Aerothermodynamics of Blunt Body Entry Vehicles. Chapter 3

NASA Technical Reports Server (NTRS)

Hollis, Brian R.; Borrelli, Salvatore

2011-01-01

In this chapter, the aerothermodynamic phenomena of blunt body entry vehicles are discussed. Four topics will be considered that present challenges to current computational modeling techniques for blunt body environments: turbulent flow, non-equilibrium flow, rarefied flow, and radiation transport. Examples of comparisons between computational tools to ground and flight-test data will be presented in order to illustrate the challenges existing in the numerical modeling of each of these phenomena and to provide test cases for evaluation of Computational Fluid Dynamics (CFD) code predictions.

Aerothermodynamics of blunt body entry vehicles

NASA Astrophysics Data System (ADS)

Hollis, Brian R.; Borrelli, Salvatore

2012-01-01

In this chapter, the aerothermodynamic phenomena of blunt body entry vehicles are discussed. Four topics will be considered that present challenges to current computational modeling techniques for blunt body environments: turbulent flow, non-equilibrium flow, rarefied flow, and radiation transport. Examples of comparisons between computational tools to ground and flight-test data will be presented in order to illustrate the challenges existing in the numerical modeling of each of these phenomena and to provide test cases for evaluation of computational fluid dynamics (CFD) code predictions.

Finite-Difference Solution for Laminar or Turbulent Boundary Layer Flow over Axisymmetric Bodies with Ideal Gas, CF4, or Equilibrium Air Chemistry

NASA Technical Reports Server (NTRS)

Hamilton, H. Harris, II; Millman, Daniel R.; Greendyke, Robert B.

1992-01-01

A computer code was developed that uses an implicit finite-difference technique to solve nonsimilar, axisymmetric boundary layer equations for both laminar and turbulent flow. The code can treat ideal gases, air in chemical equilibrium, and carbon tetrafluoride (CF4), which is a useful gas for hypersonic blunt-body simulations. This is the only known boundary layer code that can treat CF4. Comparisons with experimental data have demonstrated that accurate solutions are obtained. The method should prove useful as an analysis tool for comparing calculations with wind tunnel experiments and for making calculations about flight vehicles where equilibrium air chemistry assumptions are valid.

Finite-difference solution for laminar or turbulent boundary layer flow over axisymmetric bodies with ideal gas, CF4, or equilibrium air chemistry

NASA Astrophysics Data System (ADS)

Hamilton, H. Harris, II; Millman, Daniel R.; Greendyke, Robert B.

1992-12-01

A computer code was developed that uses an implicit finite-difference technique to solve nonsimilar, axisymmetric boundary layer equations for both laminar and turbulent flow. The code can treat ideal gases, air in chemical equilibrium, and carbon tetrafluoride (CF4), which is a useful gas for hypersonic blunt-body simulations. This is the only known boundary layer code that can treat CF4. Comparisons with experimental data have demonstrated that accurate solutions are obtained. The method should prove useful as an analysis tool for comparing calculations with wind tunnel experiments and for making calculations about flight vehicles where equilibrium air chemistry assumptions are valid.

Computing Nash equilibria through computational intelligence methods

NASA Astrophysics Data System (ADS)

Pavlidis, N. G.; Parsopoulos, K. E.; Vrahatis, M. N.

2005-03-01

Nash equilibrium constitutes a central solution concept in game theory. The task of detecting the Nash equilibria of a finite strategic game remains a challenging problem up-to-date. This paper investigates the effectiveness of three computational intelligence techniques, namely, covariance matrix adaptation evolution strategies, particle swarm optimization, as well as, differential evolution, to compute Nash equilibria of finite strategic games, as global minima of a real-valued, nonnegative function. An issue of particular interest is to detect more than one Nash equilibria of a game. The performance of the considered computational intelligence methods on this problem is investigated using multistart and deflection.

A computer graphics display technique for the examination of aircraft design data

NASA Technical Reports Server (NTRS)

Talcott, N. A., Jr.

1981-01-01

An interactive computer graphics technique has been developed for quickly sorting and interpreting large amounts of aerodynamic data. It utilizes a graphic representation rather than numbers. The geometry package represents the vehicle as a set of panels. These panels are ordered in groups of ascending values (e.g., equilibrium temperatures). The groups are then displayed successively on a CRT building up to the complete vehicle. A zoom feature allows for displaying only the panels with values between certain limits. The addition of color allows a one-time display thus eliminating the need for a display build up.

Modelling Equilibrium and Fractional Crystallization in the System MgO-FeO-CaO-Al2O3-SiO2

NASA Technical Reports Server (NTRS)

Herbert, F.

1985-01-01

A mathematical modelling technique for use in petrogenesis calculations in the system MgO-FeO-CaO-Al2O3-SiO2 is reported. Semiempirical phase boundary and elemental distribution information was combined with mass balance to compute approximate equilibrium crystallization paths for arbitrary system compositions. The calculation is applicable to a range of system compositions and fractionation calculations are possible. The goal of the calculation is the computation of the composition and quantity of each phase present as a function of the degree of solidification. The degree of solidification is parameterized by the heat released by the solidifying phases. The mathematical requirement for the solution of this problem is: (1) An equation constraining the composition of the magma for each solid phase in equilibrium with the liquidus phase, and (2) an equation for each solid phase and each component giving the distribution of that element between that phase and the magma.

Combustion of hydrogen injected into a supersonic airstream (the SHIP computer program)

NASA Technical Reports Server (NTRS)

Markatos, N. C.; Spalding, D. B.; Tatchell, D. G.

1977-01-01

The mathematical and physical basis of the SHIP computer program which embodies a finite-difference, implicit numerical procedure for the computation of hydrogen injected into a supersonic airstream at an angle ranging from normal to parallel to the airstream main flow direction is described. The physical hypotheses built into the program include: a two-equation turbulence model, and a chemical equilibrium model for the hydrogen-oxygen reaction. Typical results for equilibrium combustion are presented and exhibit qualitatively plausible behavior. The computer time required for a given case is approximately 1 minute on a CDC 7600 machine. A discussion of the assumption of parabolic flow in the injection region is given which suggests that improvement in calculation in this region could be obtained by use of the partially parabolic procedure of Pratap and Spalding. It is concluded that the technique described herein provides the basis for an efficient and reliable means for predicting the effects of hydrogen injection into supersonic airstreams and of its subsequent combustion.

Transpiration and film cooling boundary layer computer program. Volume 2: Computer program and user's manual

NASA Technical Reports Server (NTRS)

Gloss, R. J.

1971-01-01

A finite difference turbulent boundary layer computer program which allows for mass transfer wall cooling and equilibrium chemistry effects is presented. The program is capable of calculating laminar or turbulent boundary layer solutions for an arbitrary ideal gas or an equilibrium hydrogen oxygen system. Either two dimensional or axisymmetric geometric configurations may be considered. The equations are solved, in nondimension-alized physical coordinates, using the implicit Crank-Nicolson technique. The finite difference forms of the conservation of mass, momentum, total enthalpy and elements equations are linearized and uncoupled, thereby generating easily solvable tridiagonal sets of algebraic equations. A detailed description of the computer program, as well as a program user's manual is provided. Detailed descriptions of all boundary layer subroutines are included, as well as a section defining all program symbols of principal importance. Instructions are then given for preparing card input to the program and for interpreting the printed output. Finally, two sample cases are included to illustrate the use of the program.

Minimizing the Free Energy: A Computer Method for Teaching Chemical Equilibrium Concepts.

ERIC Educational Resources Information Center

Heald, Emerson F.

1978-01-01

Presents a computer method for teaching chemical equilibrium concepts using material balance conditions and the minimization of the free energy. Method for the calculation of chemical equilibrium, the computer program used to solve equilibrium problems and applications of the method are also included. (HM)

Plasma Equilibrium Control in Nuclear Fusion Devices 2. Plasma Control in Magnetic Confinement Devices 2.1 Plasma Control in Tokamaks

NASA Astrophysics Data System (ADS)

Fukuda, Takeshi

The plasma control technique for use in large tokamak devices has made great developmental strides in the last decade, concomitantly with progress in the understanding of tokamak physics and in part facilitated by the substantial advancement in the computing environment. Equilibrium control procedures have thereby been established, and it has been pervasively recognized in recent years that the real-time feedback control of physical quantities is indispensable for the improvement and sustainment of plasma performance in a quasi-steady-state. Further development is presently undertaken to realize the “advanced plasma control” concept, where integrated fusion performance is achieved by the simultaneous feedback control of multiple physical quantities, combined with equilibrium control.

Noise-induced extinction for a ratio-dependent predator-prey model with strong Allee effect in prey

NASA Astrophysics Data System (ADS)

Mandal, Partha Sarathi

2018-04-01

In this paper, we study a stochastically forced ratio-dependent predator-prey model with strong Allee effect in prey population. In the deterministic case, we show that the model exhibits the stable interior equilibrium point or limit cycle corresponding to the co-existence of both species. We investigate a probabilistic mechanism of the noise-induced extinction in a zone of stable interior equilibrium point. Computational methods based on the stochastic sensitivity function technique are applied for the analysis of the dispersion of random states near stable interior equilibrium point. This method allows to construct a confidence domain and estimate the threshold value of the noise intensity for a transition from the coexistence to the extinction.

Non-equilibrium calculations of atmospheric processes initiated by electron impact.

NASA Astrophysics Data System (ADS)

Campbell, L.; Brunger, M. J.

2007-05-01

Electron impact in the atmosphere produces ionisation, dissociation, electronic excitation and vibrational excitation of atoms and molecules. The products can then take part in chemical reactions, recombination with electrons, or radiative or collisional deactivation. While most such processes are fast, some longer--lived species do not reach equilibrium. The electron source (photoelectrons or auroral electrons) also varies over time and longer-lived species can move substantially in altitude by molecular, ambipolar or eddy diffusion. Hence non-equilibrium calculations are required in some circumstances. Such time-step calculations need to have sufficiently short steps so that the fastest processes are still calculated correctly, but this can lead to computation times that are too large. Hence techniques to allow for longer time steps by incorporating equilibrium calculations are described. Examples are given for results of atmospheric non-equilibrium calculations, including the populations of the vibrational levels of ground state N2, the electron density and its dependence on vibrationally excited N2, predictions of nitric oxide density, and detailed processes during short duration auroral events.

Nonadditivity of van der Waals forces on liquid surfaces

NASA Astrophysics Data System (ADS)

Venkataram, Prashanth S.; Whitton, Jeremy D.; Rodriguez, Alejandro W.

2016-09-01

We present an approach for modeling nanoscale wetting and dewetting of textured solid surfaces that exploits recently developed, sophisticated techniques for computing exact long-range dispersive van der Waals (vdW) or (more generally) Casimir forces in arbitrary geometries. We apply these techniques to solve the variational formulation of the Young-Laplace equation and predict the equilibrium shapes of liquid-vacuum interfaces near solid gratings. We show that commonly employed methods of computing vdW interactions based on additive Hamaker or Derjaguin approximations, which neglect important electromagnetic boundary effects, can result in large discrepancies in the shapes and behaviors of liquid surfaces compared to exact methods.

Steady-State Electrodiffusion from the Nernst-Planck Equation Coupled to Local Equilibrium Monte Carlo Simulations.

PubMed

Boda, Dezső; Gillespie, Dirk

2012-03-13

We propose a procedure to compute the steady-state transport of charged particles based on the Nernst-Planck (NP) equation of electrodiffusion. To close the NP equation and to establish a relation between the concentration and electrochemical potential profiles, we introduce the Local Equilibrium Monte Carlo (LEMC) method. In this method, Grand Canonical Monte Carlo simulations are performed using the electrochemical potential specified for the distinct volume elements. An iteration procedure that self-consistently solves the NP and flux continuity equations with LEMC is shown to converge quickly. This NP+LEMC technique can be used in systems with diffusion of charged or uncharged particles in complex three-dimensional geometries, including systems with low concentrations and small applied voltages that are difficult for other particle simulation techniques.

Monte Carlo method for computing density of states and quench probability of potential energy and enthalpy landscapes.

PubMed

Mauro, John C; Loucks, Roger J; Balakrishnan, Jitendra; Raghavan, Srikanth

2007-05-21

The thermodynamics and kinetics of a many-body system can be described in terms of a potential energy landscape in multidimensional configuration space. The partition function of such a landscape can be written in terms of a density of states, which can be computed using a variety of Monte Carlo techniques. In this paper, a new self-consistent Monte Carlo method for computing density of states is described that uses importance sampling and a multiplicative update factor to achieve rapid convergence. The technique is then applied to compute the equilibrium quench probability of the various inherent structures (minima) in the landscape. The quench probability depends on both the potential energy of the inherent structure and the volume of its corresponding basin in configuration space. Finally, the methodology is extended to the isothermal-isobaric ensemble in order to compute inherent structure quench probabilities in an enthalpy landscape.

Statistical Mechanics of Coherent Ising Machine — The Case of Ferromagnetic and Finite-Loading Hopfield Models —

NASA Astrophysics Data System (ADS)

Aonishi, Toru; Mimura, Kazushi; Utsunomiya, Shoko; Okada, Masato; Yamamoto, Yoshihisa

2017-10-01

The coherent Ising machine (CIM) has attracted attention as one of the most effective Ising computing architectures for solving large scale optimization problems because of its scalability and high-speed computational ability. However, it is difficult to implement the Ising computation in the CIM because the theories and techniques of classical thermodynamic equilibrium Ising spin systems cannot be directly applied to the CIM. This means we have to adapt these theories and techniques to the CIM. Here we focus on a ferromagnetic model and a finite loading Hopfield model, which are canonical models sharing a common mathematical structure with almost all other Ising models. We derive macroscopic equations to capture nonequilibrium phase transitions in these models. The statistical mechanical methods developed here constitute a basis for constructing evaluation methods for other Ising computation models.

Accelerating Multiagent Reinforcement Learning by Equilibrium Transfer.

PubMed

Hu, Yujing; Gao, Yang; An, Bo

2015-07-01

An important approach in multiagent reinforcement learning (MARL) is equilibrium-based MARL, which adopts equilibrium solution concepts in game theory and requires agents to play equilibrium strategies at each state. However, most existing equilibrium-based MARL algorithms cannot scale due to a large number of computationally expensive equilibrium computations (e.g., computing Nash equilibria is PPAD-hard) during learning. For the first time, this paper finds that during the learning process of equilibrium-based MARL, the one-shot games corresponding to each state's successive visits often have the same or similar equilibria (for some states more than 90% of games corresponding to successive visits have similar equilibria). Inspired by this observation, this paper proposes to use equilibrium transfer to accelerate equilibrium-based MARL. The key idea of equilibrium transfer is to reuse previously computed equilibria when each agent has a small incentive to deviate. By introducing transfer loss and transfer condition, a novel framework called equilibrium transfer-based MARL is proposed. We prove that although equilibrium transfer brings transfer loss, equilibrium-based MARL algorithms can still converge to an equilibrium policy under certain assumptions. Experimental results in widely used benchmarks (e.g., grid world game, soccer game, and wall game) show that the proposed framework: 1) not only significantly accelerates equilibrium-based MARL (up to 96.7% reduction in learning time), but also achieves higher average rewards than algorithms without equilibrium transfer and 2) scales significantly better than algorithms without equilibrium transfer when the state/action space grows and the number of agents increases.

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

Simunovic, Srdjan; Piro, Markus H.A.

Thermochimica is a software library that determines a unique combination of phases and their compositions at thermochemical equilibrium. Thermochimica can be used for stand-alone calculations or it can be directly coupled to other codes. This release of the software does not have a graphical user interface (GUI) and it can be executed from the command line or from an Application Programming Interface (API). Also, it is not intended for thermodynamic model development or for constructing phase diagrams. The main purpose of the software is to be directly coupled with a multi-physics code to provide material properties and boundary conditions formore » various physical phenomena. Significant research efforts have been dedicated to enhance computational performance through advanced algorithm development, such as improved estimation techniques and non-linear solvers. Various useful parameters can be provided as output from Thermochimica, such as: determination of which phases are stable at equilibrium, the mass of solution species and phases at equilibrium, mole fractions of solution phase constituents, thermochemical activities (which are related to partial pressures for gaseous species), chemical potentials of solution species and phases, and integral Gibbs energy (referenced relative to standard state). The overall goal is to provide an open source computational tool to enhance the predictive capability of multi-physics codes without significantly impeding computational performance.« less

Dynamic Data-Driven Reduced-Order Models of Macroscale Quantities for the Prediction of Equilibrium System State for Multiphase Porous Medium Systems

NASA Astrophysics Data System (ADS)

Talbot, C.; McClure, J. E.; Armstrong, R. T.; Mostaghimi, P.; Hu, Y.; Miller, C. T.

2017-12-01

Microscale simulation of multiphase flow in realistic, highly-resolved porous medium systems of a sufficient size to support macroscale evaluation is computationally demanding. Such approaches can, however, reveal the dynamic, steady, and equilibrium states of a system. We evaluate methods to utilize dynamic data to reduce the cost associated with modeling a steady or equilibrium state. We construct data-driven models using extensions to dynamic mode decomposition (DMD) and its connections to Koopman Operator Theory. DMD and its variants comprise a class of equation-free methods for dimensionality reduction of time-dependent nonlinear dynamical systems. DMD furnishes an explicit reduced representation of system states in terms of spatiotemporally varying modes with time-dependent oscillation frequencies and amplitudes. We use DMD to predict the steady and equilibrium macroscale state of a realistic two-fluid porous medium system imaged using micro-computed tomography (µCT) and simulated using the lattice Boltzmann method (LBM). We apply Koopman DMD to direct numerical simulation data resulting from simulations of multiphase fluid flow through a 1440x1440x4320 section of a full 1600x1600x5280 realization of imaged sandstone. We determine a representative set of system observables via dimensionality reduction techniques including linear and kernel principal component analysis. We demonstrate how this subset of macroscale quantities furnishes a representation of the time-evolution of the system in terms of dynamic modes, and discuss the selection of a subset of DMD modes yielding the optimal reduced model, as well as the time-dependence of the error in the predicted equilibrium value of each macroscale quantity. Finally, we describe how the above procedure, modified to incorporate methods from compressed sensing and random projection techniques, may be used in an online fashion to facilitate adaptive time-stepping and parsimonious storage of system states over time.

Evaluation of solution procedures for material and/or geometrically nonlinear structural analysis by the direct stiffness method.

NASA Technical Reports Server (NTRS)

Stricklin, J. A.; Haisler, W. E.; Von Riesemann, W. A.

1972-01-01

This paper presents an assessment of the solution procedures available for the analysis of inelastic and/or large deflection structural behavior. A literature survey is given which summarized the contribution of other researchers in the analysis of structural problems exhibiting material nonlinearities and combined geometric-material nonlinearities. Attention is focused at evaluating the available computation and solution techniques. Each of the solution techniques is developed from a common equation of equilibrium in terms of pseudo forces. The solution procedures are applied to circular plates and shells of revolution in an attempt to compare and evaluate each with respect to computational accuracy, economy, and efficiency. Based on the numerical studies, observations and comments are made with regard to the accuracy and economy of each solution technique.

Multiagent Reinforcement Learning With Sparse Interactions by Negotiation and Knowledge Transfer.

PubMed

Zhou, Luowei; Yang, Pei; Chen, Chunlin; Gao, Yang

2017-05-01

Reinforcement learning has significant applications for multiagent systems, especially in unknown dynamic environments. However, most multiagent reinforcement learning (MARL) algorithms suffer from such problems as exponential computation complexity in the joint state-action space, which makes it difficult to scale up to realistic multiagent problems. In this paper, a novel algorithm named negotiation-based MARL with sparse interactions (NegoSIs) is presented. In contrast to traditional sparse-interaction-based MARL algorithms, NegoSI adopts the equilibrium concept and makes it possible for agents to select the nonstrict equilibrium-dominating strategy profile (nonstrict EDSP) or meta equilibrium for their joint actions. The presented NegoSI algorithm consists of four parts: 1) the equilibrium-based framework for sparse interactions; 2) the negotiation for the equilibrium set; 3) the minimum variance method for selecting one joint action; and 4) the knowledge transfer of local Q -values. In this integrated algorithm, three techniques, i.e., unshared value functions, equilibrium solutions, and sparse interactions are adopted to achieve privacy protection, better coordination and lower computational complexity, respectively. To evaluate the performance of the presented NegoSI algorithm, two groups of experiments are carried out regarding three criteria: 1) steps of each episode; 2) rewards of each episode; and 3) average runtime. The first group of experiments is conducted using six grid world games and shows fast convergence and high scalability of the presented algorithm. Then in the second group of experiments NegoSI is applied to an intelligent warehouse problem and simulated results demonstrate the effectiveness of the presented NegoSI algorithm compared with other state-of-the-art MARL algorithms.

Computerized optimization of radioimmunoassays for hCG and estradiol: an experimental evaluation

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

Yanagishita, M.; Rodbard, D.

1978-07-15

The mathematical and statistical theory of radioimmunoassays (RIAs) has been used to develop a series of computer programs to optimize sensitivity or precision at any desired dose level for either equilibrium or nonequilibrium assays. These computer programs provide for the calculation of the equilibrium constants of association and binding capacities for antisera (parameters of Scatchard plots), the association and dissociation rate constants, and prediction of optimum concentration of labeled ligand and antibody and optimum incubation times for the assay. This paper presents an experimental evaluation of the use of these computer programs applied to RIAs for human chorionic gonadotropin (hCG)more » and estradiol. The experimental results are in reasonable semiquantitative agreement with the predictions of the computer simulations (usually within a factor of two) and thus partially validate the use of computer techniques to optimize RIAs that are reasonably well behaved, as in the case of the hCG and estradiol RIAs. Further, these programs can provide insights into the nature of the RIA system, e.g., the general nature of the sensitivity and precision surfaces. This facilitates empirical optimization of conditions.« less

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

NASA Technical Reports Server (NTRS)

Kahn, L. R.

1982-01-01

Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

Development of a computer code for calculating the steady super/hypersonic inviscid flow around real configurations. Volume 1: Computational technique

NASA Technical Reports Server (NTRS)

Marconi, F.; Salas, M.; Yaeger, L.

1976-01-01

A numerical procedure has been developed to compute the inviscid super/hypersonic flow field about complex vehicle geometries accurately and efficiently. A second order accurate finite difference scheme is used to integrate the three dimensional Euler equations in regions of continuous flow, while all shock waves are computed as discontinuities via the Rankine Hugoniot jump conditions. Conformal mappings are used to develop a computational grid. The effects of blunt nose entropy layers are computed in detail. Real gas effects for equilibrium air are included using curve fits of Mollier charts. Typical calculated results for shuttle orbiter, hypersonic transport, and supersonic aircraft configurations are included to demonstrate the usefulness of this tool.

CAG12 - A CSCM based procedure for flow of an equilibrium chemically reacting gas

NASA Technical Reports Server (NTRS)

Green, M. J.; Davy, W. C.; Lombard, C. K.

1985-01-01

The Conservative Supra Characteristic Method (CSCM), an implicit upwind Navier-Stokes algorithm, is extended to the numerical simulation of flows in chemical equilibrium. The resulting computer code known as Chemistry and Gasdynamics Implicit - Version 2 (CAG12) is described. First-order accurate results are presented for inviscid and viscous Mach 20 flows of air past a hemisphere-cylinder. The solution procedure captures the bow shock in a chemically reacting gas, a technique that is needed for simulating high altitude, rarefied flows. In an initial effort to validate the code, the inviscid results are compared with published gasdynamic and chemistry solutions and satisfactorily agreement is obtained.

Collisional-radiative switching - A powerful technique for converging non-LTE calculations

NASA Technical Reports Server (NTRS)

Hummer, D. G.; Voels, S. A.

1988-01-01

A very simple technique has been developed to converge statistical equilibrium and model atmospheric calculations in extreme non-LTE conditions when the usual iterative methods fail to converge from an LTE starting model. The proposed technique is based on a smooth transition from a collision-dominated LTE situation to the desired non-LTE conditions in which radiation dominates, at least in the most important transitions. The proposed approach was used to successfully compute stellar models with He abundances of 0.20, 0.30, and 0.50; Teff = 30,000 K, and log g = 2.9.

Development of hybrid computer plasma models for different pressure regimes

NASA Astrophysics Data System (ADS)

Hromadka, Jakub; Ibehej, Tomas; Hrach, Rudolf

2016-09-01

With increased performance of contemporary computers during last decades numerical simulations became a very powerful tool applicable also in plasma physics research. Plasma is generally an ensemble of mutually interacting particles that is out of the thermodynamic equilibrium and for this reason fluid computer plasma models give results with only limited accuracy. On the other hand, much more precise particle models are often limited only on 2D problems because of their huge demands on the computer resources. Our contribution is devoted to hybrid modelling techniques that combine advantages of both modelling techniques mentioned above, particularly to their so-called iterative version. The study is focused on mutual relations between fluid and particle models that are demonstrated on the calculations of sheath structures of low temperature argon plasma near a cylindrical Langmuir probe for medium and higher pressures. Results of a simple iterative hybrid plasma computer model are also given. The authors acknowledge the support of the Grant Agency of Charles University in Prague (project 220215).

Theory and Techniques for Assessing the Demand and Supply of Outdoor Recreation in the United States

Treesearch

H. Ken Cordell; John C. Bergstrom

1989-01-01

As the central analysis for the 1989 Renewable Resources planning Act Assessment, a household market model covering 37 recreational activities was computed for the United States. Equilibrium consumption and costs were estimated, as were likely future changes in consumption and costs in response to expected demand growth and alternative development and access policies...

A rapid method for the computation of equilibrium chemical composition of air to 15000 K

NASA Technical Reports Server (NTRS)

Prabhu, Ramadas K.; Erickson, Wayne D.

1988-01-01

A rapid computational method has been developed to determine the chemical composition of equilibrium air to 15000 K. Eleven chemically reacting species, i.e., O2, N2, O, NO, N, NO+, e-, N+, O+, Ar, and Ar+ are included. The method involves combining algebraically seven nonlinear equilibrium equations and four linear elemental mass balance and charge neutrality equations. Computational speeds for determining the equilibrium chemical composition are significantly faster than the often used free energy minimization procedure. Data are also included from which the thermodynamic properties of air can be computed. A listing of the computer program together with a set of sample results are included.

Nuclear Weak Rates and Detailed Balance in Stellar Conditions

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

Misch, G. Wendell, E-mail: wendell@sjtu.edu, E-mail: wendell.misch@gmail.com

Detailed balance is often invoked in discussions of nuclear weak transitions in astrophysical environments. Satisfaction of detailed balance is rightly touted as a virtue of some methods of computing nuclear transition strengths, but I argue that it need not necessarily be strictly obeyed in astrophysical environments, especially when the environment is far from weak equilibrium. I present the results of shell model calculations of nuclear weak strengths in both charged-current and neutral-current channels at astrophysical temperatures, finding some violation of detailed balance. I show that a slight modification of the technique to strictly obey detailed balance has little effect onmore » the reaction rates associated with these strengths under most conditions, though at high temperature the modified technique in fact misses some important strength. I comment on the relationship between detailed balance and weak equilibrium in astrophysical conditions.« less

Green's function calculations for semi-infinite carbon nanotubes

NASA Astrophysics Data System (ADS)

John, D. L.; Pulfrey, D. L.

2006-02-01

In the modeling of nanoscale electronic devices, the non-equilibrium Green's function technique is gaining increasing popularity. One complication in this method is the need for computation of the self-energy functions that account for the interactions between the active portion of a device and its leads. In the one-dimensional case, these functions may be computed analytically. In higher dimensions, a numerical approach is required. In this work, we generalize earlier methods that were developed for tight-binding Hamiltonians, and present results for the case of a carbon nanotube.

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

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

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

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

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

Partitioning and interfacial tracers for differentiating NAPL entrapment configuration: column-scale investigation.

PubMed

Dai, D; Barranco, F T; Illangasekare, T H

2001-12-15

Research on the use of partitioning and interfacial tracers has led to the development of techniques for estimating subsurface NAPL amount and NAPL-water interfacial area. Although these techniques have been utilized with some success at field sites, current application is limited largely to NAPL at residual saturation, such as for the case of post-remediation settings where mobile NAPL has been removed through product recovery. The goal of this study was to fundamentally evaluate partitioning and interfacial tracer behavior in controlled column-scale test cells for a range of entrapment configurations varying in NAPL saturation, with the results serving as a determinant of technique efficacy (and design protocol) for use with complexly distributed NAPLs, possibly at high saturation, in heterogeneous aquifers. Representative end members of the range of entrapment configurations observed under conditions of natural heterogeneity (an occurrence with residual NAPL saturation [discontinuous blobs] and an occurrence with high NAPL saturation [continuous free-phase LNAPL lens]) were evaluated. Study results indicated accurate prediction (using measured tracer retardation and equilibrium-based computational techniques) of NAPL amount and NAPL-water interfacial area for the case of residual NAPL saturation. For the high-saturation LNAPL lens, results indicated that NAPL-water interfacial area, but not NAPL amount (underpredicted by 35%), can be reasonably determined using conventional computation techniques. Underprediction of NAPL amount lead to an erroneous prediction of NAPL distribution, as indicated by the NAPL morphology index. In light of these results, careful consideration should be given to technique design and critical assumptions before applying equilibrium-based partitioning tracer methodology to settings where NAPLs are complexly entrapped, such as in naturally heterogeneous subsurface formations.

Transpiration and film cooling boundary layer computer program. Volume 1: Numerical solutions of the turbulent boundary layer equations with equilibrium chemistry

NASA Technical Reports Server (NTRS)

Levine, J. N.

1971-01-01

A finite difference turbulent boundary layer computer program has been developed. The program is primarily oriented towards the calculation of boundary layer performance losses in rocket engines; however, the solution is general, and has much broader applicability. The effects of transpiration and film cooling as well as the effect of equilibrium chemical reactions (currently restricted to the H2-O2 system) can be calculated. The turbulent transport terms are evaluated using the phenomenological mixing length - eddy viscosity concept. The equations of motion are solved using the Crank-Nicolson implicit finite difference technique. The analysis and computer program have been checked out by solving a series of both laminar and turbulent test cases and comparing the results to data or other solutions. These comparisons have shown that the program is capable of producing very satisfactory results for a wide range of flows. Further refinements to the analysis and program, especially as applied to film cooling solutions, would be aided by the acquisition of a firm data base.

State-to-State Internal Energy Relaxation Following the Quantum-Kinetic Model in DSMC

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2014-01-01

A new model for chemical reactions, the Quantum-Kinetic (Q-K) model of Bird, has recently been introduced that does not depend on macroscopic rate equations or values of local flow field data. Subsequently, the Q-K model has been extended to include reactions involving charged species and electronic energy level transitions. Although this is a phenomenological model, it has been shown to accurately reproduce both equilibrium and non-equilibrium reaction rates. The usefulness of this model becomes clear as local flow conditions either exceed the conditions used to build previous models or when they depart from an equilibrium distribution. Presently, the applicability of the relaxation technique is investigated for the vibrational internal energy mode. The Forced Harmonic Oscillator (FHO) theory for vibrational energy level transitions is combined with the Q-K energy level transition model to accurately reproduce energy level transitions at a reduced computational cost compared to the older FHO models.

Finite-size polyelectrolyte bundles at thermodynamic equilibrium

NASA Astrophysics Data System (ADS)

Sayar, M.; Holm, C.

2007-01-01

We present the results of extensive computer simulations performed on solutions of monodisperse charged rod-like polyelectrolytes in the presence of trivalent counterions. To overcome energy barriers we used a combination of parallel tempering and hybrid Monte Carlo techniques. Our results show that for small values of the electrostatic interaction the solution mostly consists of dispersed single rods. The potential of mean force between the polyelectrolyte monomers yields an attractive interaction at short distances. For a range of larger values of the Bjerrum length, we find finite-size polyelectrolyte bundles at thermodynamic equilibrium. Further increase of the Bjerrum length eventually leads to phase separation and precipitation. We discuss the origin of the observed thermodynamic stability of the finite-size aggregates.

Computational studies of thermal and quantum phase transitions approached through non-equilibrium quenching

NASA Astrophysics Data System (ADS)

Liu, Cheng-Wei

Phase transitions and their associated critical phenomena are of fundamental importance and play a crucial role in the development of statistical physics for both classical and quantum systems. Phase transitions embody diverse aspects of physics and also have numerous applications outside physics, e.g., in chemistry, biology, and combinatorial optimization problems in computer science. Many problems can be reduced to a system consisting of a large number of interacting agents, which under some circumstances (e.g., changes of external parameters) exhibit collective behavior; this type of scenario also underlies phase transitions. The theoretical understanding of equilibrium phase transitions was put on a solid footing with the establishment of the renormalization group. In contrast, non-equilibrium phase transition are relatively less understood and currently a very active research topic. One important milestone here is the Kibble-Zurek (KZ) mechanism, which provides a useful framework for describing a system with a transition point approached through a non-equilibrium quench process. I developed two efficient Monte Carlo techniques for studying phase transitions, one is for classical phase transition and the other is for quantum phase transitions, both are under the framework of KZ scaling. For classical phase transition, I develop a non-equilibrium quench (NEQ) simulation that can completely avoid the critical slowing down problem. For quantum phase transitions, I develop a new algorithm, named quasi-adiabatic quantum Monte Carlo (QAQMC) algorithm for studying quantum quenches. I demonstrate the utility of QAQMC quantum Ising model and obtain high-precision results at the transition point, in particular showing generalized dynamic scaling in the quantum system. To further extend the methods, I study more complex systems such as spin-glasses and random graphs. The techniques allow us to investigate the problems efficiently. From the classical perspective, using the NEQ approach I verify the universality class of the 3D Ising spin-glasses. I also investigate the random 3-regular graphs in terms of both classical and quantum phase transitions. I demonstrate that under this simulation scheme, one can extract information associated with the classical and quantum spin-glass transitions without any knowledge prior to the simulation.

Navier-Stokes simulation of real gas flows in nozzles

NASA Technical Reports Server (NTRS)

Nagaraj, N.; Lombard, C. K.

1987-01-01

Air flow in a hypersonic nozzle causes real gas effects due to reaction among the species constituting air. Such reactions may be in chemical equilibrium or in chemical nonequilibrium. Here using the CSCM upwind scheme for the compressible Navier-Stokes equations, the real gas flowfield in an arcjet nozzle is computed for both the equilibrium case and the nonequilibrium case. A hypersonic nozzle flow arising from a pebble bed heated plenum is also computed for the equilibrium situation. Between the equilibrium cases, the chemistry is treated by two different schemes and comments are made as to computational complexity. For the nonequilibrium case, a full set of seventeen reactions and full implicit coupling of five species with gasdynamics is employed to compute the flowfield. For all cases considered here the gas is assumed to be a calorically imperfect mixture of ideal gases in thermal equilibrium.

REACTT: an algorithm for solving spatial equilibrium problems.

Treesearch

D.J. Brooks; J. Kincaid

1987-01-01

The problem of determining equilibrium prices and quantities in spatially separated markets is reviewed. Algorithms that compute spatial equilibria are discussed. A computer program using the reactive programming algorithm for solving spatial equilibrium problems that involve multiple commodities is presented, along with detailed documentation. A sample data set,...

New phenomena in non-equilibrium quantum physics

NASA Astrophysics Data System (ADS)

Kitagawa, Takuya

From its beginning in the early 20th century, quantum theory has become progressively more important especially due to its contributions to the development of technologies. Quantum mechanics is crucial for current technology such as semiconductors, and also holds promise for future technologies such as superconductors and quantum computing. Despite of the success of quantum theory, its applications have been mostly limited to equilibrium or static systems due to 1. lack of experimental controllability of non-equilibrium quantum systems 2. lack of theoretical frameworks to understand non-equilibrium dynamics. Consequently, physicists have not yet discovered too many interesting phenomena in non-equilibrium quantum systems from both theoretical and experimental point of view and thus, non-equilibrium quantum physics did not attract too much attentions. The situation has recently changed due to the rapid development of experimental techniques in condensed matter as well as cold atom systems, which now enables a better control of non-equilibrium quantum systems. Motivated by this experimental progress, we constructed theoretical frameworks to study three different non-equilibrium regimes of transient dynamics, steady states and periodically drives. These frameworks provide new perspectives for dynamical quantum process, and help to discover new phenomena in these systems. In this thesis, we describe these frameworks through explicit examples and demonstrate their versatility. Some of these theoretical proposals have been realized in experiments, confirming the applicability of the theories to realistic experimental situations. These studies have led to not only the improved fundamental understanding of non-equilibrium processes in quantum systems, but also suggested entirely different venues for developing quantum technologies.

A numerical code for the simulation of non-equilibrium chemically reacting flows on hybrid CPU-GPU clusters

NASA Astrophysics Data System (ADS)

Kudryavtsev, Alexey N.; Kashkovsky, Alexander V.; Borisov, Semyon P.; Shershnev, Anton A.

2017-10-01

In the present work a computer code RCFS for numerical simulation of chemically reacting compressible flows on hybrid CPU/GPU supercomputers is developed. It solves 3D unsteady Euler equations for multispecies chemically reacting flows in general curvilinear coordinates using shock-capturing TVD schemes. Time advancement is carried out using the explicit Runge-Kutta TVD schemes. Program implementation uses CUDA application programming interface to perform GPU computations. Data between GPUs is distributed via domain decomposition technique. The developed code is verified on the number of test cases including supersonic flow over a cylinder.

ELAS: A general-purpose computer program for the equilibrium problems of linear structures. Volume 2: Documentation of the program. [subroutines and flow charts

NASA Technical Reports Server (NTRS)

Utku, S.

1969-01-01

A general purpose digital computer program for the in-core solution of linear equilibrium problems of structural mechanics is documented. The program requires minimum input for the description of the problem. The solution is obtained by means of the displacement method and the finite element technique. Almost any geometry and structure may be handled because of the availability of linear, triangular, quadrilateral, tetrahedral, hexahedral, conical, triangular torus, and quadrilateral torus elements. The assumption of piecewise linear deflection distribution insures monotonic convergence of the deflections from the stiffer side with decreasing mesh size. The stresses are provided by the best-fit strain tensors in the least squares at the mesh points where the deflections are given. The selection of local coordinate systems whenever necessary is automatic. The core memory is used by means of dynamic memory allocation, an optional mesh-point relabelling scheme and imposition of the boundary conditions during the assembly time.

Price schedules coordination for electricity pool markets

NASA Astrophysics Data System (ADS)

Legbedji, Alexis Motto

2002-04-01

We consider the optimal coordination of a class of mathematical programs with equilibrium constraints, which is formally interpreted as a resource-allocation problem. Many decomposition techniques were proposed to circumvent the difficulty of solving large systems with limited computer resources. The considerable improvement in computer architecture has allowed the solution of large-scale problems with increasing speed. Consequently, interest in decomposition techniques has waned. Nonetheless, there is an important class of applications for which decomposition techniques will still be relevant, among others, distributed systems---the Internet, perhaps, being the most conspicuous example---and competitive economic systems. Conceptually, a competitive economic system is a collection of agents that have similar or different objectives while sharing the same system resources. In theory, constructing a large-scale mathematical program and solving it centrally, using currently available computing power can optimize such systems of agents. In practice, however, because agents are self-interested and not willing to reveal some sensitive corporate data, one cannot solve these kinds of coordination problems by simply maximizing the sum of agent's objective functions with respect to their constraints. An iterative price decomposition or Lagrangian dual method is considered best suited because it can operate with limited information. A price-directed strategy, however, can only work successfully when coordinating or equilibrium prices exist, which is not generally the case when a weak duality is unavoidable. Showing when such prices exist and how to compute them is the main subject of this thesis. Among our results, we show that, if the Lagrangian function of a primal program is additively separable, price schedules coordination may be attained. The prices are Lagrange multipliers, and are also the decision variables of a dual program. In addition, we propose a new form of augmented or nonlinear pricing, which is an example of the use of penalty functions in mathematical programming. Applications are drawn from mathematical programming problems of the form arising in electric power system scheduling under competition.

Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?

PubMed

Knapp, B; Frantal, S; Cibena, M; Schreiner, W; Bauer, P

2011-08-01

Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

The use of interpractive graphic displays for interpretation of surface design parameters

NASA Technical Reports Server (NTRS)

Talcott, N. A., Jr.

1981-01-01

An interactive computer graphics technique known as the Graphic Display Data method has been developed to provide a convenient means for rapidly interpreting large amounts of surface design data. The display technique should prove valuable in such disciplines as aerodynamic analysis, structural analysis, and experimental data analysis. To demonstrate the system's features, an example is presented of the Graphic Data Display method used as an interpretive tool for radiation equilibrium temperature distributions over the surface of an aerodynamic vehicle. Color graphic displays were also examined as a logical extension of the technique to improve its clarity and to allow the presentation of greater detail in a single display.

Maxwell's conjecture on three point charges with equal magnitudes

NASA Astrophysics Data System (ADS)

Tsai, Ya-Lun

2015-08-01

Maxwell's conjecture on three point charges states that the number of non-degenerate equilibrium points of the electrostatic field generated by them in R3 is at most four. We prove the conjecture in the cases when three point charges have equal magnitudes and show the number of isolated equilibrium points can only be zero, two, three, or four. Specifically, fixing positions of two positive charges in R3, we know exactly where to place the third positive charge to have two, three, or four equilibrium points. All equilibrium points are isolated and there are no other possibilities for the number of isolated equilibrium points. On the other hand, if both two of the fixed charges have negative charge values, there are always two equilibrium points except when the third positive charge lies in the line segment connecting the two negative charges. The exception cases are when the field contains only a curve of equilibrium points. In this paper, computations assisted by computer involve symbolic and exact integer computations. Therefore, all the results are proved rigorously.

On the equilibrium charge density at tilt grain boundaries

NASA Astrophysics Data System (ADS)

Srikant, V.; Clarke, D. R.

1998-05-01

The equilibrium charge density and free energy of tilt grain boundaries as a function of their misorientation is computed using a Monte Carlo simulation that takes into account both the electrostatic and configurational energies associated with charges at the grain boundary. The computed equilibrium charge density increases with the grain-boundary angle and approaches a saturation value. The equilibrium charge density at large-angle grain boundaries compares well with experimental values for large-angle tilt boundaries in GaAs. The computed grain-boundary electrostatic energy is in agreement with the analytical solution to a one-dimensional Poisson equation at high donor densities but indicates that the analytical solution overestimates the electrostatic energy at lower donor densities.

Determining Equilibrium Position For Acoustical Levitation

NASA Technical Reports Server (NTRS)

Barmatz, M. B.; Aveni, G.; Putterman, S.; Rudnick, J.

1989-01-01

Equilibrium position and orientation of acoustically-levitated weightless object determined by calibration technique on Earth. From calibration data, possible to calculate equilibrium position and orientation in presence of Earth gravitation. Sample not levitated acoustically during calibration. Technique relies on Boltzmann-Ehrenfest adiabatic-invariance principle. One converts resonant-frequency-shift data into data on normalized acoustical potential energy. Minimum of energy occurs at equilibrium point. From gradients of acoustical potential energy, one calculates acoustical restoring force or torque on objects as function of deviation from equilibrium position or orientation.

Calculating binding free energies for protein-carbohydrate complexes.

PubMed

Hadden, Jodi A; Tessier, Matthew B; Fadda, Elisa; Woods, Robert J

2015-01-01

A variety of computational techniques may be applied to compute theoretical binding free energies for protein-carbohydrate complexes. Elucidation of the intermolecular interactions, as well as the thermodynamic effects, that contribute to the relative strength of receptor binding can shed light on biomolecular recognition, and the resulting initiation or inhibition of a biological process. Three types of free energy methods are discussed here, including MM-PB/GBSA, thermodynamic integration, and a non-equilibrium alternative utilizing SMD. Throughout this chapter, the well-known concanavalin A lectin is employed as a model system to demonstrate the application of these methods to the special case of carbohydrate binding.

Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

NASA Astrophysics Data System (ADS)

Tran, Diem-Trang T.; Le, Ly T.; Truong, Thanh N.

2013-08-01

Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.

Opacity probability distribution functions for electronic systems of CN and C2 molecules including their stellar isotopic forms.

NASA Technical Reports Server (NTRS)

Querci, F.; Kunde, V. G.; Querci, M.

1971-01-01

The basis and techniques are presented for generating opacity probability distribution functions for the CN molecule (red and violet systems) and the C2 molecule (Swan, Phillips, Ballik-Ramsay systems), two of the more important diatomic molecules in the spectra of carbon stars, with a view to including these distribution functions in equilibrium model atmosphere calculations. Comparisons to the CO molecule are also shown. T he computation of the monochromatic absorption coefficient uses the most recent molecular data with revision of the oscillator strengths for some of the band systems. The total molecular stellar mass absorption coefficient is established through fifteen equations of molecular dissociation equilibrium to relate the distribution functions to each other on a per gram of stellar material basis.

Soil-Moisture Retention Curves, Capillary Pressure Curves, and Mercury Porosimetry: A Theoretical and Computational Investigation of the Determination of the Geometric Properties of the Pore Space

NASA Astrophysics Data System (ADS)

Strand, T. E.; Wang, H. F.

2003-12-01

Immiscible displacement protocols have long been used to infer the geometric properties of the void space in granular porous media. The three most commonly used experimental techniques are the measurement of soil-moisture retention curves and relative permeability-capillary pressure-saturation relations, as well as mercury intrusion porosimetry experiments. A coupled theoretical and computational investigation was performed that provides insight into the limitations associated with each technique and quantifies the relationship between experimental observations and the geometric properties of the void space. It is demonstrated that the inference of the pore space geometry from both mercury porosimetry experiments and measurements of capillary pressure curves is influenced by trapping/mobilization phenomena and subject to scaling behavior. In addition, both techniques also assume that the capillary pressure at a location on the meniscus can be approximated by a pressure difference across a region or sample. For example, when performing capillary pressure measurements, the capillary pressure, taken to be the difference between the injected fluid pressure at the inlet and the defending fluid pressure at the outlet, is increased in a series of small steps and the fluid saturation is measured each time the system reaches steady. Regions of defending fluid that become entrapped by the invading fluid can be subsequently mobilized at higher flow rates (capillary pressures), contributing to a scale-dependence of the capillary pressure-saturation curve that complicates the determination of the properties of the pore space. This scale-dependence is particularly problematic for measurements performed at the core scale. Mercury porosimetry experiments are subject to similar limitations. Trapped regions of defending fluid are also present during the measurement of soil-moisture retention curves, but the effects of scaling behavior on the evaluation of the pore space properties from the immiscible displacement structure are much simpler to account for due to the control of mobilization phenomena. Some mobilization may occur due to film flow, but this can be limited by keeping time scales relatively small or exploited at longer time scales in order to quantify the rate of film flow. Computer simulations of gradient-stabilized drainage and imbibition to the (respective) equilibrium positions were performed using a pore-scale modified invasion percolation (MIP) model in order to quantify the relationship between the saturation profile and the geometric properties of the void space. These simulations are similar to the experimental measurement of soil-moisture retention curves. Results show that the equilibrium height and the width of the equilibrium fringe depend on two length scale distributions, one controlling the imbibition equilibrium structure and the other controlling the drainage structure. The equilibrium height is related to the mean value of the appropriate distribution as described by Jurin's law, and the width of the equilibrium fringe scales as a function of a combined parameter, the Bond number, Bo, divided by the coefficient of variation (cov). Simulations also demonstrate that the apparent radius distribution obtained from saturation profiles using direct inversion by Jurin's law is a subset of the actual distribution in the porous medium. The relationship between the apparent and actual radius distributions is quantified in terms of the combined parameter, Bo/cov, and the mean coordination number of the porous medium.

Thermodynamic and transport properties of gaseous tetrafluoromethane in chemical equilibrium

NASA Technical Reports Server (NTRS)

Hunt, J. L.; Boney, L. R.

1973-01-01

Equations and in computer code are presented for the thermodynamic and transport properties of gaseous, undissociated tetrafluoromethane (CF4) in chemical equilibrium. The computer code calculates the thermodynamic and transport properties of CF4 when given any two of five thermodynamic variables (entropy, temperature, volume, pressure, and enthalpy). Equilibrium thermodynamic and transport property data are tabulated and pressure-enthalpy diagrams are presented.

Development of solution techniques for nonlinear structural analysis

NASA Technical Reports Server (NTRS)

Vos, R. G.; Andrews, J. S.

1974-01-01

Nonlinear structural solution methods in the current research literature are classified according to order of the solution scheme, and it is shown that the analytical tools for these methods are uniformly derivable by perturbation techniques. A new perturbation formulation is developed for treating an arbitrary nonlinear material, in terms of a finite-difference generated stress-strain expansion. Nonlinear geometric effects are included in an explicit manner by appropriate definition of an applicable strain tensor. A new finite-element pilot computer program PANES (Program for Analysis of Nonlinear Equilibrium and Stability) is presented for treatment of problems involving material and geometric nonlinearities, as well as certain forms on nonconservative loading.

Entropy production in a fluid-solid system far from thermodynamic equilibrium.

PubMed

Chung, Bong Jae; Ortega, Blas; Vaidya, Ashwin

2017-11-24

The terminal orientation of a rigid body in a moving fluid is an example of a dissipative system, out of thermodynamic equilibrium and therefore a perfect testing ground for the validity of the maximum entropy production principle (MaxEP). Thus far, dynamical equations alone have been employed in studying the equilibrium states in fluid-solid interactions, but these are far too complex and become analytically intractable when inertial effects come into play. At that stage, our only recourse is to rely on numerical techniques which can be computationally expensive. In our past work, we have shown that the MaxEP is a reliable tool to help predict orientational equilibrium states of highly symmetric bodies such as cylinders, spheroids and toroidal bodies. The MaxEP correctly helps choose the stable equilibrium in these cases when the system is slightly out of thermodynamic equilibrium. In the current paper, we expand our analysis to examine i) bodies with fewer symmetries than previously reported, for instance, a half-ellipse and ii) when the system is far from thermodynamic equilibrium. Using two-dimensional numerical studies at Reynolds numbers ranging between 0 and 14, we examine the validity of the MaxEP. Our analysis of flow past a half-ellipse shows that overall the MaxEP is a good predictor of the equilibrium states but, in the special case of the half-ellipse with aspect ratio much greater than unity, the MaxEP is replaced by the Min-MaxEP, at higher Reynolds numbers when inertial effects come into play. Experiments in sedimentation tanks and with hinged bodies in a flow tank confirm these calculations.

Theoretical and experimental morphologies of 4-aminobenzophenone (ABP) crystals

NASA Astrophysics Data System (ADS)

Wang, Qingwu; Sheen, D. B.; Shepherd, E. E. A.; Sherwood, J. N.; Simpson, G. S.; Hammond, R. B.

1997-11-01

The lattice energy (Elatt), slice energies (Eslice) and attachment energies (Eatt) of the different habit faces of ABP crystals have been calculated using the computer program HABIT. On the basis of the attachment energies of different crystal faces, the morphology was defined as {1 0 0}, {0 0 1}, {1 1 0}, {11bar0} and {1 01bar}. To confirm this theoretical prediction, we have grown ABP films and ABP crystals from the vapour phase. In both cases, the morphologically most important face was defined as {1 0 0} face using X-ray diffraction techniques. The remaining faces of the vapour-grown crystals were defined using a projection method, while the crystallites in the films were morphologically analysed by means of atomic force microscopy (AFM). The experimental morphologies are basically in agreement with the computation. Deviations from the equilibrium morphology can be ascribed to departure from equilibrium conditions during growth. For completeness, the results are compared with those for crystals grown from solutions for which deviations in morphology from the theoretical predictions can be ascribed to interaction between the crystal faces and solvent molecules.

Computing Equilibrium Chemical Compositions

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford

1995-01-01

Chemical Equilibrium With Transport Properties, 1993 (CET93) computer program provides data on chemical-equilibrium compositions. Aids calculation of thermodynamic properties of chemical systems. Information essential in design and analysis of such equipment as compressors, turbines, nozzles, engines, shock tubes, heat exchangers, and chemical-processing equipment. CET93/PC is version of CET93 specifically designed to run within 640K memory limit of MS-DOS operating system. CET93/PC written in FORTRAN.

Auxiliary principle technique and iterative algorithm for a perturbed system of generalized multi-valued mixed quasi-equilibrium-like problems.

PubMed

Rahaman, Mijanur; Pang, Chin-Tzong; Ishtyak, Mohd; Ahmad, Rais

2017-01-01

In this article, we introduce a perturbed system of generalized mixed quasi-equilibrium-like problems involving multi-valued mappings in Hilbert spaces. To calculate the approximate solutions of the perturbed system of generalized multi-valued mixed quasi-equilibrium-like problems, firstly we develop a perturbed system of auxiliary generalized multi-valued mixed quasi-equilibrium-like problems, and then by using the celebrated Fan-KKM technique, we establish the existence and uniqueness of solutions of the perturbed system of auxiliary generalized multi-valued mixed quasi-equilibrium-like problems. By deploying an auxiliary principle technique and an existence result, we formulate an iterative algorithm for solving the perturbed system of generalized multi-valued mixed quasi-equilibrium-like problems. Lastly, we study the strong convergence analysis of the proposed iterative sequences under monotonicity and some mild conditions. These results are new and generalize some known results in this field.

Computer program determines chemical equilibria in complex systems

NASA Technical Reports Server (NTRS)

Gordon, S.; Zeleznik, F. J.

1966-01-01

Computer program numerically solves nonlinear algebraic equations for chemical equilibrium based on iteration equations independent of choice of components. This program calculates theoretical performance for frozen and equilibrium composition during expansion and Chapman-Jouguet flame properties, studies combustion, and designs hardware.

A Newton method for the magnetohydrodynamic equilibrium equations

NASA Astrophysics Data System (ADS)

Oliver, Hilary James

We have developed and implemented a (J, B) space Newton method to solve the full nonlinear three dimensional magnetohydrodynamic equilibrium equations in toroidal geometry. Various cases have been run successfully, demonstrating significant improvement over Picard iteration, including a 3D stellarator equilibrium at β = 2%. The algorithm first solves the equilibrium force balance equation for the current density J, given a guess for the magnetic field B. This step is taken from the Picard-iterative PIES 3D equilibrium code. Next, we apply Newton's method to Ampere's Law by expansion of the functional J(B), which is defined by the first step. An analytic calculation in magnetic coordinates, of how the Pfirsch-Schlüter currents vary in the plasma in response to a small change in the magnetic field, yields the Newton gradient term (analogous to ∇f . δx in Newton's method for f(x) = 0). The algorithm is computationally feasible because we do this analytically, and because the gradient term is flux surface local when expressed in terms of a vector potential in an Ar=0 gauge. The equations are discretized by a hybrid spectral/offset grid finite difference technique, and leading order radial dependence is factored from Fourier coefficients to improve finite- difference accuracy near the polar-like origin. After calculating the Newton gradient term we transfer the equation from the magnetic grid to a fixed background grid, which greatly improves the code's performance.

Vibrational study and Natural Bond Orbital analysis of serotonin in monomer and dimer states by density functional theory

NASA Astrophysics Data System (ADS)

Borah, Mukunda Madhab; Devi, Th. Gomti

2018-06-01

The vibrational spectral analysis of Serotonin and its dimer were carried out using the Fourier Transform Infrared (FTIR) and Raman techniques. The equilibrium geometrical parameters, harmonic vibrational wavenumbers, Frontier orbitals, Mulliken atomic charges, Natural Bond orbitals, first order hyperpolarizability and some optimized energy parameters were computed by density functional theory with 6-31G(d,p) basis set. The detailed analysis of the vibrational spectra have been carried out by computing Potential Energy Distribution (PED, %) with the help of Vibrational Energy Distribution Analysis (VEDA) program. The second order delocalization energies E(2) confirms the occurrence of intramolecular Charge Transfer (ICT) within the molecule. The computed wavenumbers of Serotonin monomer and dimer were found in good agreement with the experimental Raman and IR values.

Vapor-liquid equilibrium thermodynamics of N2 + CH4 - Model and Titan applications

NASA Technical Reports Server (NTRS)

Thompson, W. R.; Zollweg, John A.; Gabis, David H.

1992-01-01

A thermodynamic model is presented for vapor-liquid equilibrium in the N2 + CH4 system, which is implicated in calculations of the Titan tropospheric clouds' vapor-liquid equilibrium thermodynamics. This model imposes constraints on the consistency of experimental equilibrium data, and embodies temperature effects by encompassing enthalpy data; it readily calculates the saturation criteria, condensate composition, and latent heat for a given pressure-temperature profile of the Titan atmosphere. The N2 content of condensate is about half of that computed from Raoult's law, and about 30 percent greater than that computed from Henry's law.

Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.

PubMed

Awasthi, Shalini; Kapil, Venkat; Nair, Nisanth N

2016-06-15

Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad, and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Efficient grid-based techniques for density functional theory

NASA Astrophysics Data System (ADS)

Rodriguez-Hernandez, Juan Ignacio

Understanding the chemical and physical properties of molecules and materials at a fundamental level often requires quantum-mechanical models for these substance's electronic structure. This type of many body quantum mechanics calculation is computationally demanding, hindering its application to substances with more than a few hundreds atoms. The supreme goal of many researches in quantum chemistry---and the topic of this dissertation---is to develop more efficient computational algorithms for electronic structure calculations. In particular, this dissertation develops two new numerical integration techniques for computing molecular and atomic properties within conventional Kohn-Sham-Density Functional Theory (KS-DFT) of molecular electronic structure. The first of these grid-based techniques is based on the transformed sparse grid construction. In this construction, a sparse grid is generated in the unit cube and then mapped to real space according to the pro-molecular density using the conditional distribution transformation. The transformed sparse grid was implemented in program deMon2k, where it is used as the numerical integrator for the exchange-correlation energy and potential in the KS-DFT procedure. We tested our grid by computing ground state energies, equilibrium geometries, and atomization energies. The accuracy on these test calculations shows that our grid is more efficient than some previous integration methods: our grids use fewer points to obtain the same accuracy. The transformed sparse grids were also tested for integrating, interpolating and differentiating in different dimensions (n = 1,2,3,6). The second technique is a grid-based method for computing atomic properties within QTAIM. It was also implemented in deMon2k. The performance of the method was tested by computing QTAIM atomic energies, charges, dipole moments, and quadrupole moments. For medium accuracy, our method is the fastest one we know of.

Computer program for calculating and fitting thermodynamic functions

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford

1992-01-01

A computer program is described which (1) calculates thermodynamic functions (heat capacity, enthalpy, entropy, and free energy) for several optional forms of the partition function, (2) fits these functions to empirical equations by means of a least-squares fit, and (3) calculates, as a function of temperture, heats of formation and equilibrium constants. The program provides several methods for calculating ideal gas properties. For monatomic gases, three methods are given which differ in the technique used for truncating the partition function. For diatomic and polyatomic molecules, five methods are given which differ in the corrections to the rigid-rotator harmonic-oscillator approximation. A method for estimating thermodynamic functions for some species is also given.

Irreducible Green's functions method for a quantum dot coupled to metallic and superconducting leads

NASA Astrophysics Data System (ADS)

Górski, Grzegorz; Kucab, Krzysztof

2017-05-01

Using irreducible Green's functions (IGF) method we analyse the Coulomb interaction dependence of the spectral functions and the transport properties of a quantum dot coupled to isotropic superconductor and metallic leads (SC-QD-N). The irreducible Green's functions method is the modification of classical equation of motion technique. The IGF scheme is based on differentiation of double-time Green's functions, both over the primary and secondary times. The IGF method allows to obtain the spectral functions for equilibrium and non-equilibrium impurity Anderson model used for SC-QD-N system. By the numerical computations, we show the change of spectral and the anomalous densities under the influence of the Coulomb interactions. The observed sign change of the anomalous spectral density can be used as the criterion of the SC singlet-Kondo singlet transition.

A review on the solution of Grad-Shafranov equation in the cylindrical coordinates based on the Chebyshev collocation technique

NASA Astrophysics Data System (ADS)

Amerian, Z.; Salem, M. K.; Salar Elahi, A.; Ghoranneviss, M.

2017-03-01

Equilibrium reconstruction consists of identifying, from experimental measurements, a distribution of the plasma current density that satisfies the pressure balance constraint. Numerous methods exist to solve the Grad-Shafranov equation, describing the equilibrium of plasma confined by an axisymmetric magnetic field. In this paper, we have proposed a new numerical solution to the Grad-Shafranov equation (an axisymmetric, magnetic field transformed in cylindrical coordinates solved with the Chebyshev collocation method) when the source term (current density function) on the right-hand side is linear. The Chebyshev collocation method is a method for computing highly accurate numerical solutions of differential equations. We describe a circular cross-section of the tokamak and present numerical result of magnetic surfaces on the IR-T1 tokamak and then compare the results with an analytical solution.

Equilibrium chemical reaction of supersonic hydrogen-air jets (the ALMA computer program)

NASA Technical Reports Server (NTRS)

Elghobashi, S.

1977-01-01

The ALMA (axi-symmetrical lateral momentum analyzer) program is concerned with the computation of two dimensional coaxial jets with large lateral pressure gradients. The jets may be free or confined, laminar or turbulent, reacting or non-reacting. Reaction chemistry is equilibrium.

On the computational modeling of the viscosity of colloidal dispersions and its relation with basic molecular interactions

NASA Astrophysics Data System (ADS)

Gama Goicochea, A.; Balderas Altamirano, M. A.; Lopez-Esparza, R.; Waldo-Mendoza, Miguel A.; Perez, E.

2015-09-01

The connection between fundamental interactions acting in molecules in a fluid and macroscopically measured properties, such as the viscosity between colloidal particles coated with polymers, is studied here. The role that hydrodynamic and Brownian forces play in colloidal dispersions is also discussed. It is argued that many-body systems in which all these interactions take place can be accurately solved using computational simulation tools. One of those modern tools is the technique known as dissipative particle dynamics, which incorporates Brownian and hydrodynamic forces, as well as basic conservative interactions. A case study is reported, as an example of the applications of this technique, which consists of the prediction of the viscosity and friction between two opposing parallel surfaces covered with polymer chains, under the influence of a steady flow. This work is intended to serve as an introduction to the subject of colloidal dispersions and computer simulations, for final-year undergraduate students and beginning graduate students who are interested in beginning research in soft matter systems. To that end, a computational code is included that students can use right away to study complex fluids in equilibrium.

Rapid computation of chemical equilibrium composition - An application to hydrocarbon combustion

NASA Technical Reports Server (NTRS)

Erickson, W. D.; Prabhu, R. K.

1986-01-01

A scheme for rapidly computing the chemical equilibrium composition of hydrocarbon combustion products is derived. A set of ten governing equations is reduced to a single equation that is solved by the Newton iteration method. Computation speeds are approximately 80 times faster than the often used free-energy minimization method. The general approach also has application to many other chemical systems.

An approximate viscous shock layer technique for calculating chemically reacting hypersonic flows about blunt-nosed bodies

NASA Technical Reports Server (NTRS)

Cheatwood, F. Mcneil; Dejarnette, Fred R.

1991-01-01

An approximate axisymmetric method was developed which can reliably calculate fully viscous hypersonic flows over blunt nosed bodies. By substituting Maslen's second order pressure expression for the normal momentum equation, a simplified form of the viscous shock layer (VSL) equations is obtained. This approach can solve both the subsonic and supersonic regions of the shock layer without a starting solution for the shock shape. The approach is applicable to perfect gas, equilibrium, and nonequilibrium flowfields. Since the method is fully viscous, the problems associated with a boundary layer solution with an inviscid layer solution are avoided. This procedure is significantly faster than the parabolized Navier-Stokes (PNS) or VSL solvers and would be useful in a preliminary design environment. Problems associated with a previously developed approximate VSL technique are addressed before extending the method to nonequilibrium calculations. Perfect gas (laminar and turbulent), equilibrium, and nonequilibrium solutions were generated for airflows over several analytic body shapes. Surface heat transfer, skin friction, and pressure predictions are comparable to VSL results. In addition, computed heating rates are in good agreement with experimental data. The present technique generates its own shock shape as part of its solution, and therefore could be used to provide more accurate initial shock shapes for higher order procedures which require starting solutions.

Numerical techniques in radiative heat transfer for general, scattering, plane-parallel media

NASA Technical Reports Server (NTRS)

Sharma, A.; Cogley, A. C.

1982-01-01

The study of radiative heat transfer with scattering usually leads to the solution of singular Fredholm integral equations. The present paper presents an accurate and efficient numerical method to solve certain integral equations that govern radiative equilibrium problems in plane-parallel geometry for both grey and nongrey, anisotropically scattering media. In particular, the nongrey problem is represented by a spectral integral of a system of nonlinear integral equations in space, which has not been solved previously. The numerical technique is constructed to handle this unique nongrey governing equation as well as the difficulties caused by singular kernels. Example problems are solved and the method's accuracy and computational speed are analyzed.

Thermodynamic modeling using BINGO-ANTIDOTE: A new strategy to investigate metamorphic rocks

NASA Astrophysics Data System (ADS)

Lanari, Pierre; Duesterhoeft, Erik

2016-04-01

BINGO-ANTIDOTE is a new program, combing the achievements of the two petrological software packages XMAPTOOLS[1] and THERIAK-DOMINO[2]. XMAPTOOLS affords information about compositional zoning in mineral and local bulk composition of domains at the thin sections scale. THERIAK-DOMINO calculates equilibrium phase assemblages from given bulk rock composition, temperature T and pressure P. Primarily BINGO-ANTIDOTE can be described as an inverse THERIAK-DOMINO, because it uses the information provided by XMAPTOOLS to calculate the probable P-T equilibrium conditions of metamorphic rocks. Consequently, the introduced program combines the strengths of forward Gibbs free energy minimization models with the intuitive output of inverse thermobarometry models. In order to get "best" P-T equilibrium conditions of a metamorphic rock sample and thus estimating the degree of agreement between the observed and calculated mineral assemblage, it is critical to define a reliable scoring strategy. BINGO uses the THERIAKD ADD-ON[3] (Duesterhoeft and de Capitani, 2013) and is a flexible model scorer with 3+1 evaluation criteria. These criteria are the statistical agreement between the observed and calculated mineral-assemblage, -proportions (vol%) and -composition (mol). Additionally, a total likelihood, consisting of the first three criteria, allows the user an evaluation of the most probable equilibrium P-T condition. ANTIDOTE is an interactive user interface, displaying the 3+1 evaluation criteria as probability P-T-maps. It can be used with and without XMAPTOOLS. As a stand-alone program, the user is able to give the program macroscopic observations (i.e., mineral names and proportions), which ANTIDOTE converts to a readable BINGO input. In this manner, the use of BINGO-ANTIDOTE opens up thermodynamics to students and people with only a basic knowledge of phase diagrams and thermodynamic modeling techniques. This presentation introduces BINGO-ANTIDOTE and includes typical examples of its functionality, such as the determination of P-T conditions of high-grade rocks. BINGO-ANTIDOTE is still under development and will soon be freely available online. References: [1] Lanari P., Vidal O., De Andrade V., Dubacq B., Lewin E., Grosch E. G. and Schwartz S. (2013) XMapTools: a MATLAB©-based program for electron microprobe X-ray image processing and geothermobarometry. Comput. Geosci. 62, 227-240. [2] de Capitani C. and Petrakakis K. (2010) The computation of equilibrium assemblage diagrams with Theriak/Domino software. Am. Mineral. 95, 1006-1016. [3] Duesterhoeft E. and de Capitani C. (2013) Theriak_D: An add-on to implement equilibrium computations in geodynamic models. Geochem. Geophys. Geosyst. 14, 4962-4967.

Computer program determines chemical composition of physical system at equilibrium

NASA Technical Reports Server (NTRS)

Kwong, S. S.

1966-01-01

FORTRAN 4 digital computer program calculates equilibrium composition of complex, multiphase chemical systems. This is a free energy minimization method with solution of the problem reduced to mathematical operations, without concern for the chemistry involved. Also certain thermodynamic properties are determined as byproducts of the main calculations.

Computer Assisted Instruction in Economics: An Approach for Illustrating General Equilibrium Concepts.

ERIC Educational Resources Information Center

Gillespie, Robert W.

A market exchange simulation utilizing the PLATO computer-assisted instructional system at the University of Illinois has been designed to teach students the principles of a general equilibrium system. It serves a laboratory function which supplements traditional instruction by stimulating students' interests and providing them with illustrations…

Data Science Innovations That Streamline Development, Documentation, Reproducibility, and Dissemination of Models in Computational Thermodynamics: An Application of Image Processing Techniques for Rapid Computation, Parameterization and Modeling of Phase Diagrams

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2014-12-01

Computational thermodynamics (CT) represents a collection of numerical techniques that are used to calculate quantitative results from thermodynamic theory. In the Earth sciences, CT is most often applied to estimate the equilibrium properties of solutions, to calculate phase equilibria from models of the thermodynamic properties of materials, and to approximate irreversible reaction pathways by modeling these as a series of local equilibrium steps. The thermodynamic models that underlie CT calculations relate the energy of a phase to temperature, pressure and composition. These relationships are not intuitive and they are seldom well constrained by experimental data; often, intuition must be applied to generate a robust model that satisfies the expectations of use. As a consequence of this situation, the models and databases the support CT applications in geochemistry and petrology are tedious to maintain as new data and observations arise. What is required to make the process more streamlined and responsive is a computational framework that permits the rapid generation of observable outcomes from the underlying data/model collections, and importantly, the ability to update and re-parameterize the constitutive models through direct manipulation of those outcomes. CT procedures that take models/data to the experiential reference frame of phase equilibria involve function minimization, gradient evaluation, the calculation of implicit lines, curves and surfaces, contour extraction, and other related geometrical measures. All these procedures are the mainstay of image processing analysis. Since the commercial escalation of video game technology, open source image processing libraries have emerged (e.g., VTK) that permit real time manipulation and analysis of images. These tools find immediate application to CT calculations of phase equilibria by permitting rapid calculation and real time feedback between model outcome and the underlying model parameters.

A "User-Friendly" Program for Vapor-Liquid Equilibrium.

ERIC Educational Resources Information Center

Da Silva, Francisco A.; And Others

1991-01-01

Described is a computer software package suitable for teaching and research in the area of multicomponent vapor-liquid equilibrium. This program, which has a complete database, can accomplish phase-equilibrium calculations using various models and graph the results. (KR)

Unified gas-kinetic scheme with multigrid convergence for rarefied flow study

NASA Astrophysics Data System (ADS)

Zhu, Yajun; Zhong, Chengwen; Xu, Kun

2017-09-01

The unified gas kinetic scheme (UGKS) is based on direct modeling of gas dynamics on the mesh size and time step scales. With the modeling of particle transport and collision in a time-dependent flux function in a finite volume framework, the UGKS can connect the flow physics smoothly from the kinetic particle transport to the hydrodynamic wave propagation. In comparison with the direct simulation Monte Carlo (DSMC) method, the current equation-based UGKS can implement implicit techniques in the updates of macroscopic conservative variables and microscopic distribution functions. The implicit UGKS significantly increases the convergence speed for steady flow computations, especially in the highly rarefied and near continuum regimes. In order to further improve the computational efficiency, for the first time, a geometric multigrid technique is introduced into the implicit UGKS, where the prediction step for the equilibrium state and the evolution step for the distribution function are both treated with multigrid acceleration. More specifically, a full approximate nonlinear system is employed in the prediction step for fast evaluation of the equilibrium state, and a correction linear equation is solved in the evolution step for the update of the gas distribution function. As a result, convergent speed has been greatly improved in all flow regimes from rarefied to the continuum ones. The multigrid implicit UGKS (MIUGKS) is used in the non-equilibrium flow study, which includes microflow, such as lid-driven cavity flow and the flow passing through a finite-length flat plate, and high speed one, such as supersonic flow over a square cylinder. The MIUGKS shows 5-9 times efficiency increase over the previous implicit scheme. For the low speed microflow, the efficiency of MIUGKS is several orders of magnitude higher than the DSMC. Even for the hypersonic flow at Mach number 5 and Knudsen number 0.1, the MIUGKS is still more than 100 times faster than the DSMC method for obtaining a convergent steady state solution.

Out of equilibrium transport through an Anderson impurity: probing scaling laws within the equation of motion approach.

PubMed

Balseiro, C A; Usaj, G; Sánchez, M J

2010-10-27

We study non-equilibrium electron transport through a quantum impurity coupled to metallic leads using the equation of motion technique at finite temperature T. Assuming that the interactions are taking place solely in the impurity and focusing on the infinite Hubbard limit, we compute the out of equilibrium density of states and the differential conductance G(2)(T, V) in order to test several scaling laws. We find that G(2)(T, V)/G(2)(T, 0) is a universal function of both eV/T(K) and T/T(K), T(K) being the Kondo temperature. The effect of an in-plane magnetic field on the splitting of the zero bias anomaly in the differential conductance is also analyzed. For a Zeeman splitting Δ, the computed differential conductance peak splitting depends only on Δ/T(K), and for large fields approaches the value of 2Δ. Besides studying the traditional two leads setup, we also consider other configurations that mimic recent experiments, namely, an impurity embedded in a mesoscopic wire and the presence of a third weakly coupled lead. In these cases, a double peak structure of the Kondo resonance is clearly obtained in the differential conductance while the amplitude of the highest peak is shown to decrease as ln(eV/T(K)). Several features of these results are in qualitative agreement with recent experimental observations reported on quantum dots.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

NASA Technical Reports Server (NTRS)

Glass, Christopher E.

1990-01-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

NASA Astrophysics Data System (ADS)

Glass, Christopher E.

1990-08-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

Wavelet Algorithms for Illumination Computations

NASA Astrophysics Data System (ADS)

Schroder, Peter

One of the core problems of computer graphics is the computation of the equilibrium distribution of light in a scene. This distribution is given as the solution to a Fredholm integral equation of the second kind involving an integral over all surfaces in the scene. In the general case such solutions can only be numerically approximated, and are generally costly to compute, due to the geometric complexity of typical computer graphics scenes. For this computation both Monte Carlo and finite element techniques (or hybrid approaches) are typically used. A simplified version of the illumination problem is known as radiosity, which assumes that all surfaces are diffuse reflectors. For this case hierarchical techniques, first introduced by Hanrahan et al. (32), have recently gained prominence. The hierarchical approaches lead to an asymptotic improvement when only finite precision is required. The resulting algorithms have cost proportional to O(k^2 + n) versus the usual O(n^2) (k is the number of input surfaces, n the number of finite elements into which the input surfaces are meshed). Similarly a hierarchical technique has been introduced for the more general radiance problem (which allows glossy reflectors) by Aupperle et al. (6). In this dissertation we show the equivalence of these hierarchical techniques to the use of a Haar wavelet basis in a general Galerkin framework. By so doing, we come to a deeper understanding of the properties of the numerical approximations used and are able to extend the hierarchical techniques to higher orders. In particular, we show the correspondence of the geometric arguments underlying hierarchical methods to the theory of Calderon-Zygmund operators and their sparse realization in wavelet bases. The resulting wavelet algorithms for radiosity and radiance are analyzed and numerical results achieved with our implementation are reported. We find that the resulting algorithms achieve smaller and smoother errors at equivalent work.

I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.

PubMed

Procacci, Piero

2016-06-01

In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non-covalent bonding in drug-receptor systems. I show that most of the pitfalls and entanglements for the binding free energy evaluation in computer simulations are rooted in the equilibrium assumption that is implicit in the reversible method. These critical issues can be resolved by using a non-equilibrium variant of the alchemical method in molecular dynamics simulations, relying on the production of many independent trajectories with a continuous dynamical evolution of an externally driven alchemical coordinate, completing the decoupling of the ligand in a matter of a few tens of picoseconds rather than nanoseconds. The absolute binding free energy can be recovered from the annihilation work distributions by applying an unbiased unidirectional free energy estimate, on the assumption that any observed work distribution is given by a mixture of normal distributions, whose components are identical in either direction of the non-equilibrium process, with weights regulated by the Crooks theorem. I finally show that the inherent reliability and accuracy of the unidirectional estimate of the decoupling free energies, based on the production of a few hundreds of non-equilibrium independent sub-nanosecond unrestrained alchemical annihilation processes, is a direct consequence of the funnel-like shape of the free energy surface in molecular recognition. An application of the technique to a real drug-receptor system is presented in the companion paper.

A General Method for Automatic Computation of Equilibrium Compositions and Theoretical Rocket Performance of Propellants

NASA Technical Reports Server (NTRS)

Gordon, Sanford; Zeleznik, Frank J.; Huff, Vearl N.

1959-01-01

A general computer program for chemical equilibrium and rocket performance calculations was written for the IBM 650 computer with 2000 words of drum storage, 60 words of high-speed core storage, indexing registers, and floating point attachments. The program is capable of carrying out combustion and isentropic expansion calculations on a chemical system that may include as many as 10 different chemical elements, 30 reaction products, and 25 pressure ratios. In addition to the equilibrium composition, temperature, and pressure, the program calculates specific impulse, specific impulse in vacuum, characteristic velocity, thrust coefficient, area ratio, molecular weight, Mach number, specific heat, isentropic exponent, enthalpy, entropy, and several thermodynamic first derivatives.

Phase equilibrium of methane and nitrogen at low temperatures - Application to Titan

NASA Technical Reports Server (NTRS)

Kouvaris, Louis C.; Flasar, F. M.

1991-01-01

Since the vapor phase composition of Titan's methane-nitrogen lower atmosphere is uniquely determined as a function of the Gibbs phase rule, these data are presently computed via integration of the Gibbs-Duhem equation. The thermodynamic consistency of published measurements and calculations of the vapor phase composition is then examined, and the saturated mole fraction of gaseous methane is computed as a function of altitude up to the 700-mbar level. The mole fraction is found to lie approximately halfway between that computed from Raoult's law, for a gas in equilibrium with an ideal solution of liquid nitrogen and methane, and that for a gas in equilibrium with pure liquid methane.

Numerical study of the geometry of the phase space of the Augmented Hill Three-Body problem

NASA Astrophysics Data System (ADS)

Farrés, Ariadna; Jorba, Àngel; Mondelo, Josep-Maria

2017-09-01

The Augmented Hill Three-Body problem is an extension of the classical Hill problem that, among other applications, has been used to model the motion of a solar sail around an asteroid. This model is a 3 degrees of freedom (3DoF) Hamiltonian system that depends on four parameters. This paper describes the bounded motions (periodic orbits and invariant tori) in an extended neighbourhood of some of the equilibrium points of the model. An interesting feature is the existence of equilibrium points with a 1:1 resonance, whose neighbourhood we also describe. The main tools used are the computation of periodic orbits (including their stability and bifurcations), the reduction of the Hamiltonian to centre manifolds at equilibria, and the numerical approximation of invariant tori. It is remarkable how the combination of these techniques allows the description of the dynamics of a 3DoF Hamiltonian system.

Improvements on non-equilibrium and transport Green function techniques: The next-generation TRANSIESTA

NASA Astrophysics Data System (ADS)

Papior, Nick; Lorente, Nicolás; Frederiksen, Thomas; García, Alberto; Brandbyge, Mads

2017-03-01

We present novel methods implemented within the non-equilibrium Green function code (NEGF) TRANSIESTA based on density functional theory (DFT). Our flexible, next-generation DFT-NEGF code handles devices with one or multiple electrodes (Ne ≥ 1) with individual chemical potentials and electronic temperatures. We describe its novel methods for electrostatic gating, contour optimizations, and assertion of charge conservation, as well as the newly implemented algorithms for optimized and scalable matrix inversion, performance-critical pivoting, and hybrid parallelization. Additionally, a generic NEGF "post-processing" code (TBTRANS/PHTRANS) for electron and phonon transport is presented with several novelties such as Hamiltonian interpolations, Ne ≥ 1 electrode capability, bond-currents, generalized interface for user-defined tight-binding transport, transmission projection using eigenstates of a projected Hamiltonian, and fast inversion algorithms for large-scale simulations easily exceeding 106 atoms on workstation computers. The new features of both codes are demonstrated and bench-marked for relevant test systems.

Understanding the connection between conformational changes of peptides and equilibrium thermal fluctuations.

PubMed

Soler, Miguel A; Zúñiga, José; Requena, Alberto; Bastida, Adolfo

2017-02-01

Despite the increasing evidence that conformational transitions in peptides and proteins are driven by specific vibrational energy pathways along the molecule, the current experimental techniques of analysis do as yet not allow to study these biophysical processes in terms of anisotropic energy flows. Computational methods offer a complementary approach to obtain a more detailed understanding of the vibrational and conformational dynamics of these systems. Accordingly, in this work we investigate jointly the vibrational energy distribution and the conformational dynamics of trialanine peptide in water solution at room temperature by applying the Instantaneous Normal Mode analysis to the results derived from equilibrium molecular dynamics simulations. It is shown that conformational changes in trialanine are triggered by the vibrational energy accumulated in the low-frequency modes of the molecule, and that excitation is caused exclusively by thermal fluctuations of the solute-solvent system, thus excluding the possibility of an intramolecular vibrational energy redistribution process.

Crystal structure optimisation using an auxiliary equation of state

NASA Astrophysics Data System (ADS)

Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; Walsh, Aron

2015-11-01

Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

Study of Stark broadening of Li I 460 and 497 nm spectral lines with independent plasma diagnostics by Thomson scattering

NASA Astrophysics Data System (ADS)

Dzierżȩga, Krzysztof; Piȩta, Tomasz; Zawadzki, Witold; Stambulchik, Evgeny; Gavrilović-Božović, Marijana; Jovićević, Sonja; Pokrzywka, Bartłomiej

2018-02-01

We present results of experimental and theoretical studies of the Stark broadening of the Li I 460 nm spectral line with forbidden components and of the isolated 497 nm line. Plasma was induced by Nd:YAG laser radiation at 1064 nm with pulse duration ˜4.5 ns. Laser-induced plasma was generated in front of the alumina pellet, with some content of Li2CO3, placed in a vacuum chamber filled with argon under reduced pressure. Plasma diagnostics was performed using the laser Thomson scattering technique, free from assumptions about the plasma equilibrium state and its composition and so independently of plasma emission spectra. Spatially resolved spectra with Li lines were obtained from the measured, laterally integrated ones applying the inverse Abel transform. The Stark profiles were calculated by computer simulation method assuming a plasma in the local thermodynamic equilibrium. Calculations were performed for experimentally-inferred electron densities and temperatures, from 1.422 × 1023 to 3.55 × 1022 m-3 and from 1.96 eV to 1.04 eV, respectively. Our studies show very good agreement between experimental Stark profiles and those computer simulated.

Mechanical behavior of cells in microinjection: a minimum potential energy study.

PubMed

Liu, Fei; Wu, Dan; Chen, Ken

2013-08-01

Microinjection is a widely used technique to deliver foreign materials into biological cells. We propose a mathematical model to study the mechanical behavior of a cell in microinjection. Firstly, a cell is modeled by a hyperelastic membrane and interior cytoplasm. Then, based on the fact that the equilibrium configuration of a cell would minimize the potential energy, the energy function during microinjection is analyzed. With Lagrange multiplier and Rayleigh-Ritz technique, we successfully minimize the potential energy and obtain the equilibrium configuration. Upon this model, the injection force, the injection distance, the radius of the microinjector and the membrane stress are studied. The analysis demonstrates that the microinjector radius has a significant influence on the cell mechanical behavior: (1) the larger radius generates larger injection force and larger interior pressure at the same injection distance; (2) the radius determines the place where the membrane is most likely to rupture by governing the membrane stress distribution. For a fine microinjector with radius less than 20% of the cell radius, the most likely rupture point located at the edge of the contact area between the microinjector and the membrane; however, it may move to the middle of the equilibrium configuration as the radius increases. To verify our model, some experiments were conducted on zebrafish egg cells. The results show that the computational analysis agrees with the experimental data, which supports the findings from the theoretical model. Copyright © 2013 Elsevier Ltd. All rights reserved.

The Nash Equilibrium Revisited: Chaos and Complexity Hidden in Simplicity

NASA Astrophysics Data System (ADS)

Fellman, Philip V.

The Nash Equilibrium is a much discussed, deceptively complex, method for the analysis of non-cooperative games (McLennan and Berg, 2005). If one reads many of the commonly available definitions the description of the Nash Equilibrium is deceptively simple in appearance. Modern research has discovered a number of new and important complex properties of the Nash Equilibrium, some of which remain as contemporary conundrums of extraordinary difficulty and complexity (Quint and Shubik, 1997). Among the recently discovered features which the Nash Equilibrium exhibits under various conditions are heteroclinic Hamiltonian dynamics, a very complex asymptotic structure in the context of two-player bi-matrix games and a number of computationally complex or computationally intractable features in other settings (Sato, Akiyama and Farmer, 2002). This paper reviews those findings and then suggests how they may inform various market prediction strategies.

Thermodynamic properties of gaseous fluorocarbons and isentropic equilibrium expansions of two binary mixtures of fluorocarbons and argon

NASA Technical Reports Server (NTRS)

Talcott, N. A., Jr.

1977-01-01

Equations and computer code are given for the thermodynamic properties of gaseous fluorocarbons in chemical equilibrium. In addition, isentropic equilibrium expansions of two binary mixtures of fluorocarbons and argon are included. The computer code calculates the equilibrium thermodynamic properties and, in some cases, the transport properties for the following fluorocarbons: CCl2F, CCl2F2, CBrF3, CF4, CHCl2F, CHF3, CCL2F-CCl2F, CCLF2-CClF2, CF3-CF3, and C4F8. Equilibrium thermodynamic properties are tabulated for six of the fluorocarbons(CCl3F, CCL2F2, CBrF3, CF4, CF3-CF3, and C4F8) and pressure-enthalpy diagrams are presented for CBrF3.

Thermal conductivity of MgO and MgSiO3 at lower mantle conditions from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Jahn, S.; Haigis, V.; Salanne, M.

2011-12-01

Thermal conductivity is an important physical parameter that controls the heat flow in the Earth's core and mantle. The heat flow from the core to the mantle influences mantle dynamics and the convective regime of the liquid outer core, which drives the geodynamo. Although thermal conductivities of important mantle minerals at ambient pressure are well-known (Hofmeister, 1999), experimentalists encounter major difficulties to measure thermal conductivities at high pressures and temperatures. Extrapolations of experimental data to high pressures have a large uncertainty and hence the heat transport in minerals at conditions of the deep mantle is not well constrained. Recently, the thermal conductivity of MgO at lower mantle conditions was computed from first-principles simulations (e.g. de Koker (2009), Stackhouse et al. (2010)). Here, we used classical molecular dynamics to calculate thermal conductivities of MgO and MgSiO3 in the perovskite and post-perovskite structures at different pressures and temperatures. The interactions between atoms were treated by an advanced ionic interaction model which was shown to describe the behavior of materials reliably within a wide pressure and temperature range (Jahn & Madden, 2007). Two alternative techniques were used and compared. In non-equilibrium MD, an energy flow is imposed on the system, and the thermal conductivity is taken to be inversely proportional to the temperature gradient that builds up in response to this flow. The other technique (which is still too expensive for first principles methods) uses standard equilibrium MD and extracts the thermal conductivity from energy current correlation functions, according to the Green-Kubo formula. As a benchmark for the interaction potential, we calculated the thermal conductivity of fcc MgO at 2000K and 149GPa, where data from ab-initio non-equilibrium MD are available (Stackhouse et al., 2010). The results agree within the error bars, which justifies the use of the model for the calculation of thermal conductivities. However, with the non-equilibrium technique, the conductivity depends strongly on the size of the simulation box. Therefore, a scaling to infinite system size has to be applied, which introduces some uncertainty to the final result. The equilibrium MD method, on the other hand, seems to be less sensitive to finite-size effects. We will present computed thermal conductivities of MgO and MgSiO3 in the perovskite and post-perovskite structures at 138 GPa and temperatures of 300 K and 3000 K, the latter corresponding to conditions in the D'' layer. This allows an assessment of the extrapolations to high pressures and temperatures used in the literature. Jahn S & Madden PA (2007) Phys. Earth Planet. Int. 162, 129 de Koker N (2009) Phys. Rev. Lett. 103, 125902 Hofmeister AM (1999) Science 283, 1699 Stackhouse S et al. (2010) Phys. Rev. Lett. 104, 208501

Myoglobin structure and function: A multiweek biochemistry laboratory project.

PubMed

Silverstein, Todd P; Kirk, Sarah R; Meyer, Scott C; Holman, Karen L McFarlane

2015-01-01

We have developed a multiweek laboratory project in which students isolate myoglobin and characterize its structure, function, and redox state. The important laboratory techniques covered in this project include size-exclusion chromatography, electrophoresis, spectrophotometric titration, and FTIR spectroscopy. Regarding protein structure, students work with computer modeling and visualization of myoglobin and its homologues, after which they spectroscopically characterize its thermal denaturation. Students also study protein function (ligand binding equilibrium) and are instructed on topics in data analysis (calibration curves, nonlinear vs. linear regression). This upper division biochemistry laboratory project is a challenging and rewarding one that not only exposes students to a wide variety of important biochemical laboratory techniques but also ties those techniques together to work with a single readily available and easily characterized protein, myoglobin. © 2015 International Union of Biochemistry and Molecular Biology.

Computer simulation of surface and film processes

NASA Technical Reports Server (NTRS)

Tiller, W. A.; Halicioglu, M. T.

1984-01-01

All the investigations which were performed employed in one way or another a computer simulation technique based on atomistic level considerations. In general, three types of simulation methods were used for modeling systems with discrete particles that interact via well defined potential functions: molecular dynamics (a general method for solving the classical equations of motion of a model system); Monte Carlo (the use of Markov chain ensemble averaging technique to model equilibrium properties of a system); and molecular statics (provides properties of a system at T = 0 K). The effects of three-body forces on the vibrational frequencies of triatomic cluster were investigated. The multilayer relaxation phenomena for low index planes of an fcc crystal was analyzed also as a function of the three-body interactions. Various surface properties for Si and SiC system were calculated. Results obtained from static simulation calculations for slip formation were presented. The more elaborate molecular dynamics calculations on the propagation of cracks in two-dimensional systems were outlined.

Thermal characterization assessment of rigid and flexible water models in a nanogap using molecular dynamics

NASA Astrophysics Data System (ADS)

Akıner, Tolga; Mason, Jeremy; Ertürk, Hakan

2017-11-01

The thermal properties of the TIP3P and TIP5P water models are investigated using equilibrium and non-equilibrium molecular dynamics techniques in the presence of solid surfaces. The performance of the non-equilibrium technique for rigid molecules is found to depend significantly on the distribution of atomic degrees of freedom. An improved approach to distribute atomic degrees of freedom is proposed for which the thermal conductivity of the TIP5P model agrees more closely with equilibrium molecular dynamics and experimental results than the existing state of the art.

Performance Modeling of Experimental Laser Lightcrafts

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Chen, Yen-Sen; Liu, Jiwen; Myrabo, Leik N.; Mead, Franklin B., Jr.; Turner, Jim (Technical Monitor)

2001-01-01

A computational plasma aerodynamics model is developed to study the performance of a laser propelled Lightcraft. The computational methodology is based on a time-accurate, three-dimensional, finite-difference, chemically reacting, unstructured grid, pressure-based formulation. The underlying physics are added and tested systematically using a building-block approach. The physics modeled include non-equilibrium thermodynamics, non-equilibrium air-plasma finite-rate kinetics, specular ray tracing, laser beam energy absorption and refraction by plasma, non-equilibrium plasma radiation, and plasma resonance. A series of transient computations are performed at several laser pulse energy levels and the simulated physics are discussed and compared with those of tests and literatures. The predicted coupling coefficients for the Lightcraft compared reasonably well with those of tests conducted on a pendulum apparatus.

Multiscale analysis of heart rate dynamics: entropy and time irreversibility measures.

PubMed

Costa, Madalena D; Peng, Chung-Kang; Goldberger, Ary L

2008-06-01

Cardiovascular signals are largely analyzed using traditional time and frequency domain measures. However, such measures fail to account for important properties related to multiscale organization and non-equilibrium dynamics. The complementary role of conventional signal analysis methods and emerging multiscale techniques, is, therefore, an important frontier area of investigation. The key finding of this presentation is that two recently developed multiscale computational tools--multiscale entropy and multiscale time irreversibility--are able to extract information from cardiac interbeat interval time series not contained in traditional methods based on mean, variance or Fourier spectrum (two-point correlation) techniques. These new methods, with careful attention to their limitations, may be useful in diagnostics, risk stratification and detection of toxicity of cardiac drugs.

Criticality of the random field Ising model in and out of equilibrium: A nonperturbative functional renormalization group description

NASA Astrophysics Data System (ADS)

Balog, Ivan; Tarjus, Gilles; Tissier, Matthieu

2018-03-01

We show that, contrary to previous suggestions based on computer simulations or erroneous theoretical treatments, the critical points of the random-field Ising model out of equilibrium, when quasistatically changing the applied source at zero temperature, and in equilibrium are not in the same universality class below some critical dimension dD R≈5.1 . We demonstrate this by implementing a nonperturbative functional renormalization group for the associated dynamical field theory. Above dD R, the avalanches, which characterize the evolution of the system at zero temperature, become irrelevant at large distance, and hysteresis and equilibrium critical points are then controlled by the same fixed point. We explain how to use computer simulation and finite-size scaling to check the correspondence between in and out of equilibrium criticality in a far less ambiguous way than done so far.

Combustion of hydrogen injected into a supersonic airstream (a guide to the HISS computer program)

NASA Technical Reports Server (NTRS)

Dyer, D. F.; Maples, G.; Spalding, D. B.

1976-01-01

A computer program based on a finite-difference, implicit numerical integration scheme is described for the prediction of hydrogen injected into a supersonic airstream at an angle ranging from normal to parallel to the airstream main flow direction. Results of calculations for flow and thermal property distributions were compared with 'cold flow data' taken by NASA/Langley and show excellent correlation. Typical results for equilibrium combustion are presented and exhibit qualitatively plausible behavior. Computer time required for a given case is approximately one minute on a CDC 7600. A discussion of the assumption of parabolic flow in the injection region is given which demonstrates that improvement in calculation in this region could be obtained by a partially-parabolic procedure which has been developed. It is concluded that the technique described provides an efficient and reliable means for analyzing hydrogen injection into supersonic airstreams and the subsequent combustion.

Investigation on imperfection sensitivity of composite cylindrical shells using the nonlinearity reduction technique and the polynomial chaos method

NASA Astrophysics Data System (ADS)

Liang, Ke; Sun, Qin; Liu, Xiaoran

2018-05-01

The theoretical buckling load of a perfect cylinder must be reduced by a knock-down factor to account for structural imperfections. The EU project DESICOS proposed a new robust design for imperfection-sensitive composite cylindrical shells using the combination of deterministic and stochastic simulations, however the high computational complexity seriously affects its wider application in aerospace structures design. In this paper, the nonlinearity reduction technique and the polynomial chaos method are implemented into the robust design process, to significantly lower computational costs. The modified Newton-type Koiter-Newton approach which largely reduces the number of degrees of freedom in the nonlinear finite element model, serves as the nonlinear buckling solver to trace the equilibrium paths of geometrically nonlinear structures efficiently. The non-intrusive polynomial chaos method provides the buckling load with an approximate chaos response surface with respect to imperfections and uses buckling solver codes as black boxes. A fast large-sample study can be applied using the approximate chaos response surface to achieve probability characteristics of buckling loads. The performance of the method in terms of reliability, accuracy and computational effort is demonstrated with an unstiffened CFRP cylinder.

Sedimentation equilibrium analysis of protein interactions with global implicit mass conservation constraints and systematic noise decomposition.

PubMed

Vistica, Jennifer; Dam, Julie; Balbo, Andrea; Yikilmaz, Emine; Mariuzza, Roy A; Rouault, Tracey A; Schuck, Peter

2004-03-15

Sedimentation equilibrium is a powerful tool for the characterization of protein self-association and heterogeneous protein interactions. Frequently, it is applied in a configuration with relatively long solution columns and with equilibrium profiles being acquired sequentially at several rotor speeds. The present study proposes computational tools, implemented in the software SEDPHAT, for the global analysis of equilibrium data at multiple rotor speeds with multiple concentrations and multiple optical detection methods. The detailed global modeling of such equilibrium data can be a nontrivial computational problem. It was shown previously that mass conservation constraints can significantly improve and extend the analysis of heterogeneous protein interactions. Here, a method for using conservation of mass constraints for the macromolecular redistribution is proposed in which the effective loading concentrations are calculated from the sedimentation equilibrium profiles. The approach is similar to that described by Roark (Biophys. Chem. 5 (1976) 185-196), but its utility is extended by determining the bottom position of the solution columns from the macromolecular redistribution. For analyzing heterogeneous associations at multiple protein concentrations, additional constraints that relate the effective loading concentrations of the different components or their molar ratio in the global analysis are introduced. Equilibrium profiles at multiple rotor speeds also permit the algebraic determination of radial-dependent baseline profiles, which can govern interference optical ultracentrifugation data, but usually also occur, to a smaller extent, in absorbance optical data. Finally, the global analysis of equilibrium profiles at multiple rotor speeds with implicit mass conservation and computation of the bottom of the solution column provides an unbiased scale for determining molar mass distributions of noninteracting species. The properties of these tools are studied with theoretical and experimental data sets.

Algorithmic Mechanism Design of Evolutionary Computation.

PubMed

Pei, Yan

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.

Algorithmic Mechanism Design of Evolutionary Computation

PubMed Central

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

A Simple Method for Automated Equilibration Detection in Molecular Simulations.

PubMed

Chodera, John D

2016-04-12

Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure and demonstrate its utility on typical molecular simulation data.

A simple method for automated equilibration detection in molecular simulations

PubMed Central

Chodera, John D.

2016-01-01

Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest, in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure, and demonstrate its utility on typical molecular simulation data. PMID:26771390

Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

2016-02-01

We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

NON-EQUILIBRIUM HELIUM IONIZATION IN AN MHD SIMULATION OF THE SOLAR ATMOSPHERE

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

Golding, Thomas Peter; Carlsson, Mats; Leenaarts, Jorrit, E-mail: thomas.golding@astro.uio.no, E-mail: mats.carlsson@astro.uio.no, E-mail: jorrit.leenaarts@astro.su.se

The ionization state of the gas in the dynamic solar chromosphere can depart strongly from the instantaneous statistical equilibrium commonly assumed in numerical modeling. We improve on earlier simulations of the solar atmosphere that only included non-equilibrium hydrogen ionization by performing a 2D radiation-magnetohydrodynamics simulation featuring non-equilibrium ionization of both hydrogen and helium. The simulation includes the effect of hydrogen Lyα and the EUV radiation from the corona on the ionization and heating of the atmosphere. Details on code implementation are given. We obtain helium ion fractions that are far from their equilibrium values. Comparison with models with local thermodynamicmore » equilibrium (LTE) ionization shows that non-equilibrium helium ionization leads to higher temperatures in wavefronts and lower temperatures in the gas between shocks. Assuming LTE ionization results in a thermostat-like behavior with matter accumulating around the temperatures where the LTE ionization fractions change rapidly. Comparison of DEM curves computed from our models shows that non-equilibrium ionization leads to more radiating material in the temperature range 11–18 kK, compared to models with LTE helium ionization. We conclude that non-equilibrium helium ionization is important for the dynamics and thermal structure of the upper chromosphere and transition region. It might also help resolve the problem that intensities of chromospheric lines computed from current models are smaller than those observed.« less

First-principles simulations of heat transport

NASA Astrophysics Data System (ADS)

Puligheddu, Marcello; Gygi, Francois; Galli, Giulia

2017-11-01

Advances in understanding heat transport in solids were recently reported by both experiment and theory. However an efficient and predictive quantum simulation framework to investigate thermal properties of solids, with the same complexity as classical simulations, has not yet been developed. Here we present a method to compute the thermal conductivity of solids by performing ab initio molecular dynamics at close to equilibrium conditions, which only requires calculations of first-principles trajectories and atomic forces, thus avoiding direct computation of heat currents and energy densities. In addition the method requires much shorter sequential simulation times than ordinary molecular dynamics techniques, making it applicable within density functional theory. We discuss results for a representative oxide, MgO, at different temperatures and for ordered and nanostructured morphologies, showing the performance of the method in different conditions.

The analysis of composite laminated beams using a 2D interpolating meshless technique

NASA Astrophysics Data System (ADS)

Sadek, S. H. M.; Belinha, J.; Parente, M. P. L.; Natal Jorge, R. M.; de Sá, J. M. A. César; Ferreira, A. J. M.

2018-02-01

Laminated composite materials are widely implemented in several engineering constructions. For its relative light weight, these materials are suitable for aerospace, military, marine, and automotive structural applications. To obtain safe and economical structures, the modelling analysis accuracy is highly relevant. Since meshless methods in the recent years achieved a remarkable progress in computational mechanics, the present work uses one of the most flexible and stable interpolation meshless technique available in the literature—the Radial Point Interpolation Method (RPIM). Here, a 2D approach is considered to numerically analyse composite laminated beams. Both the meshless formulation and the equilibrium equations ruling the studied physical phenomenon are presented with detail. Several benchmark beam examples are studied and the results are compared with exact solutions available in the literature and the results obtained from a commercial finite element software. The results show the efficiency and accuracy of the proposed numeric technique.

The solution of radiative transfer problems in molecular bands without the LTE assumption by accelerated lambda iteration methods

NASA Technical Reports Server (NTRS)

Kutepov, A. A.; Kunze, D.; Hummer, D. G.; Rybicki, G. B.

1991-01-01

An iterative method based on the use of approximate transfer operators, which was designed initially to solve multilevel NLTE line formation problems in stellar atmospheres, is adapted and applied to the solution of the NLTE molecular band radiative transfer in planetary atmospheres. The matrices to be constructed and inverted are much smaller than those used in the traditional Curtis matrix technique, which makes possible the treatment of more realistic problems using relatively small computers. This technique converges much more rapidly than straightforward iteration between the transfer equation and the equations of statistical equilibrium. A test application of this new technique to the solution of NLTE radiative transfer problems for optically thick and thin bands (the 4.3 micron CO2 band in the Venusian atmosphere and the 4.7 and 2.3 micron CO bands in the earth's atmosphere) is described.

Application of an enriched FEM technique in thermo-mechanical contact problems

NASA Astrophysics Data System (ADS)

Khoei, A. R.; Bahmani, B.

2018-02-01

In this paper, an enriched FEM technique is employed for thermo-mechanical contact problem based on the extended finite element method. A fully coupled thermo-mechanical contact formulation is presented in the framework of X-FEM technique that takes into account the deformable continuum mechanics and the transient heat transfer analysis. The Coulomb frictional law is applied for the mechanical contact problem and a pressure dependent thermal contact model is employed through an explicit formulation in the weak form of X-FEM method. The equilibrium equations are discretized by the Newmark time splitting method and the final set of non-linear equations are solved based on the Newton-Raphson method using a staggered algorithm. Finally, in order to illustrate the capability of the proposed computational model several numerical examples are solved and the results are compared with those reported in literature.

Using a Microcomputer in the Teaching of Gas-Phase Equilibria: A Numerical Simulation.

ERIC Educational Resources Information Center

Hayward, Roger

1995-01-01

Describes a computer program that can model the equilibrium processes in the production of ammonia from hydrogen and nitrogen, sulfur trioxide from sulfur dioxide and oxygen, and the nitrogen dioxide-dinitrogen tetroxide equilibrium. Provides information about downloading the program ChemEquilibrium from the World Wide Web. (JRH)

Description of the General Equilibrium Model of Ecosystem Services (GEMES)

Treesearch

Travis Warziniack; David Finnoff; Jenny Apriesnig

2017-01-01

This paper serves as documentation for the General Equilibrium Model of Ecosystem Services (GEMES). GEMES is a regional computable general equilibrium model that is composed of values derived from natural capital and ecosystem services. It models households, producing sectors, and governments, linked to one another through commodity and factor markets. GEMES was...

Technique for Calculating Solution Derivatives With Respect to Geometry Parameters in a CFD Code

NASA Technical Reports Server (NTRS)

Mathur, Sanjay

2011-01-01

A solution has been developed to the challenges of computation of derivatives with respect to geometry, which is not straightforward because these are not typically direct inputs to the computational fluid dynamics (CFD) solver. To overcome these issues, a procedure has been devised that can be used without having access to the mesh generator, while still being applicable to all types of meshes. The basic approach is inspired by the mesh motion algorithms used to deform the interior mesh nodes in a smooth manner when the surface nodes, for example, are in a fluid structure interaction problem. The general idea is to model the mesh edges and nodes as constituting a spring-mass system. Changes to boundary node locations are propagated to interior nodes by allowing them to assume their new equilibrium positions, for instance, one where the forces on each node are in balance. The main advantage of the technique is that it is independent of the volumetric mesh generator, and can be applied to structured, unstructured, single- and multi-block meshes. It essentially reduces the problem down to defining the surface mesh node derivatives with respect to the geometry parameters of interest. For analytical geometries, this is quite straightforward. In the more general case, one would need to be able to interrogate the underlying parametric CAD (computer aided design) model and to evaluate the derivatives either analytically, or by a finite difference technique. Because the technique is based on a partial differential equation (PDE), it is applicable not only to forward mode problems (where derivatives of all the output quantities are computed with respect to a single input), but it could also be extended to the adjoint problem, either by using an analytical adjoint of the PDE or a discrete analog.

Variability of radon and thoron equilibrium factors in indoor environment of Garhwal Himalaya.

PubMed

Prasad, Mukesh; Rawat, Mukesh; Dangwal, Anoop; Kandari, Tushar; Gusain, G S; Mishra, Rosaline; Ramola, R C

2016-01-01

The measurements of radon, thoron and their progeny concentrations have been carried out in the dwellings of Uttarkashi and Tehri districts of Garhwal Himalaya, India using LR-115 detector based pin-hole dosimeter and DRPS/DTPS techniques. The equilibrium factors for radon, thoron and their progeny were calculated by using the values measured with these techniques. The average values of equilibrium factor between radon and its progeny have been found to be 0.44, 0.39, 0.39 and 0.28 for rainy, autumn, winter and summer seasons, respectively. For thoron and its progeny, the average values of equilibrium factor have been found to be 0.04, 0.04, 0.04 and 0.03 for rainy, autumn, winter and summer seasons, respectively. The equilibrium factor between radon and its progeny has been found to be dependent on the seasonal changes. However, the equilibrium factor for thoron and progeny has been found to be same for rainy, autumn and winter seasons but slightly different for summer season. The annual average equilibrium factors for radon and thoron have been found to vary from 0.23 to 0.80 with an average of 0.42 and from 0.01 to 0.29 with an average of 0.07, respectively. The detailed discussion of the measurement techniques and the explanation for the results obtained is given in the paper. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational models for the analysis of three-dimensional internal and exhaust plume flowfields

NASA Technical Reports Server (NTRS)

Dash, S. M.; Delguidice, P. D.

1977-01-01

This paper describes computational procedures developed for the analysis of three-dimensional supersonic ducted flows and multinozzle exhaust plume flowfields. The models/codes embodying these procedures cater to a broad spectrum of geometric situations via the use of multiple reference plane grid networks in several coordinate systems. Shock capturing techniques are employed to trace the propagation and interaction of multiple shock surfaces while the plume interface, separating the exhaust and external flows, and the plume external shock are discretely analyzed. The computational grid within the reference planes follows the trace of streamlines to facilitate the incorporation of finite-rate chemistry and viscous computational capabilities. Exhaust gas properties consist of combustion products in chemical equilibrium. The computational accuracy of the models/codes is assessed via comparisons with exact solutions, results of other codes and experimental data. Results are presented for the flows in two-dimensional convergent and divergent ducts, expansive and compressive corner flows, flow in a rectangular nozzle and the plume flowfields for exhausts issuing out of single and multiple rectangular nozzles.

3D equilibrium reconstruction with islands

NASA Astrophysics Data System (ADS)

Cianciosa, M.; Hirshman, S. P.; Seal, S. K.; Shafer, M. W.

2018-04-01

This paper presents the development of a 3D equilibrium reconstruction tool and the results of the first-ever reconstruction of an island equilibrium. The SIESTA non-nested equilibrium solver has been coupled to the V3FIT 3D equilibrium reconstruction code. Computed from a coupled VMEC and SIESTA model, synthetic signals are matched to measured signals by finding an optimal set of equilibrium parameters. By using the normalized pressure in place of normalized flux, non-equilibrium quantities needed by diagnostic signals can be efficiently mapped to the equilibrium. The effectiveness of this tool is demonstrated by reconstructing an island equilibrium of a DIII-D inner wall limited L-mode case with an n = 1 error field applied. Flat spots in Thomson and ECE temperature diagnostics show the reconstructed islands have the correct size and phase. ).

Ab Initio Infrared and Raman Spectra.

DTIC Science & Technology

1982-08-01

equilibrium and non -equilibrium systems. It b pointed out that a similar ab !ni- te QFC molecular dynamic approach could be used to compute other types of...applied to -2- equilibrium and non -equilibrium system. It is pointed out that a similar oh im- ib QFCT molecular dynamic approach could be used to...desire to be able to experimentally identify and understand transient species or states (such as those existing during the course of chemical

Simulation studies of carbon nanotube field-effect transistors

NASA Astrophysics Data System (ADS)

John, David Llewellyn

Simulation studies of carbon nanotube field-effect transistors (CNFETs) are presented using models of increasing rigour and versatility that have been systematically developed. Firstly, it is demonstrated how one may compute the standard tight-binding band structure. From this foundation, a self-consistent solution for computing the equilibrium energy band diagram of devices with Schottky-barrier source and drain contacts is developed. While this does provide insight into the likely behaviour of CNFETs, a non-equilibrium model is required in order to predict the current-voltage relation. To this end, the effective-mass approximation is utilized, where a parabolic fit to the band structure is used in order to develop a Schrodinger-Poisson solver. This model is employed to predict both DC behaviour and switching times for CNFETs, and was one of the first models that captured quantum effects, such as tunneling and resonance, in these devices. In addition, this model has been used in order to validate compact models that incorporated tunneling via the WKB approximation. A modified WKB derivation is provided in order to account for the non-zero reflection of carriers above a potential energy step. In order to allow for greater flexibility in the CNFET geometries, and to lift the effective-mass approximation, a non-equilibrium Green's function method is finally developed, which uses an atomistic tight-binding Hamiltonian to model doped-contact, as opposed to Schottky-barrier-contact, devices. This approach benefits by being able to account for both inter- and intra-band tunneling, and by utilizing a quadratic matrix equation in order to improve the computation time for the required self-energy matrices. Within this technique, an expression for the local inter-atomic current is derived in order to provide more detailed information than the usual compact expression for the terminal current. With this final model, an investigation is presented into the effects of geometrical variations, contact thicknesses, and azimuthal variation in the surface potential of the nanotube.

Equilibrium Propagation: Bridging the Gap between Energy-Based Models and Backpropagation

PubMed Central

Scellier, Benjamin; Bengio, Yoshua

2017-01-01

We introduce Equilibrium Propagation, a learning framework for energy-based models. It involves only one kind of neural computation, performed in both the first phase (when the prediction is made) and the second phase of training (after the target or prediction error is revealed). Although this algorithm computes the gradient of an objective function just like Backpropagation, it does not need a special computation or circuit for the second phase, where errors are implicitly propagated. Equilibrium Propagation shares similarities with Contrastive Hebbian Learning and Contrastive Divergence while solving the theoretical issues of both algorithms: our algorithm computes the gradient of a well-defined objective function. Because the objective function is defined in terms of local perturbations, the second phase of Equilibrium Propagation corresponds to only nudging the prediction (fixed point or stationary distribution) toward a configuration that reduces prediction error. In the case of a recurrent multi-layer supervised network, the output units are slightly nudged toward their target in the second phase, and the perturbation introduced at the output layer propagates backward in the hidden layers. We show that the signal “back-propagated” during this second phase corresponds to the propagation of error derivatives and encodes the gradient of the objective function, when the synaptic update corresponds to a standard form of spike-timing dependent plasticity. This work makes it more plausible that a mechanism similar to Backpropagation could be implemented by brains, since leaky integrator neural computation performs both inference and error back-propagation in our model. The only local difference between the two phases is whether synaptic changes are allowed or not. We also show experimentally that multi-layer recurrently connected networks with 1, 2, and 3 hidden layers can be trained by Equilibrium Propagation on the permutation-invariant MNIST task. PMID:28522969

A nonlinear model for gas chromatograph systems

NASA Technical Reports Server (NTRS)

Feinberg, M. P.

1975-01-01

Fundamental engineering design techniques and concepts were studied for the optimization of a gas chromatograph-mass spectrometer chemical analysis system suitable for use on an unmanned, Martian roving vehicle. Previously developed mathematical models of the gas chromatograph are found to be inadequate for predicting peak heights and spreading for some experimental conditions and chemical systems. A modification to the existing equilibrium adsorption model is required; the Langmuir isotherm replaces the linear isotherm. The numerical technique of Crank-Nicolson was studied for use with the linear isotherm to determine the utility of the method. Modifications are made to the method eliminate unnecessary calculations which result in an overall reduction of the computation time of about 42 percent. The Langmuir isotherm is considered which takes into account the composition-dependent effects on the thermodynamic parameter, mRo.

Improving high-altitude emp modeling capabilities by using a non-equilibrium electron swarm model to monitor conduction electron evolution

NASA Astrophysics Data System (ADS)

Pusateri, Elise Noel

An Electromagnetic Pulse (EMP) can severely disrupt the use of electronic devices in its path causing a significant amount of infrastructural damage. EMP can also cause breakdown of the surrounding atmosphere during lightning discharges. This makes modeling EMP phenomenon an important research effort in many military and atmospheric physics applications. EMP events include high-energy Compton electrons or photoelectrons that ionize air and produce low energy conduction electrons. A sufficient number of conduction electrons will damp or alter the EMP through conduction current. Therefore, it is important to understand how conduction electrons interact with air in order to accurately predict the EMP evolution and propagation in the air. It is common for EMP simulation codes to use an equilibrium ohmic model for computing the conduction current. Equilibrium ohmic models assume the conduction electrons are always in equilibrium with the local instantaneous electric field, i.e. for a specific EMP electric field, the conduction electrons instantaneously reach steady state without a transient process. An equilibrium model will work well if the electrons have time to reach their equilibrium distribution with respect to the rise time or duration of the EMP. If the time to reach equilibrium is comparable or longer than the rise time or duration of the EMP then the equilibrium model would not accurately predict the conduction current necessary for the EMP simulation. This is because transport coefficients used in the conduction current calculation will be found based on equilibrium reactions rates which may differ significantly from their non-equilibrium values. We see this deficiency in Los Alamos National Laboratory's EMP code, CHAP-LA (Compton High Altitude Pulse-Los Alamos), when modeling certain EMP scenarios at high altitudes, such as upward EMP, where the ionization rate by secondary electrons is over predicted by the equilibrium model, causing the EMP to short abruptly. The objective of the PhD research is to mitigate this effect by integrating a conduction electron model into CHAP-LA which can calculate the conduction current based on a non-equilibrium electron distribution. We propose to use an electron swarm model to monitor the time evolution of conduction electrons in the EMP environment which is characterized by electric field and pressure. Swarm theory uses various collision frequencies and reaction rates to study how the electron distribution and the resultant transport coefficients change with time, ultimately reaching an equilibrium distribution. Validation of the swarm model we develop is a necessary step for completion of the thesis work. After validation, the swarm model is integrated in the air chemistry model CHAP-LA employs for conduction electron simulations. We test high altitude EMP simulations with the swarm model option in the air chemistry model to show improvements in the computational capability of CHAP-LA. A swarm model has been developed that is based on a previous swarm model developed by Higgins, Longmire and O'Dell 1973, hereinafter HLO. The code used for the swarm model calculation solves a system of coupled differential equations for electric field, electron temperature, electron number density, and drift velocity. Important swarm parameters, including the momentum transfer collision frequency, energy transfer collision frequency, and ionization rate, are recalculated and compared to the previously reported empirical results given by HLO. These swarm parameters are found using BOLSIG+, a two term Boltzmann solver developed by Hagelaar and Pitchford 2005. BOLSIG+ utilizes updated electron scattering cross sections that are defined over an expanded energy range found in the atomic and molecular cross section database published by Phelps in the Phelps Database 2014 on the LXcat website created by Pancheshnyi et al. 2012. The swarm model is also updated from the original HLO model by including additional physical parameters such as the O2 electron attachment rate, recombination rate, and mutual neutralization rate. This necessitates tracking the positive and negative ion densities in the swarm model. Adding these parameters, especially electron attachment, is important at lower EMP altitudes where atmospheric density is high. We compare swarm model equilibrium temperatures and times using the HLO and BOLSIG+ coefficients for a uniform electric field of 1 StatV/cm for a range of atmospheric heights. This is done in order to test sensitivity to the swarm parameters used in the swarm model. It is shown that the equilibrium temperature and time are sensitive to the modifications in the collision frequency and ionization rate based on the updated electron interaction cross sections. We validate the swarm model by comparing ionization coefficients and equilibrium drift velocities to experimental results over a wide range of reduced electric field values. The final part of the PhD thesis work includes integrating the swarm model into CHAP-LA. We discuss the physics included in the CHAP-LA EMP model and demonstrate EMP damping behavior caused by the ohmic model at high altitudes. We report on numerical techniques for incorporation of the swarm model into CHAP-LA's Maxwell solver. This includes a discussion of integration techniques for Maxwell's equations in CHAP-LA using the swarm model calculated conduction current. We show improvements on EMP parameter calculations when modeling a high altitude, upward EMP scenario. This provides a novel computational capability that will have an important impact on the atmospheric and EMP research community.

A Computational Method for Determining the Equilibrium Composition and Product Temperature in a LH2/LOX Combustor

NASA Technical Reports Server (NTRS)

Sozen, Mehmet

2003-01-01

In what follows, the model used for combustion of liquid hydrogen (LH2) with liquid oxygen (LOX) using chemical equilibrium assumption, and the novel computational method developed for determining the equilibrium composition and temperature of the combustion products by application of the first and second laws of thermodynamics will be described. The modular FORTRAN code developed as a subroutine that can be incorporated into any flow network code with little effort has been successfully implemented in GFSSP as the preliminary runs indicate. The code provides capability of modeling the heat transfer rate to the coolants for parametric analysis in system design.

Computational Study of a McDonnell Douglas Single-Stage-to-Orbit Vehicle Concept for Aerodynamic Analysis

NASA Technical Reports Server (NTRS)

Prabhu, Ramadas K.

1996-01-01

This paper presents the results of a computational flow analysis of the McDonnell Douglas single-stage-to-orbit vehicle concept designated as the 24U. This study was made to determine the aerodynamic characteristics of the vehicle with and without body flaps over an angle of attack range of 20-40 deg. Computations were made at a flight Mach number of 20 at 200,000 ft. altitude with equilibrium air, and a Mach number of 6 with CF4 gas. The software package FELISA (Finite Element Langley imperial College Sawansea Ames) was used for all the computations. The FELISA software consists of unstructured surface and volume grid generators, and inviscid flow solvers with (1) perfect gas option for subsonic, transonic, and low supersonic speeds, and (2) perfect gas, equilibrium air, and CF4 options for hypersonic speeds. The hypersonic flow solvers with equilibrium air and CF4 options were used in the present studies. Results are compared with other computational results and hypersonic CF4 tunnel test data.

Computer simulations of equilibrium magnetization and microstructure in magnetic fluids

NASA Astrophysics Data System (ADS)

Rosa, A. P.; Abade, G. C.; Cunha, F. R.

2017-09-01

In this work, Monte Carlo and Brownian Dynamics simulations are developed to compute the equilibrium magnetization of a magnetic fluid under action of a homogeneous applied magnetic field. The particles are free of inertia and modeled as hard spheres with the same diameters. Two different periodic boundary conditions are implemented: the minimum image method and Ewald summation technique by replicating a finite number of particles throughout the suspension volume. A comparison of the equilibrium magnetization resulting from the minimum image approach and Ewald sums is performed by using Monte Carlo simulations. The Monte Carlo simulations with minimum image and lattice sums are used to investigate suspension microstructure by computing the important radial pair-distribution function go(r), which measures the probability density of finding a second particle at a distance r from a reference particle. This function provides relevant information on structure formation and its anisotropy through the suspension. The numerical results of go(r) are compared with theoretical predictions based on quite a different approach in the absence of the field and dipole-dipole interactions. A very good quantitative agreement is found for a particle volume fraction of 0.15, providing a validation of the present simulations. In general, the investigated suspensions are dominated by structures like dimmer and trimmer chains with trimmers having probability to form an order of magnitude lower than dimmers. Using Monte Carlo with lattice sums, the density distribution function g2(r) is also examined. Whenever this function is different from zero, it indicates structure-anisotropy in the suspension. The dependence of the equilibrium magnetization on the applied field, the magnetic particle volume fraction, and the magnitude of the dipole-dipole magnetic interactions for both boundary conditions are explored in this work. Results show that at dilute regimes and with moderate dipole-dipole interactions, the standard method of minimum image is both accurate and computationally efficient. Otherwise, lattice sums of magnetic particle interactions are required to accelerate convergence of the equilibrium magnetization. The accuracy of the numerical code is also quantitatively verified by comparing the magnetization obtained from numerical results with asymptotic predictions of high order in the particle volume fraction, in the presence of dipole-dipole interactions. In addition, Brownian Dynamics simulations are used in order to examine magnetization relaxation of a ferrofluid and to calculate the magnetic relaxation time as a function of the magnetic particle interaction strength for a given particle volume fraction and a non-dimensional applied field. The simulations of magnetization relaxation have shown the existence of a critical value of the dipole-dipole interaction parameter. For strength of the interactions below the critical value at a given particle volume fraction, the magnetic relaxation time is close to the Brownian relaxation time and the suspension has no appreciable memory. On the other hand, for strength of dipole interactions beyond its critical value, the relaxation time increases exponentially with the strength of dipole-dipole interaction. Although we have considered equilibrium conditions, the obtained results have far-reaching implications for the analysis of magnetic suspensions under external flow.

Characterization and Detection of ϵ-Berge-Zhukovskii Equilibria

PubMed Central

Lung, Rodica Ioana; Suciu, Mihai; Gaskó, Noémi; Dumitrescu, D.

2015-01-01

The Berge-Zhukovskii equilibrium is an alternate solution concept in non-cooperative game theory that formalizes cooperation in a noncooperative setting. In this paper, the ϵ-Berge-Zhukovskii equilibrium is introduced and characterized by using a generative relation. The generative relation also provides a solution to the problem of computing the ϵ-Berge-Zhukovskii equilibrium for large games, by using evolutionary algorithms. Numerical examples illustrate the approach and provide a possible application for this equilibrium concept. PMID:26177217

Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

NASA Astrophysics Data System (ADS)

Philip, B.; Wang, Z.; Berrill, M. A.; Birke, M.; Pernice, M.

2014-04-01

The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

Bilevel formulation of a policy design problem considering multiple objectives and incomplete preferences

NASA Astrophysics Data System (ADS)

Hawthorne, Bryant; Panchal, Jitesh H.

2014-07-01

A bilevel optimization formulation of policy design problems considering multiple objectives and incomplete preferences of the stakeholders is presented. The formulation is presented for Feed-in-Tariff (FIT) policy design for decentralized energy infrastructure. The upper-level problem is the policy designer's problem and the lower-level problem is a Nash equilibrium problem resulting from market interactions. The policy designer has two objectives: maximizing the quantity of energy generated and minimizing policy cost. The stakeholders decide on quantities while maximizing net present value and minimizing capital investment. The Nash equilibrium problem in the presence of incomplete preferences is formulated as a stochastic linear complementarity problem and solved using expected value formulation, expected residual minimization formulation, and the Monte Carlo technique. The primary contributions in this article are the mathematical formulation of the FIT policy, the extension of computational policy design problems to multiple objectives, and the consideration of incomplete preferences of stakeholders for policy design problems.

Fisher-Wright model with deterministic seed bank and selection.

PubMed

Koopmann, Bendix; Müller, Johannes; Tellier, Aurélien; Živković, Daniel

2017-04-01

Seed banks are common characteristics to many plant species, which allow storage of genetic diversity in the soil as dormant seeds for various periods of time. We investigate an above-ground population following a Fisher-Wright model with selection coupled with a deterministic seed bank assuming the length of the seed bank is kept constant and the number of seeds is large. To assess the combined impact of seed banks and selection on genetic diversity, we derive a general diffusion model. The applied techniques outline a path of approximating a stochastic delay differential equation by an appropriately rescaled stochastic differential equation. We compute the equilibrium solution of the site-frequency spectrum and derive the times to fixation of an allele with and without selection. Finally, it is demonstrated that seed banks enhance the effect of selection onto the site-frequency spectrum while slowing down the time until the mutation-selection equilibrium is reached. Copyright © 2016 Elsevier Inc. All rights reserved.

3D equilibrium reconstruction with islands

DOE PAGES

Cianciosa, M.; Hirshman, S. P.; Seal, S. K.; ...

2018-02-15

This study presents the development of a 3D equilibrium reconstruction tool and the results of the first-ever reconstruction of an island equilibrium. The SIESTA non-nested equilibrium solver has been coupled to the V3FIT 3D equilibrium reconstruction code. Computed from a coupled VMEC and SIESTA model, synthetic signals are matched to measured signals by finding an optimal set of equilibrium parameters. By using the normalized pressure in place of normalized flux, non-equilibrium quantities needed by diagnostic signals can be efficiently mapped to the equilibrium. The effectiveness of this tool is demonstrated by reconstructing an island equilibrium of a DIII-D inner wallmore » limited L-mode case with an n = 1 error field applied. Finally, flat spots in Thomson and ECE temperature diagnostics show the reconstructed islands have the correct size and phase.« less

3D equilibrium reconstruction with islands

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

Cianciosa, M.; Hirshman, S. P.; Seal, S. K.

This study presents the development of a 3D equilibrium reconstruction tool and the results of the first-ever reconstruction of an island equilibrium. The SIESTA non-nested equilibrium solver has been coupled to the V3FIT 3D equilibrium reconstruction code. Computed from a coupled VMEC and SIESTA model, synthetic signals are matched to measured signals by finding an optimal set of equilibrium parameters. By using the normalized pressure in place of normalized flux, non-equilibrium quantities needed by diagnostic signals can be efficiently mapped to the equilibrium. The effectiveness of this tool is demonstrated by reconstructing an island equilibrium of a DIII-D inner wallmore » limited L-mode case with an n = 1 error field applied. Finally, flat spots in Thomson and ECE temperature diagnostics show the reconstructed islands have the correct size and phase.« less

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

Ivanov, Sergei D., E-mail: sergei.ivanov@unirostock.de; Grant, Ian M.; Marx, Dominik

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently andmore » thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.« less

On Social Optima of Non-Cooperative Mean Field Games

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

Li, Sen; Zhang, Wei; Zhao, Lin

This paper studies the social optima in noncooperative mean-field games for a large population of agents with heterogeneous stochastic dynamic systems. Each agent seeks to maximize an individual utility functional, and utility functionals of different agents are coupled through a mean field term that depends on the mean of the population states/controls. The paper has the following contributions. First, we derive a set of control strategies for the agents that possess *-Nash equilibrium property, and converge to the mean-field Nash equilibrium as the population size goes to infinity. Second, we study the social optimal in the mean field game. Wemore » derive the conditions, termed the socially optimal conditions, under which the *-Nash equilibrium of the mean field game maximizes the social welfare. Third, a primal-dual algorithm is proposed to compute the *-Nash equilibrium of the mean field game. Since the *-Nash equilibrium of the mean field game is socially optimal, we can compute the equilibrium by solving the social welfare maximization problem, which can be addressed by a decentralized primal-dual algorithm. Numerical simulations are presented to demonstrate the effectiveness of the proposed approach.« less

CO2 and humidity removal system for extended Shuttle missions - CO2, H2O, and trace contaminant equilibrium testing

NASA Technical Reports Server (NTRS)

Davis, S. H.; Kissinger, L. D.

1977-01-01

The equilibrium relationships for the co-adsorption of CO2 and H2O on an amine coated acrylic ester are presented. The equilibrium data collection and reduction techniques are discussed. Based on the equilibrium relationship, other modes of operation of systems containing HS-C are discussed and specific space applications for HS-C are presented. Equilibrium data for 10 compounds which are found as trace contaminants in closed environments are also presented.

Fast equilibration protocol for million atom systems of highly entangled linear polyethylene chains

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

Sliozberg, Yelena R.; TKC Global, Inc., Aberdeen Proving Ground, Maryland 21005; Kröger, Martin

Equilibrated systems of entangled polymer melts cannot be produced using direct brute force equilibration due to the slow reptation dynamics exhibited by high molecular weight chains. Instead, these dense systems are produced using computational techniques such as Monte Carlo-Molecular Dynamics hybrid algorithms, though the use of soft potentials has also shown promise mainly for coarse-grained polymeric systems. Through the use of soft-potentials, the melt can be equilibrated via molecular dynamics at intermediate and long length scales prior to switching to a Lennard-Jones potential. We will outline two different equilibration protocols, which use various degrees of information to produce the startingmore » configurations. In one protocol, we use only the equilibrium bond angle, bond length, and target density during the construction of the simulation cell, where the information is obtained from available experimental data and extracted from the force field without performing any prior simulation. In the second protocol, we moreover utilize the equilibrium radial distribution function and dihedral angle distribution. This information can be obtained from experimental data or from a simulation of short unentangled chains. Both methods can be used to prepare equilibrated and highly entangled systems, but the second protocol is much more computationally efficient. These systems can be strictly monodisperse or optionally polydisperse depending on the starting chain distribution. Our protocols, which utilize a soft-core harmonic potential, will be applied for the first time to equilibrate a million particle system of polyethylene chains consisting of 1000 united atoms at various temperatures. Calculations of structural and entanglement properties demonstrate that this method can be used as an alternative towards the generation of entangled equilibrium structures.« less

Implicit unified gas-kinetic scheme for steady state solutions in all flow regimes

NASA Astrophysics Data System (ADS)

Zhu, Yajun; Zhong, Chengwen; Xu, Kun

2016-06-01

This paper presents an implicit unified gas-kinetic scheme (UGKS) for non-equilibrium steady state flow computation. The UGKS is a direct modeling method for flow simulation in all regimes with the updates of both macroscopic flow variables and microscopic gas distribution function. By solving the macroscopic equations implicitly, a predicted equilibrium state can be obtained first through iterations. With the newly predicted equilibrium state, the evolution equation of the gas distribution function and the corresponding collision term can be discretized in a fully implicit way for fast convergence through iterations as well. The lower-upper symmetric Gauss-Seidel (LU-SGS) factorization method is implemented to solve both macroscopic and microscopic equations, which improves the efficiency of the scheme. Since the UGKS is a direct modeling method and its physical solution depends on the mesh resolution and the local time step, a physical time step needs to be fixed before using an implicit iterative technique with a pseudo-time marching step. Therefore, the physical time step in the current implicit scheme is determined by the same way as that in the explicit UGKS for capturing the physical solution in all flow regimes, but the convergence to a steady state speeds up through the adoption of a numerical time step with large CFL number. Many numerical test cases in different flow regimes from low speed to hypersonic ones, such as the Couette flow, cavity flow, and the flow passing over a cylinder, are computed to validate the current implicit method. The overall efficiency of the implicit UGKS can be improved by one or two orders of magnitude in comparison with the explicit one.

PIES free boundary stellarator equilibria with improved initial conditions

NASA Astrophysics Data System (ADS)

Drevlak, M.; Monticello, D.; Reiman, A.

2005-07-01

The MFBE procedure developed by Strumberger (1997 Nucl. Fusion 37 19) is used to provide an improved starting point for free boundary equilibrium computations in the case of W7-X (Nührenberg and Zille 1986 Phys. Lett. A 114 129) using the Princeton iterative equilibrium solver (PIES) code (Reiman and Greenside 1986 Comput. Phys. Commun. 43 157). Transferring the consistent field found by the variational moments equilibrium code (VMEC) (Hirshmann and Whitson 1983 Phys. Fluids 26 3553) to an extended coordinate system using the VMORPH code, a safe margin between plasma boundary and PIES domain is established. The new EXTENDER_P code implements a generalization of the virtual casing principle, which allows field extension both for VMEC and PIES equilibria. This facilitates analysis of the 5/5 islands of the W7-X standard case without including them in the original PIES computation.

Thermodynamic model effects on the design and optimization of natural gas plants

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

Diaz, S.; Zabaloy, M.; Brignole, E.A.

1999-07-01

The design and optimization of natural gas plants is carried out on the basis of process simulators. The physical property package is generally based on cubic equations of state. By rigorous thermodynamics phase equilibrium conditions, thermodynamic functions, equilibrium phase separations, work and heat are computed. The aim of this work is to analyze the NGL turboexpansion process and identify possible process computations that are more sensitive to model predictions accuracy. Three equations of state, PR, SRK and Peneloux modification, are used to study the effect of property predictions on process calculations and plant optimization. It is shown that turboexpander plantsmore » have moderate sensitivity with respect to phase equilibrium computations, but higher accuracy is required for the prediction of enthalpy and turboexpansion work. The effect of modeling CO{sub 2} solubility is also critical in mixtures with high CO{sub 2} content in the feed.« less

Comparison of equilibrium and non-equilibrium distribution coefficients for the human drug carbamazepine

USDA-ARS?s Scientific Manuscript database

The distribution coefficient (KD) for the human drug carbamazepine was measured using a non-equilibrium technique. Repacked soil columns were prepared using an Airport silt loam (Typic Natrustalf) with an average organic matter content of 2.45%. Carbamazepine solutions were then leached through th...

Laminar or turbulent boundary-layer flows of perfect gases or reacting gas mixtures in chemical equilibrium

NASA Technical Reports Server (NTRS)

Anderson, E. C.; Lewis, C. H.

1971-01-01

Turbulent boundary layer flows of non-reacting gases are predicted for both interal (nozzle) and external flows. Effects of favorable pressure gradients on two eddy viscosity models were studied in rocket and hypervelocity wind tunnel flows. Nozzle flows of equilibrium air with stagnation temperatures up to 10,000 K were computed. Predictions of equilibrium nitrogen flows through hypervelocity nozzles were compared with experimental data. A slender spherically blunted cone was studied at 70,000 ft altitude and 19,000 ft/sec. in the earth's atmosphere. Comparisons with available experimental data showed good agreement. A computer program was developed and fully documented during this investigation for use by interested individuals.

A survey of upwind methods for flows with equilibrium and non-equilibrium chemistry and thermodynamics

NASA Technical Reports Server (NTRS)

Grossman, B.; Garrett, J.; Cinnella, P.

1989-01-01

Several versions of flux-vector split and flux-difference split algorithms were compared with regard to general applicability and complexity. Test computations were performed using curve-fit equilibrium air chemistry for an M = 5 high-temperature inviscid flow over a wedge, and an M = 24.5 inviscid flow over a blunt cylinder for test computations; for these cases, little difference in accuracy was found among the versions of the same flux-split algorithm. For flows with nonequilibrium chemistry, the effects of the thermodynamic model on the development of flux-vector split and flux-difference split algorithms were investigated using an equilibrium model, a general nonequilibrium model, and a simplified model based on vibrational relaxation. Several numerical examples are presented, including nonequilibrium air chemistry in a high-temperature shock tube and nonequilibrium hydrogen-air chemistry in a supersonic diffuser.

An interactive computer code for calculation of gas-phase chemical equilibrium (EQLBRM)

NASA Technical Reports Server (NTRS)

Pratt, B. S.; Pratt, D. T.

1984-01-01

A user friendly, menu driven, interactive computer program known as EQLBRM which calculates the adiabatic equilibrium temperature and product composition resulting from the combustion of hydrocarbon fuels with air, at specified constant pressure and enthalpy is discussed. The program is developed primarily as an instructional tool to be run on small computers to allow the user to economically and efficiency explore the effects of varying fuel type, air/fuel ratio, inlet air and/or fuel temperature, and operating pressure on the performance of continuous combustion devices such as gas turbine combustors, Stirling engine burners, and power generation furnaces.

Combustion of hydrogen-air jets in local chemical equilibrium: A guide to the CHARNAL computer program

NASA Technical Reports Server (NTRS)

Spalding, D. B.; Launder, B. E.; Morse, A. P.; Maples, G.

1974-01-01

A guide to a computer program, written in FORTRAN 4, for predicting the flow properties of turbulent mixing with combustion of a circular jet of hydrogen into a co-flowing stream of air is presented. The program, which is based upon the Imperial College group's PASSA series, solves differential equations for diffusion and dissipation of turbulent kinetic energy and also of the R.M.S. fluctuation of hydrogen concentration. The effective turbulent viscosity for use in the shear stress equation is computed. Chemical equilibrium is assumed throughout the flow.

The Lewis Chemical Equilibrium Program with parametric study capability

NASA Technical Reports Server (NTRS)

Sevigny, R.

1981-01-01

The program was developed to determine chemical equilibrium in complex systems. Using a free energy minimization technique, the program permits calculations such as: chemical equilibrium for assigned thermodynamic states; theoretical rocket performance for both equilibrium and frozen compositions during expansion; incident and reflected shock properties; and Chapman-Jouget detonation properties. It is shown that the same program can handle solid coal in an entrained flow coal gasification problem.

Linearized Flux Evolution (LiFE): A technique for rapidly adapting fluxes from full-physics radiative transfer models

NASA Astrophysics Data System (ADS)

Robinson, Tyler D.; Crisp, David

2018-05-01

Solar and thermal radiation are critical aspects of planetary climate, with gradients in radiative energy fluxes driving heating and cooling. Climate models require that radiative transfer tools be versatile, computationally efficient, and accurate. Here, we describe a technique that uses an accurate full-physics radiative transfer model to generate a set of atmospheric radiative quantities which can be used to linearly adapt radiative flux profiles to changes in the atmospheric and surface state-the Linearized Flux Evolution (LiFE) approach. These radiative quantities describe how each model layer in a plane-parallel atmosphere reflects and transmits light, as well as how the layer generates diffuse radiation by thermal emission and by scattering light from the direct solar beam. By computing derivatives of these layer radiative properties with respect to dynamic elements of the atmospheric state, we can then efficiently adapt the flux profiles computed by the full-physics model to new atmospheric states. We validate the LiFE approach, and then apply this approach to Mars, Earth, and Venus, demonstrating the information contained in the layer radiative properties and their derivatives, as well as how the LiFE approach can be used to determine the thermal structure of radiative and radiative-convective equilibrium states in one-dimensional atmospheric models.

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Sagui, Celeste

2010-03-01

We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a nonequilibrium umbrella sampling method, in this case, the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the weighted histogram analysis technique applied to all the replicas, and equilibrium properties of the solute are computed from the unbiased trajectory. We illustrate the approach by applying it to the study of the puckering landscapes of the methyl glycosides of α-L-iduronic acid and its C5 epimer β-D-glucuronic acid in water. Big savings in computational resources are gained in comparison to the standard parallel tempering method.

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water.

PubMed

Babin, Volodymyr; Sagui, Celeste

2010-03-14

We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a nonequilibrium umbrella sampling method, in this case, the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the weighted histogram analysis technique applied to all the replicas, and equilibrium properties of the solute are computed from the unbiased trajectory. We illustrate the approach by applying it to the study of the puckering landscapes of the methyl glycosides of alpha-L-iduronic acid and its C5 epimer beta-D-glucuronic acid in water. Big savings in computational resources are gained in comparison to the standard parallel tempering method.

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models.

PubMed

Poitevin, Frédéric; Orland, Henri; Doniach, Sebastian; Koehl, Patrice; Delarue, Marc

2011-07-01

Small Angle X-ray Scattering (SAXS) techniques are becoming more and more useful for structural biologists and biochemists, thanks to better access to dedicated synchrotron beamlines, better detectors and the relative easiness of sample preparation. The ability to compute the theoretical SAXS profile of a given structural model, and to compare this profile with the measured scattering intensity, yields crucial structural informations about the macromolecule under study and/or its complexes in solution. An important contribution to the profile, besides the macromolecule itself and its solvent-excluded volume, is the excess density due to the hydration layer. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. Here, we describe the interface architecture and capabilities of the AquaSAXS web server (http://lorentz.dynstr.pasteur.fr/aquasaxs.php).

Computational technique and performance of Transient Inundation Model for Rivers--2 Dimensional (TRIM2RD) : a depth-averaged two-dimensional flow model

USGS Publications Warehouse

Fulford, Janice M.

2003-01-01

A numerical computer model, Transient Inundation Model for Rivers -- 2 Dimensional (TrimR2D), that solves the two-dimensional depth-averaged flow equations is documented and discussed. The model uses a semi-implicit, semi-Lagrangian finite-difference method. It is a variant of the Trim model and has been used successfully in estuarine environments such as San Francisco Bay. The abilities of the model are documented for three scenarios: uniform depth flows, laboratory dam-break flows, and large-scale riverine flows. The model can start computations from a ?dry? bed and converge to accurate solutions. Inflows are expressed as source terms, which limits the use of the model to sufficiently long reaches where the flow reaches equilibrium with the channel. The data sets used by the investigation demonstrate that the model accurately propagates flood waves through long river reaches and simulates dam breaks with abrupt water-surface changes.

User's guide for the computer code COLTS for calculating the coupled laminar and turbulent flow over a Jovian entry probe

NASA Technical Reports Server (NTRS)

Kumar, A.; Graeves, R. A.

1980-01-01

A user's guide for a computer code 'COLTS' (Coupled Laminar and Turbulent Solutions) is provided which calculates the laminar and turbulent hypersonic flows with radiation and coupled ablation injection past a Jovian entry probe. Time-dependent viscous-shock-layer equations are used to describe the flow field. These equations are solved by an explicit, two-step, time-asymptotic finite-difference method. Eddy viscosity in the turbulent flow is approximated by a two-layer model. In all, 19 chemical species are used to describe the injection of carbon-phenolic ablator in the hydrogen-helium gas mixture. The equilibrium composition of the mixture is determined by a free-energy minimization technique. A detailed frequency dependence of the absorption coefficient for various species is considered to obtain the radiative flux. The code is written for a CDC-CYBER-203 computer and is capable of providing solutions for ablated probe shapes also.

Computational methods for reactive transport modeling: An extended law of mass-action, xLMA, method for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg; Saar, Martin O.

2016-10-01

We present an extended law of mass-action (xLMA) method for multiphase equilibrium calculations and apply it in the context of reactive transport modeling. This extended LMA formulation differs from its conventional counterpart in that (i) it is directly derived from the Gibbs energy minimization (GEM) problem (i.e., the fundamental problem that describes the state of equilibrium of a chemical system under constant temperature and pressure); and (ii) it extends the conventional mass-action equations with Lagrange multipliers from the Gibbs energy minimization problem, which can be interpreted as stability indices of the chemical species. Accounting for these multipliers enables the method to determine all stable phases without presuming their types (e.g., aqueous, gaseous) or their presence in the equilibrium state. Therefore, the here proposed xLMA method inherits traits of Gibbs energy minimization algorithms that allow it to naturally detect the phases present in equilibrium, which can be single-component phases (e.g., pure solids or liquids) or non-ideal multi-component phases (e.g., aqueous, melts, gaseous, solid solutions, adsorption, or ion exchange). Moreover, our xLMA method requires no technique that tentatively adds or removes reactions based on phase stability indices (e.g., saturation indices for minerals), since the extended mass-action equations are valid even when their corresponding reactions involve unstable species. We successfully apply the proposed method to a reactive transport modeling problem in which we use PHREEQC and GEMS as alternative backends for the calculation of thermodynamic properties such as equilibrium constants of reactions, standard chemical potentials of species, and activity coefficients. Our tests show that our algorithm is efficient and robust for demanding applications, such as reactive transport modeling, where it converges within 1-3 iterations in most cases. The proposed xLMA method is implemented in Reaktoro, a unified open-source framework for modeling chemically reactive systems.

Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption.

PubMed

Lu, Wen-Jie; Yamada, Yoshiji; Sakuma, Jun

2015-01-01

Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Our solution supports evaluation of the D' measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical.

Implementation of Premixed Equilibrium Chemistry Capability in OVERFLOW

NASA Technical Reports Server (NTRS)

Olsen, M. E.; Liu, Y.; Vinokur, M.; Olsen, T.

2003-01-01

An implementation of premixed equilibrium chemistry has been completed for the OVERFLOW code, a chimera capable, complex geometry flow code widely used to predict transonic flowfields. The implementation builds on the computational efficiency and geometric generality of the solver.

Implementation of Premixed Equilibrium Chemistry Capability in OVERFLOW

NASA Technical Reports Server (NTRS)

Olsen, Mike E.; Liu, Yen; Vinokur, M.; Olsen, Tom

2004-01-01

An implementation of premixed equilibrium chemistry has been completed for the OVERFLOW code, a chimera capable, complex geometry flow code widely used to predict transonic flowfields. The implementation builds on the computational efficiency and geometric generality of the solver.

Development and application of a three dimensional numerical model for predicting pollutant and sediment transport using an Eulerian-Lagrangian marker particle technique

NASA Technical Reports Server (NTRS)

Pavish, D. L.; Spaulding, M. L.

1977-01-01

A computer coded Lagrangian marker particle in Eulerian finite difference cell solution to the three dimensional incompressible mass transport equation, Water Advective Particle in Cell Technique, WAPIC, was developed, verified against analytic solutions, and subsequently applied in the prediction of long term transport of a suspended sediment cloud resulting from an instantaneous dredge spoil release. Numerical results from WAPIC were verified against analytic solutions to the three dimensional incompressible mass transport equation for turbulent diffusion and advection of Gaussian dye releases in unbounded uniform and uniformly sheared uni-directional flow, and for steady-uniform plug channel flow. WAPIC was utilized to simulate an analytic solution for non-equilibrium sediment dropout from an initially vertically uniform particle distribution in one dimensional turbulent channel flow.

Effects of resident water and non-equilibrium adsorption on the primary and enhanced coalbed methane gas recovery

NASA Astrophysics Data System (ADS)

Jahediesfanjani, Hossein

The major part of the gas in coalbed methane and shale gas reservoirs is stored as the adsorbed gas in the coal and organic materials of the black shale internal surfaces. The sorption sites in both reservoirs are composed of several macropores that contain very small pore sizes. Therefore, the adsorption/desorption is very slow process and follows a non-equilibrium trend. The time-dependency of the sorption process is further affected by the reservoir resident water. Water can diffuse into the matrix and adsorption sites, plug the pores and affect the reservoir gas production. This study presents an experimental and theoretical procedure to investigate the effects of the resident water and time-dependency of the sorption process on coalbed and shale gas primary and enhanced recovery by simultaneous CO 2/N2 injection. Series of the experiments are conducted to construct both equilibrium and non-equilibrium single and multi-component isotherms with the presence of water. A novel and rapid data interpretation technique is developed based on the nonequilibrium adsorption/desorption thermodynamics, mass conservation law, and volume filling adsorption theory. The developed technique is implemented to construct both equilibrium and non-equilibrium multi-component multi-phase isotherms from the early time experimental measurements. The non-equilibrium isotherms are incorporated in the coalbed methane/shale gas reservoir simulations to account for the time-dependency of the sorption process. The experimental results indicate that the presence of water in the sorption system reduces both carbon dioxide and nitrogen adsorption rates. Reduction in the adsorption rate for carbon dioxide is more than nitrogen. The results also indicate that the resident water reduces the adsorption ability of low rank coals more than high rank ones. The results of the multi-component sorption tests indicate that increasing the initial mole fraction of the nitrogen gas in the injected CO2/N2 mixture will increase the net carbon dioxide sequestration rate on coals in the presence of water. The optimum CO2/N2 ratio that can result in the maximum carbon dioxide sequestration rate can be obtained by conducting the experiments for various CO2/N2 ratios. The results of applying the developed non-equilibrium interpretation technique for several literature and in-house data indicate that both the equilibrium and non-equilibrium isotherms can be constructed in shorter time period (around 70 times less than the time required with the equilibrium techniques) and with higher accuracy using this method. (Abstract shortened by UMI.)

User's guide for vectorized code EQUIL for calculating equilibrium chemistry on Control Data STAR-100 computer

NASA Technical Reports Server (NTRS)

Kumar, A.; Graves, R. A., Jr.; Weilmuenster, K. J.

1980-01-01

A vectorized code, EQUIL, was developed for calculating the equilibrium chemistry of a reacting gas mixture on the Control Data STAR-100 computer. The code provides species mole fractions, mass fractions, and thermodynamic and transport properties of the mixture for given temperature, pressure, and elemental mass fractions. The code is set up for the electrons H, He, C, O, N system of elements. In all, 24 chemical species are included.

Validation of vibration-dissociation coupling models in hypersonic non-equilibrium separated flows

NASA Astrophysics Data System (ADS)

Shoev, G.; Oblapenko, G.; Kunova, O.; Mekhonoshina, M.; Kustova, E.

2018-03-01

The validation of recently developed models of vibration-dissociation coupling is discussed in application to numerical solutions of the Navier-Stokes equations in a two-temperature approximation for a binary N2/N flow. Vibrational-translational relaxation rates are computed using the Landau-Teller formula generalized for strongly non-equilibrium flows obtained in the framework of the Chapman-Enskog method. Dissociation rates are calculated using the modified Treanor-Marrone model taking into account the dependence of the model parameter on the vibrational state. The solutions are compared to those obtained using traditional Landau-Teller and Treanor-Marrone models, and it is shown that for high-enthalpy flows, the traditional and recently developed models can give significantly different results. The computed heat flux and pressure on the surface of a double cone are in a good agreement with experimental data available in the literature on low-enthalpy flow with strong thermal non-equilibrium. The computed heat flux on a double wedge qualitatively agrees with available data for high-enthalpy non-equilibrium flows. Different contributions to the heat flux calculated using rigorous kinetic theory methods are evaluated. Quantitative discrepancy of numerical and experimental data is discussed.

Equilibrium Distribution Functions: Another Look.

ERIC Educational Resources Information Center

Waite, Boyd A.

1986-01-01

Discusses equilibrium distribution functions and provides an alternative "derivation" that allows the student, with the help of a computer, to gain intuitive insight as to the nature of distributions in general and the precise nature of the dominance of the Boltzmann distribution. (JN)

Calculation of the equilibrium distribution for a deleterious gene by the finite Fourier transform.

PubMed

Lange, K

1982-03-01

In a population of constant size every deleterious gene eventually attains a stochastic equilibrium between mutation and selection. The individual probabilities of this equilibrium distribution can be computed by an application of the finite Fourier transform to an appropriate branching process formula. Specific numerical examples are discussed for the autosomal dominants, Huntington's chorea and chondrodystrophy, and for the X-linked recessive, Becker's muscular dystrophy.

Computer model of one-dimensional equilibrium controlled sorption processes

USGS Publications Warehouse

Grove, D.B.; Stollenwerk, K.G.

1984-01-01

A numerical solution to the one-dimensional solute-transport equation with equilibrium-controlled sorption and a first-order irreversible-rate reaction is presented. The computer code is written in FORTRAN language, with a variety of options for input and output for user ease. Sorption reactions include Langmuir, Freundlich, and ion-exchange, with or without equal valance. General equations describing transport and reaction processes are solved by finite-difference methods, with nonlinearities accounted for by iteration. Complete documentation of the code, with examples, is included. (USGS)

Computer code for single-point thermodynamic analysis of hydrogen/oxygen expander-cycle rocket engines

NASA Technical Reports Server (NTRS)

Glassman, Arthur J.; Jones, Scott M.

1991-01-01

This analysis and this computer code apply to full, split, and dual expander cycles. Heat regeneration from the turbine exhaust to the pump exhaust is allowed. The combustion process is modeled as one of chemical equilibrium in an infinite-area or a finite-area combustor. Gas composition in the nozzle may be either equilibrium or frozen during expansion. This report, which serves as a users guide for the computer code, describes the system, the analysis methodology, and the program input and output. Sample calculations are included to show effects of key variables such as nozzle area ratio and oxidizer-to-fuel mass ratio.

Chemical equilibrium of ablation materials including condensed species

NASA Technical Reports Server (NTRS)

Stroud, C. W.; Brinkley, K. L.

1975-01-01

Equilibrium is determined by finding chemical composition with minimum free energy. Method of steepest descent is applied to quadratic representation of free-energy surface. Solution is initiated by selecting arbitrary set of mole fractions, from which point on free-energy surface is computed.

Equilibrium gas-oil ratio measurements using a microfluidic technique.

PubMed

Fisher, Robert; Shah, Mohammad Khalid; Eskin, Dmitry; Schmidt, Kurt; Singh, Anil; Molla, Shahnawaz; Mostowfi, Farshid

2013-07-07

A method for measuring the equilibrium GOR (gas-oil ratio) of reservoir fluids using microfluidic technology is developed. Live crude oils (crude oil with dissolved gas) are injected into a long serpentine microchannel at reservoir pressure. The fluid forms a segmented flow as it travels through the channel. Gas and liquid phases are produced from the exit port of the channel that is maintained at atmospheric conditions. The process is analogous to the production of crude oil from a formation. By using compositional analysis and thermodynamic principles of hydrocarbon fluids, we show excellent equilibrium between the produced gas and liquid phases is achieved. The GOR of a reservoir fluid is a key parameter in determining the equation of state of a crude oil. Equations of state that are commonly used in petroleum engineering and reservoir simulations describe the phase behaviour of a fluid at equilibrium state. Therefore, to accurately determine the coefficients of an equation of state, the produced gas and liquid phases have to be as close to the thermodynamic equilibrium as possible. In the examples presented here, the GORs measured with the microfluidic technique agreed with GOR values obtained from conventional methods. Furthermore, when compared to conventional methods, the microfluidic technique was simpler to perform, required less equipment, and yielded better repeatability.

Solar flare model atmospheres

NASA Technical Reports Server (NTRS)

Hawley, Suzanne L.; Fisher, George H.

1993-01-01

Solar flare model atmospheres computed under the assumption of energetic equilibrium in the chromosphere are presented. The models use a static, one-dimensional plane parallel geometry and are designed within a physically self-consistent coronal loop. Assumed flare heating mechanisms include collisions from a flux of non-thermal electrons and x-ray heating of the chromosphere by the corona. The heating by energetic electrons accounts explicitly for variations of the ionized fraction with depth in the atmosphere. X-ray heating of the chromosphere by the corona incorporates a flare loop geometry by approximating distant portions of the loop with a series of point sources, while treating the loop leg closest to the chromospheric footpoint in the plane-parallel approximation. Coronal flare heating leads to increased heat conduction, chromospheric evaporation and subsequent changes in coronal pressure; these effects are included self-consistently in the models. Cooling in the chromosphere is computed in detail for the important optically thick HI, CaII and MgII transitions using the non-LTE prescription in the program MULTI. Hydrogen ionization rates from x-ray photo-ionization and collisional ionization by non-thermal electrons are included explicitly in the rate equations. The models are computed in the 'impulsive' and 'equilibrium' limits, and in a set of intermediate 'evolving' states. The impulsive atmospheres have the density distribution frozen in pre-flare configuration, while the equilibrium models assume the entire atmosphere is in hydrostatic and energetic equilibrium. The evolving atmospheres represent intermediate stages where hydrostatic equilibrium has been established in the chromosphere and corona, but the corona is not yet in energetic equilibrium with the flare heating source. Thus, for example, chromospheric evaporation is still in the process of occurring.

Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties.

PubMed

Scheraga, H A; Paine, G H

1986-01-01

We are using a variety of theoretical and computational techniques to study protein structure, protein folding, and higher-order structures. Our earlier work involved treatments of liquid water and aqueous solutions of nonpolar and polar solutes, computations of the stabilities of the fundamental structures of proteins and their packing arrangements, conformations of small cyclic and open-chain peptides, structures of fibrous proteins (collagen), structures of homologous globular proteins, introduction of special procedures as constraints during energy minimization of globular proteins, and structures of enzyme-substrate complexes. Recently, we presented a new methodology for predicting polypeptide structure (described here); the method is based on the calculation of the probable and average conformation of a polypeptide chain by the application of equilibrium statistical mechanics in conjunction with an adaptive, importance sampling Monte Carlo algorithm. As a test, it was applied to Met-enkephalin.

Information thermodynamics of near-equilibrium computation

NASA Astrophysics Data System (ADS)

Prokopenko, Mikhail; Einav, Itai

2015-06-01

In studying fundamental physical limits and properties of computational processes, one is faced with the challenges of interpreting primitive information-processing functions through well-defined information-theoretic as well as thermodynamic quantities. In particular, transfer entropy, characterizing the function of computational transmission and its predictability, is known to peak near critical regimes. We focus on a thermodynamic interpretation of transfer entropy aiming to explain the underlying critical behavior by associating information flows intrinsic to computational transmission with particular physical fluxes. Specifically, in isothermal systems near thermodynamic equilibrium, the gradient of the average transfer entropy is shown to be dynamically related to Fisher information and the curvature of system's entropy. This relationship explicitly connects the predictability, sensitivity, and uncertainty of computational processes intrinsic to complex systems and allows us to consider thermodynamic interpretations of several important extreme cases and trade-offs.

A Computational Study of the Rheology and Structure of Surfactant Covered Droplets

NASA Astrophysics Data System (ADS)

Maia, Joao; Boromand, Arman; Jamali, Safa

2015-11-01

The use of different types of surface-active agents is ubiquitous practice in different industrial applications ranging from cosmetic and food industries to polymeric nano-composite and blends. This allows stable multiphasic systems like foams and emulsions to be produced. Stability and shelf-life of those products are directly determined by the efficiency of the surfactant molecules. Although the effect of molecular configuration of the surface-active molecules on the planar interfaces has been studied both experimentally and computationally, it remains challenging to track the efficiency and effectiveness of different surfactant molecules on curved interfaces. In this study we address this gap by using Dissipative Particle Dynamics, to study the effectiveness and efficiency of different surfactant molecules (linear vs. branched) on a curved interface in equilibrium and far from equilibrium. In particular, we are interested to relate interfacial properties of the surface covered droplets and its dynamics to the molecular configuration of the surface active molecules under equilibrium and far from equilibrium condition.

Development and Assessment of a Computer-Based Equation of State for Equilibrium Air

DTIC Science & Technology

2013-09-01

for very low energies. However, the ideal gas EOS is appropriate for atmospheric flight at subsonic, transonic, and low supersonic flight speeds...Flow Properties About Blunt Bodies Moving at Supersonic Speeds in an Equilibrium Gas ,” NASA TR R-204, July 1964. 21. Tannehill, John C., and Mugge...changes are made. 15. Subject Terms Air, thermodynamic properties, equation of state, chemical equilibrium, real- gas 16. SECURITY CLASSIFICATION

Free energy landscape from path-sampling: application to the structural transition in LJ38

NASA Astrophysics Data System (ADS)

Adjanor, G.; Athènes, M.; Calvo, F.

2006-09-01

We introduce a path-sampling scheme that allows equilibrium state-ensemble averages to be computed by means of a biased distribution of non-equilibrium paths. This non-equilibrium method is applied to the case of the 38-atom Lennard-Jones atomic cluster, which has a double-funnel energy landscape. We calculate the free energy profile along the Q4 bond orientational order parameter. At high or moderate temperature the results obtained using the non-equilibrium approach are consistent with those obtained using conventional equilibrium methods, including parallel tempering and Wang-Landau Monte Carlo simulations. At lower temperatures, the non-equilibrium approach becomes more efficient in exploring the relevant inherent structures. In particular, the free energy agrees with the predictions of the harmonic superposition approximation.

Influence of neural adaptation on dynamics and equilibrium state of neural activities in a ring neural network

NASA Astrophysics Data System (ADS)

Takiyama, Ken

2017-12-01

How neural adaptation affects neural information processing (i.e. the dynamics and equilibrium state of neural activities) is a central question in computational neuroscience. In my previous works, I analytically clarified the dynamics and equilibrium state of neural activities in a ring-type neural network model that is widely used to model the visual cortex, motor cortex, and several other brain regions. The neural dynamics and the equilibrium state in the neural network model corresponded to a Bayesian computation and statistically optimal multiple information integration, respectively, under a biologically inspired condition. These results were revealed in an analytically tractable manner; however, adaptation effects were not considered. Here, I analytically reveal how the dynamics and equilibrium state of neural activities in a ring neural network are influenced by spike-frequency adaptation (SFA). SFA is an adaptation that causes gradual inhibition of neural activity when a sustained stimulus is applied, and the strength of this inhibition depends on neural activities. I reveal that SFA plays three roles: (1) SFA amplifies the influence of external input in neural dynamics; (2) SFA allows the history of the external input to affect neural dynamics; and (3) the equilibrium state corresponds to the statistically optimal multiple information integration independent of the existence of SFA. In addition, the equilibrium state in a ring neural network model corresponds to the statistically optimal integration of multiple information sources under biologically inspired conditions, independent of the existence of SFA.

Electric power and the global economy: Advances in database construction and sector representation

NASA Astrophysics Data System (ADS)

Peters, Jeffrey C.

The electricity sector plays a crucial role in the global economy. The sector is a major consumer of fossil fuel resources, producer of greenhouse gas emissions, and an important indicator and correlate of economic development. As such, the sector is a primary target for policy-makers seeking to address these issues. The sector is also experiencing rapid technological change in generation (e.g. renewables), primary inputs (e.g. horizontal drilling and hydraulic fracturing), and end-use efficiency. This dissertation seeks to further our understanding of the role of the electricity sector as part of the dynamic global energy-economy, which requires significant research advances in both database construction and modeling techniques. Chapter 2 identifies useful engineering-level data and presents a novel matrix balancing method for integrating these data in global economic databases. Chapter 3 demonstrates the relationship between matrix balancing method and modeling results, and Chapter 4 presents the full construction methodology for GTAP-Power, the foremost, publicly-available global computable general equilibrium database. Chapter 5 presents an electricity-detailed computational equilibrium model that explicitly and endogenously captures capacity utilization, capacity expansion, and their interdependency - important aspects of technological substitution in the electricity sector. The individual, but interrelated, research contributions to database construction and electricity modeling in computational equilibrium are placed in the context of analyzing the US EPA Clean Power Plan (CPP) CO 2 target of 32 percent reduction of CO2 emissions in the US electricity sector from a 2005 baseline by 2030. Assuming current fuel prices, the model predicts an almost 28 percent CO2 reduction without further policy intervention. Next, a carbon tax and investment subsidies for renewable technologies to meet the CPP full targets are imposed and compared (Chapter 6). The carbon tax achieves the target via both utilization and expansion, while the renewable investment subsidies lead to over-expansion and compromises some of the possibilities via utilization. In doing so, this dissertation furthers our understanding of the role of the electricity sector as part of the dynamic global energy-economy.

Variable horizon in a peridynamic medium

DOE PAGES

Silling, Stewart A.; Littlewood, David J.; Seleson, Pablo

2015-12-10

Here, a notion of material homogeneity is proposed for peridynamic bodies with variable horizon but constant bulk properties. A relation is derived that scales the force state according to the position-dependent horizon while keeping the bulk properties unchanged. Using this scaling relation, if the horizon depends on position, artifacts called ghost forces may arise in a body under a homogeneous deformation. These artifacts depend on the second derivative of the horizon and can be reduced by employing a modified equilibrium equation using a new quantity called the partial stress. Bodies with piecewise constant horizon can be modeled without ghost forcesmore » by using a simpler technique called a splice. As a limiting case of zero horizon, both the partial stress and splice techniques can be used to achieve local-nonlocal coupling. Computational examples, including dynamic fracture in a one-dimensional model with local-nonlocal coupling, illustrate the methods.« less

Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation

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

Schnell, Sondre K.; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720; Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim

2014-10-14

We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtainedmore » with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation.« less

Computations of ideal and real gas high altitude plume flows

NASA Technical Reports Server (NTRS)

Feiereisen, William J.; Venkatapathy, Ethiraj

1988-01-01

In the present work, complete flow fields around generic space vehicles in supersonic and hypersonic flight regimes are studied numerically. Numerical simulation is performed with a flux-split, time asymptotic viscous flow solver that incorporates a generalized equilibrium chemistry model. Solutions to generic problems at various altitude and flight conditions show the complexity of the flow, the equilibrium chemical dissociation and its effect on the overall flow field. Viscous ideal gas solutions are compared against equilibrium gas solutions to illustrate the effect of equilibrium chemistry. Improved solution accuracy is achieved through adaptive grid refinement.

A novel Kinetic Monte Carlo algorithm for Non-Equilibrium Simulations

NASA Astrophysics Data System (ADS)

Jha, Prateek; Kuzovkov, Vladimir; Grzybowski, Bartosz; Olvera de La Cruz, Monica

2012-02-01

We have developed an off-lattice kinetic Monte Carlo simulation scheme for reaction-diffusion problems in soft matter systems. The definition of transition probabilities in the Monte Carlo scheme are taken identical to the transition rates in a renormalized master equation of the diffusion process and match that of the Glauber dynamics of Ising model. Our scheme provides several advantages over the Brownian dynamics technique for non-equilibrium simulations. Since particle displacements are accepted/rejected in a Monte Carlo fashion as opposed to moving particles following a stochastic equation of motion, nonphysical movements (e.g., violation of a hard core assumption) are not possible (these moves have zero acceptance). Further, the absence of a stochastic ``noise'' term resolves the computational difficulties associated with generating statistically independent trajectories with definitive mean properties. Finally, since the timestep is independent of the magnitude of the interaction forces, much longer time-steps can be employed than Brownian dynamics. We discuss the applications of this scheme for dynamic self-assembly of photo-switchable nanoparticles and dynamical problems in polymeric systems.

Final Technical Report: Mathematical Foundations for Uncertainty Quantification in Materials Design

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

Plechac, Petr; Vlachos, Dionisios G.

We developed path-wise information theory-based and goal-oriented sensitivity analysis and parameter identification methods for complex high-dimensional dynamics and in particular of non-equilibrium extended molecular systems. The combination of these novel methodologies provided the first methods in the literature which are capable to handle UQ questions for stochastic complex systems with some or all of the following features: (a) multi-scale stochastic models such as (bio)chemical reaction networks, with a very large number of parameters, (b) spatially distributed systems such as Kinetic Monte Carlo or Langevin Dynamics, (c) non-equilibrium processes typically associated with coupled physico-chemical mechanisms, driven boundary conditions, hybrid micro-macro systems,more » etc. A particular computational challenge arises in simulations of multi-scale reaction networks and molecular systems. Mathematical techniques were applied to in silico prediction of novel materials with emphasis on the effect of microstructure on model uncertainty quantification (UQ). We outline acceleration methods to make calculations of real chemistry feasible followed by two complementary tasks on structure optimization and microstructure-induced UQ.« less

A pseudo-equilibrium thermodynamic model of information processing in nonlinear brain dynamics.

PubMed

Freeman, Walter J

2008-01-01

Computational models of brain dynamics fall short of performance in speed and robustness of pattern recognition in detecting minute but highly significant pattern fragments. A novel model employs the properties of thermodynamic systems operating far from equilibrium, which is analyzed by linearization near adaptive operating points using root locus techniques. Such systems construct order by dissipating energy. Reinforcement learning of conditioned stimuli creates a landscape of attractors and their basins in each sensory cortex by forming nerve cell assemblies in cortical connectivity. Retrieval of a selected category of stored knowledge is by a phase transition that is induced by a conditioned stimulus, and that leads to pattern self-organization. Near self-regulated criticality the cortical background activity displays aperiodic null spikes at which analytic amplitude nears zero, and which constitute a form of Rayleigh noise. Phase transitions in recognition and recall are initiated at null spikes in the presence of an input signal, owing to the high signal-to-noise ratio that facilitates capture of cortex by an attractor, even by very weak activity that is typically evoked by a conditioned stimulus.

Unsteady Computational Tests of a Non-Equilibrium

NASA Astrophysics Data System (ADS)

Jirasek, Adam; Hamlington, Peter; Lofthouse, Andrew; Usafa Collaboration; Cu Boulder Collaboration

2017-11-01

A non-equilibrium turbulence model is assessed on simulations of three practically-relevant unsteady test cases; oscillating channel flow, transonic flow around an oscillating airfoil, and transonic flow around the Benchmark Super-Critical Wing. The first case is related to piston-driven flows while the remaining cases are relevant to unsteady aerodynamics at high angles of attack and transonic speeds. Non-equilibrium turbulence effects arise in each of these cases in the form of a lag between the mean strain rate and Reynolds stresses, resulting in reduced kinetic energy production compared to classical equilibrium turbulence models that are based on the gradient transport (or Boussinesq) hypothesis. As a result of the improved representation of unsteady flow effects, the non-equilibrium model provides substantially better agreement with available experimental data than do classical equilibrium turbulence models. This suggests that the non-equilibrium model may be ideally suited for simulations of modern high-speed, high angle of attack aerodynamics problems.

Statics and dynamics of DNA knotting

NASA Astrophysics Data System (ADS)

Orlandini, Enzo

2018-02-01

Knots and entanglement in polymers and biopolymers such as DNA and proteins constitute a timely topic that spans various scientific disciplines ranging from physics to chemistry, biology and mathematics. Although in the past many advancements have been made in understanding the equilibrium knotting probability and knot complexity of long polymer chains in solutions, many questions have been addressed in recent years by both experimental and theoretical means—for instance, how the knotting probability depends on the quality of the solvent, the elastic properties of the molecule and its degree of confinement. How knots form, evolve and eventually disappear in a fluctuating chain. Are the equilibrium and non-equilibrium properties of knotted molecules affected by the knot swelling/shrinking dynamics? Moreover, thanks to the great advance in nanotechnology and micromanipulation techniques, nowadays knots can be ‘manually’ tied in a single DNA molecule, followed during their motion along the chains, forced to pass through nanopores, or stretched by external forces or elongational flows. All these experimental approaches allow access to new information on the interplay of topology and polymer physics, and this has opened new perspectives in the field. Here, we provide an overview of the current knowledge of this topic, stressing the main results obtained, including the recent developments in experimental and computational approaches. Since almost all experiments on knotting involve DNA, the review will be mainly focused on the topological properties of this fascinating and biologically relevant molecule.

Equilibrium and stability of a satellite influenced by gravitational and aerodynamic torques

NASA Technical Reports Server (NTRS)

Galaboff, Z. J.

1981-01-01

A circular orbit and constant atmospheric density was assumed. A computer program which determines equilibrium attitudes and the associated eigenvalues of these attitudes is presented. Demonstration of the use of this program was made using the former Skylab satellite as an example.

Computer Series, 67: Bits and Pieces, 27.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1986-01-01

Discusses a computer interfacing course using Commodore 64 microcomputers; a computer program for radioactive equilibrium; analysis of near infrared spectrum of hydrochloric acid molecules using Apple II microcomputers; microcomputer approach to conductivity titrations; balancing equations with Commodore 64's; formulation of mathematical…

Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated.

PubMed

Ivanov, Sergei D; Grant, Ian M; Marx, Dominik

2015-09-28

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.

Nicholas Metropolis Award for Outstanding Doctoral Thesis Work in Computational Physics Lecture: The Janus computer, a new window into spin-glass physics

NASA Astrophysics Data System (ADS)

Yllanes, David

2013-03-01

Spin glasses are a longstanding model for the sluggish dynamics that appears at the glass transition. They enjoy a privileged status in this context, as they provide the simplest model system both for theoretical and experimental studies of glassy dynamics. However, in spite of forty years of intensive investigation, spin glasses still pose a formidable challenge to theoretical, computational and experimental physics. The main difficulty lies in their incredibly slow dynamics. A recent breakthrough has been made possible by our custom-built computer, Janus, designed and built in a collaboration formed by five universities in Spain and Italy. By employing a purpose-driven architecture, capable of fully exploiting the parallelization possibilities intrinsic to these simulations, Janus outperforms conventional computers by several orders of magnitude. After a brief introduction to spin glasses, the talk will focus on the new physics unearthed by Janus. In particular, we recall our numerical study of the nonequilibrium dynamics of the Edwards-Anderson Ising Spin Glass, for a time that spans eleven orders of magnitude, thus approaching the experimentally relevant scale (i.e. seconds). We have also studied the equilibrium properties of the spin-glass phase, with an emphasis on the quantitative matching between non-equilibrium and equilibrium correlation functions, through a time-length dictionary. Last but not least, we have clarified the existence of a glass transition in the presence of a magnetic field for a finite-range spin glass (the so-called de Almeida-Thouless line). We will finally mention some of the currently ongoing work of the collaboration, such as the characterization of the non-equilibrium dynamics in a magnetic field and the existence of a statics-dynamics dictionary in these conditions.

Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption

PubMed Central

2015-01-01

Objective Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. Methods To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Results Our solution supports evaluation of the D′ measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. Conclusions With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical. PMID:26732892

Microwave Spectra of the Two Conformers of PROPENE-3-{d}_1 and a Semiexperimental Equilibrium Structure of Propene

NASA Astrophysics Data System (ADS)

Craig, Norman C.; Demaison, J.; Rudolph, Heinz Dieter; Gurusinghe, Ranil M.; Tubergen, Michael; Coudert, L. H.; Szalay, Peter; Császár, Attila

2017-06-01

FT microwave spectra have been observed and analyzed for the S (in-plane) and A (out-of-plane) conformers of propene-3-{d}_1 in the 10-22 GHz region. Both conformers display splittings due to deuterium quadrupole coupling; for the latter one only, a 19 MHz splitting due to internal rotation of the partially deuterated methyl group has been observed. In addition to rotational constants, the analysis yielded quadrupole coupling constants and parameters describing the tunneling splitting and its rotational dependence. Improved rotational constants for parent propene and the three ^{13}C_1 species are recently available. Use of vibration-rotation interaction constants computed at the MP2(FC)/cc-pVTZ level gave equilibrium rotational constants for these six species and for fourteen more deuterium isotopologues with diminished accuracy from early literature data. A semiexperimental equilibrium structure, r_e^{SE}, has been determined for propene by fitting fourteen structural parameters to the equilibrium rotational constants. The new r_e^{SE} structure compares well with an ab initio equilibrium structure computed with the all-electron CCSD(T)/cc-pV(Q,T)Z model and with a structure obtained using the mixed regression method with predicates and equilibrium rotational constants. N. C. Craig, P. Groner, A. R. Conrad, R. Gurusinghe, M. J. Tubergen J. Mol. Spectrosc. 248, 1-6 (2016).

Computation material science of structural-phase transformation in casting aluminium alloys

NASA Astrophysics Data System (ADS)

Golod, V. M.; Dobosh, L. Yu

2017-04-01

Successive stages of computer simulation the formation of the casting microstructure under non-equilibrium conditions of crystallization of multicomponent aluminum alloys are presented. On the basis of computer thermodynamics and heat transfer during solidification of macroscale shaped castings are specified the boundary conditions of local heat exchange at mesoscale modeling of non-equilibrium formation the solid phase and of the component redistribution between phases during coalescence of secondary dendrite branches. Computer analysis of structural - phase transitions based on the principle of additive physico-chemical effect of the alloy components in the process of diffusional - capillary morphological evolution of the dendrite structure and the o of local dendrite heterogeneity which stochastic nature and extent are revealed under metallographic study and modeling by the Monte Carlo method. The integrated computational materials science tools at researches of alloys are focused and implemented on analysis the multiple-factor system of casting processes and prediction of casting microstructure.

FORTRAN 4 computer program for calculation of thermodynamic and transport properties of complex chemical systems

NASA Technical Reports Server (NTRS)

Svehla, R. A.; Mcbride, B. J.

1973-01-01

A FORTRAN IV computer program for the calculation of the thermodynamic and transport properties of complex mixtures is described. The program has the capability of performing calculations such as:(1) chemical equilibrium for assigned thermodynamic states, (2) theoretical rocket performance for both equilibrium and frozen compositions during expansion, (3) incident and reflected shock properties, and (4) Chapman-Jouguet detonation properties. Condensed species, as well as gaseous species, are considered in the thermodynamic calculation; but only the gaseous species are considered in the transport calculations.

Iterative algorithms for computing the feedback Nash equilibrium point for positive systems

NASA Astrophysics Data System (ADS)

Ivanov, I.; Imsland, Lars; Bogdanova, B.

2017-03-01

The paper studies N-player linear quadratic differential games on an infinite time horizon with deterministic feedback information structure. It introduces two iterative methods (the Newton method as well as its accelerated modification) in order to compute the stabilising solution of a set of generalised algebraic Riccati equations. The latter is related to the Nash equilibrium point of the considered game model. Moreover, we derive the sufficient conditions for convergence of the proposed methods. Finally, we discuss two numerical examples so as to illustrate the performance of both of the algorithms.

Equilibrium paths analysis of materials with rheological properties by using the chaos theory

NASA Astrophysics Data System (ADS)

Bednarek, Paweł; Rządkowski, Jan

2018-01-01

The numerical equilibrium path analysis of the material with random rheological properties by using standard procedures and specialist computer programs was not successful. The proper solution for the analysed heuristic model of the material was obtained on the base of chaos theory elements and neural networks. The paper deals with mathematical reasons of used computer programs and also are elaborated the properties of the attractor used in analysis. There are presented results of conducted numerical analysis both in a numerical and in graphical form for the used procedures.

Thermodynamic equilibrium-air correlations for flowfield applications

NASA Technical Reports Server (NTRS)

Zoby, E. V.; Moss, J. N.

1981-01-01

Equilibrium-air thermodynamic correlations have been developed for flowfield calculation procedures. A comparison between the postshock results computed by the correlation equations and detailed chemistry calculations is very good. The thermodynamic correlations are incorporated in an approximate inviscid flowfield code with a convective heating capability for the purpose of defining the thermodynamic environment through the shock layer. Comparisons of heating rates computed by the approximate code and a viscous-shock-layer method are good. In addition to presenting the thermodynamic correlations, the impact of several viscosity models on the convective heat transfer is demonstrated.

Calculating Shocks In Flows At Chemical Equilibrium

NASA Technical Reports Server (NTRS)

Eberhardt, Scott; Palmer, Grant

1988-01-01

Boundary conditions prove critical. Conference paper describes algorithm for calculation of shocks in hypersonic flows of gases at chemical equilibrium. Although algorithm represents intermediate stage in development of reliable, accurate computer code for two-dimensional flow, research leading up to it contributes to understanding of what is needed to complete task.

Analysis of non-equilibrium phenomena in inductively coupled plasma generators

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

Zhang, W.; Panesi, M., E-mail: mpanesi@illinois.edu; Lani, A.

This work addresses the modeling of non-equilibrium phenomena in inductively coupled plasma discharges. In the proposed computational model, the electromagnetic induction equation is solved together with the set of Navier-Stokes equations in order to compute the electromagnetic and flow fields, accounting for their mutual interaction. Semi-classical statistical thermodynamics is used to determine the plasma thermodynamic properties, while transport properties are obtained from kinetic principles, with the method of Chapman and Enskog. Particle ambipolar diffusive fluxes are found by solving the Stefan-Maxwell equations with a simple iterative method. Two physico-mathematical formulations are used to model the chemical reaction processes: (1) Amore » Local Thermodynamics Equilibrium (LTE) formulation and (2) a thermo-chemical non-equilibrium (TCNEQ) formulation. In the TCNEQ model, thermal non-equilibrium between the translational energy mode of the gas and the vibrational energy mode of individual molecules is accounted for. The electronic states of the chemical species are assumed in equilibrium with the vibrational temperature, whereas the rotational energy mode is assumed to be equilibrated with translation. Three different physical models are used to account for the coupling of chemistry and energy transfer processes. Numerical simulations obtained with the LTE and TCNEQ formulations are used to characterize the extent of non-equilibrium of the flow inside the Plasmatron facility at the von Karman Institute. Each model was tested using different kinetic mechanisms to assess the sensitivity of the results to variations in the reaction parameters. A comparison of temperatures and composition profiles at the outlet of the torch demonstrates that the flow is in non-equilibrium for operating conditions characterized by pressures below 30 000 Pa, frequency 0.37 MHz, input power 80 kW, and mass flow 8 g/s.« less

Analysis of non-equilibrium phenomena in inductively coupled plasma generators

NASA Astrophysics Data System (ADS)

Zhang, W.; Lani, A.; Panesi, M.

2016-07-01

This work addresses the modeling of non-equilibrium phenomena in inductively coupled plasma discharges. In the proposed computational model, the electromagnetic induction equation is solved together with the set of Navier-Stokes equations in order to compute the electromagnetic and flow fields, accounting for their mutual interaction. Semi-classical statistical thermodynamics is used to determine the plasma thermodynamic properties, while transport properties are obtained from kinetic principles, with the method of Chapman and Enskog. Particle ambipolar diffusive fluxes are found by solving the Stefan-Maxwell equations with a simple iterative method. Two physico-mathematical formulations are used to model the chemical reaction processes: (1) A Local Thermodynamics Equilibrium (LTE) formulation and (2) a thermo-chemical non-equilibrium (TCNEQ) formulation. In the TCNEQ model, thermal non-equilibrium between the translational energy mode of the gas and the vibrational energy mode of individual molecules is accounted for. The electronic states of the chemical species are assumed in equilibrium with the vibrational temperature, whereas the rotational energy mode is assumed to be equilibrated with translation. Three different physical models are used to account for the coupling of chemistry and energy transfer processes. Numerical simulations obtained with the LTE and TCNEQ formulations are used to characterize the extent of non-equilibrium of the flow inside the Plasmatron facility at the von Karman Institute. Each model was tested using different kinetic mechanisms to assess the sensitivity of the results to variations in the reaction parameters. A comparison of temperatures and composition profiles at the outlet of the torch demonstrates that the flow is in non-equilibrium for operating conditions characterized by pressures below 30 000 Pa, frequency 0.37 MHz, input power 80 kW, and mass flow 8 g/s.

Budget Allocation in a Competitive Communication Spectrum Economy

NASA Astrophysics Data System (ADS)

Lin, Ming-Hua; Tsai, Jung-Fa; Ye, Yinyu

2009-12-01

This study discusses how to adjust "monetary budget" to meet each user's physical power demand, or balance all individual utilities in a competitive "spectrum market" of a communication system. In the market, multiple users share a common frequency or tone band and each of them uses the budget to purchase its own transmit power spectra (taking others as given) in maximizing its Shannon utility or pay-off function that includes the effect of interferences. A market equilibrium is a budget allocation, price spectrum, and tone power distribution that independently and simultaneously maximizes each user's utility. The equilibrium conditions of the market are formulated and analyzed, and the existence of an equilibrium is proved. Computational results and comparisons between the competitive equilibrium and Nash equilibrium solutions are also presented, which show that the competitive market equilibrium solution often provides more efficient power distribution.

New Computer Automated Holo-Photoelastic Method For Measuring Planar Principal Stress Magnitudes And Orientation

NASA Astrophysics Data System (ADS)

Brown, G. M.; Sullivan, J. L.

1987-09-01

A complete experimental determination of the stress and strain fields in an arbitrary deformed structure is generally unavailable. However, for two dimensional elasticity problems, such determinations are possible since in those cases one needs only to solve for three stresses (two normal and one shear). In fact, such determinations have been conducted quite often. By using isochromatic and isoclinic photoelastic data, the shear difference and numerical iteration techniques (1) and the least squares techniques (2) have been successfully used for complete stress field determinations of two dimensional elasticity problems. Though the shear difference technique can be particularly sensitive to cumulative errors resulting from numerical integration, the least squares technique is not affected by this and appears to yield better accuracy. The methods just cited use both experimental data and one or more mechanics conditions(e.g., the equations of equilibrium) to determine the stress field. However, the stress field can also be obtained from experimental data alone for planar elasticity problems, if there is enough of it to solve for the three stresses. For example, the Moire* technique or the combination of isochromatic, isoclinic, and isopachic data (for transparent models) can be used for such determinations. Further, with the marriage of advanced image processing equipment to computers, such analyses using this type of data can be conveniently conducted. It is even possible that such analyses could be more accurate than those using the combined experimental/numerical techniques cited above. The purposes of this report are two fold: i) to describe a single apparatus for obtaining isochromatic, isopachic, and isoclinic results for complete stress field determinations of two dimensional transparent models, and ii) to compare experimental and theoretical stress field values for an antisymmetrically loaded beam obtained using that apparatus.

Theoretical studies of UO(2)(OH)(H(2)O)(n) (+), UO(2)(OH)(2)(H(2)O)(n), NpO(2)(OH)(H(2)O)(n), and PuO(2)(OH)(H(2)O)(n) (+) (n

PubMed

Cao, Zhiji; Balasubramanian, K

2009-10-28

Extensive ab initio calculations have been carried out to study equilibrium structures, vibrational frequencies, and the nature of chemical bonds of hydrated UO(2)(OH)(+), UO(2)(OH)(2), NpO(2)(OH), and PuO(2)(OH)(+) complexes that contain up to 21 water molecules both in first and second hydration spheres in both aqueous solution and the gas phase. The structures have been further optimized by considering long-range solvent effects through a polarizable continuum dielectric model. The hydrolysis reaction Gibbs free energy of UO(2)(H(2)O)(5) (2+) is computed to be 8.11 kcal/mol at the MP2 level in good agreement with experiments. Our results reveal that it is necessary to include water molecules bound to the complex in the first hydration sphere for proper treatment of the hydrated complex and the dielectric cavity although water molecules in the second hydration sphere do not change the coordination complex. Structural reoptimization of the complex in a dielectric cavity seems inevitable to seek subtle structural variations in the solvent and to correlate with the observed spectra and thermodynamic properties in the aqueous environment. Our computations reveal dramatically different equilibrium structures in the gas phase and solution and also confirm the observed facile exchanges between the complex and bulk solvent. Complete active space multiconfiguration self-consistent field followed by multireference singles+doubles CI (MRSDCI) computations on smaller complexes confirm predominantly single-configurational nature of these species and the validity of B3LYP and MP2 techniques for these complexes in their ground states.

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

Kenik, E.A.

X-ray microanalysis in an analytical electron microscope is a proven technique for the measurement of solute segregation in alloys. Solute segregation under equilibrium or nonequilibrium conditions can strongly influence material performance. X-ray microanalysis in an analytical electron microscope provides an alternative technique to measure grain boundary segregation, as well as segregation to other defects not accessible to Auger analysis. The utility of the technique is demonstrated by measurements of equilibrium segregation to boundaries in an antimony containing stainless steel, including the variation of segregation with boundary character and by measurements of nonequilibrium segregation to boundaries and dislocations in an ion-irradiatedmore » stainless steel.« less

Microgravity Diode Laser Spectroscopy Measurements in a Reacting Vortex Ring

NASA Technical Reports Server (NTRS)

Chen, Shin-Juh; Dahm, Werner J. A.; Silver, Joel A.; Piltch, Nancy D.

2001-01-01

The technique of Diode Laser Spectroscopy (DLS) with wavelength modulation is utilized to measure the concentration of methane in reacting vortex rings under microgravity conditions. From the measured concentration of methane, other major species such as water, carbon dioxide, nitrogen, and oxygen can be easily computed under the assumption of equilibrium chemistry with the method of Interactive Temperature with Assumed Chemistry (ITAC). The conserved scalar approach in modelling the coupling between fluid dynamics and combustion is utilized to represent the unknown variables in terms of the mixture fraction and scalar dissipation rate in conjunction with ITAC. Post-processing of the DLS measurements and the method of ITAC used in computing the species concentration are discussed. From the flame luminosity results, the increase in ring circulation appears to increase the fuel consumption rate inside the reacting vortex ring and the flame height for cases with similar fuel volumes. Preliminary results and application of ITAC show some potential capabilities of ITAC in DLS. The measured concentration of methane, and computed concentrations of water and carbon dioxide agree well with available results from numerical simulations.

A computer program for two-dimensional and axisymmetric nonreacting perfect gas and equilibrium chemically reacting laminar, transitional and-or turbulent boundary layer flows

NASA Technical Reports Server (NTRS)

Miner, E. W.; Anderson, E. C.; Lewis, C. H.

1971-01-01

A computer program is described in detail for laminar, transitional, and/or turbulent boundary-layer flows of non-reacting (perfect gas) and reacting gas mixtures in chemical equilibrium. An implicit finite difference scheme was developed for both two dimensional and axisymmetric flows over bodies, and in rocket nozzles and hypervelocity wind tunnel nozzles. The program, program subroutines, variables, and input and output data are described. Also included is the output from a sample calculation of fully developed turbulent, perfect gas flow over a flat plate. Input data coding forms and a FORTRAN source listing of the program are included. A method is discussed for obtaining thermodynamic and transport property data which are required to perform boundary-layer calculations for reacting gases in chemical equilibrium.

Computing Properties Of Chemical Mixtures At Equilibrium

NASA Technical Reports Server (NTRS)

Mcbride, B. J.; Gordon, S.

1995-01-01

Scientists and engineers need data on chemical equilibrium compositions to calculate theoretical thermodynamic properties of chemical systems. Information essential in design and analysis of such equipment as compressors, turbines, nozzles, engines, shock tubes, heat exchangers, and chemical-processing equipment. CET93 is general program that calculates chemical equilibrium compositions and properties of mixtures for any chemical system for which thermodynamic data are available. Includes thermodynamic data for more than 1,300 gaseous and condensed species and thermal-transport data for 151 gases. Written in FORTRAN 77.

Algorithmic mechanisms for reliable crowdsourcing computation under collusion.

PubMed

Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A; Pareja, Daniel

2015-01-01

We consider a computing system where a master processor assigns a task for execution to worker processors that may collude. We model the workers' decision of whether to comply (compute the task) or not (return a bogus result to save the computation cost) as a game among workers. That is, we assume that workers are rational in a game-theoretic sense. We identify analytically the parameter conditions for a unique Nash Equilibrium where the master obtains the correct result. We also evaluate experimentally mixed equilibria aiming to attain better reliability-profit trade-offs. For a wide range of parameter values that may be used in practice, our simulations show that, in fact, both master and workers are better off using a pure equilibrium where no worker cheats, even under collusion, and even for colluding behaviors that involve deviating from the game.

Algorithmic Mechanisms for Reliable Crowdsourcing Computation under Collusion

PubMed Central

Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A.; Pareja, Daniel

2015-01-01

We consider a computing system where a master processor assigns a task for execution to worker processors that may collude. We model the workers’ decision of whether to comply (compute the task) or not (return a bogus result to save the computation cost) as a game among workers. That is, we assume that workers are rational in a game-theoretic sense. We identify analytically the parameter conditions for a unique Nash Equilibrium where the master obtains the correct result. We also evaluate experimentally mixed equilibria aiming to attain better reliability-profit trade-offs. For a wide range of parameter values that may be used in practice, our simulations show that, in fact, both master and workers are better off using a pure equilibrium where no worker cheats, even under collusion, and even for colluding behaviors that involve deviating from the game. PMID:25793524

Statistical equilibrium calculations for silicon in early-type model stellar atmospheres

NASA Technical Reports Server (NTRS)

Kamp, L. W.

1976-01-01

Line profiles of 36 multiplets of silicon (Si) II, III, and IV were computed for a grid of model atmospheres covering the range from 15,000 to 35,000 K in effective temperature and 2.5 to 4.5 in log (gravity). The computations involved simultaneous solution of the steady-state statistical equilibrium equations for the populations and of the equation of radiative transfer in the lines. The variables were linearized, and successive corrections were computed until a minimal accuracy of 1/1000 in the line intensities was reached. The common assumption of local thermodynamic equilibrium (LTE) was dropped. The model atmospheres used also were computed by non-LTE methods. Some effects that were incorporated into the calculations were the depression of the continuum by free electrons, hydrogen and ionized helium line blocking, and auto-ionization and dielectronic recombination, which later were found to be insignificant. Use of radiation damping and detailed electron (quadratic Stark) damping constants had small but significant effects on the strong resonance lines of Si III and IV. For weak and intermediate-strength lines, large differences with respect to LTE computations, the results of which are also presented, were found in line shapes and strengths. For the strong lines the differences are generally small, except for the models at the hot, low-gravity extreme of our range. These computations should be useful in the interpretation of the spectra of stars in the spectral range B0-B5, luminosity classes III, IV, and V.

The Voronoi volume and molecular representation of molar volume: equilibrium simple fluids.

PubMed

Hunjan, Jagtar Singh; Eu, Byung Chan

2010-04-07

The Voronoi volume of simple fluids was previously made use of in connection with volume transport phenomena in nonequilibrium simple fluids. To investigate volume transport phenomena, it is important to develop a method to compute the Voronoi volume of fluids in nonequilibrium. In this work, as a first step to this goal, we investigate the equilibrium limit of the nonequilibrium Voronoi volume together with its attendant related molar (molal) and specific volumes. It is proved that the equilibrium Voronoi volume is equivalent to the molar (molal) volume. The latter, in turn, is proved equivalent to the specific volume. This chain of equivalences provides an alternative procedure of computing the equilibrium Voronoi volume from the molar volume/specific volume. We also show approximate methods of computing the Voronoi and molar volumes from the information on the pair correlation function. These methods may be employed for their quick estimation, but also provide some aspects of the fluid structure and its relation to the Voronoi volume. The Voronoi volume obtained from computer simulations is fitted to a function of temperature and pressure in the region above the triple point but below the critical point. Since the fitting function is given in terms of reduced variables for the Lennard-Jones (LJ) model and the kindred volumes (i.e., specific and molar volumes) are in essence equivalent to the equation of state, the formula obtained is a reduced equation state for simple fluids obeying the LJ model potential in the range of temperature and pressure examined and hence can be used for other simple fluids.

Hammett analyses of halocarbene-halocarbanion equilibria.

PubMed

Wang, Lei; Moss, Robert A; Krogh-Jespersen, Karsten

2013-04-19

Substituted arylchlorocarbenes (X = H, p-Cl, p-CF3, p-F, m-Cl) reacted reversibly with Cl(-) in dichloroethane to form the corresponding aryldichloromethide carbanions. Equilibrium constants and rate constants for the forward and reverse reactions were correlated by the Hammett equation. DFT methods were used to compute equilibrium constants and electronic absorption spectra.

Helping Students Revise Disruptive Experientially Supported Ideas about Thermodynamics: Computer Visualizations and Tactile Models

ERIC Educational Resources Information Center

Clark, Douglas; Jorde, Doris

2004-01-01

This study analyzes the impact of an integrated sensory model within a thermal equilibrium visualization. We hypothesized that this intervention would not only help students revise their disruptive experientially supported ideas about why objects feel hot or cold, but also increase their understanding of thermal equilibrium. The analysis…

Surface currents on the plasma-vacuum interface in MHD equilibria

NASA Astrophysics Data System (ADS)

Hanson, James

2017-10-01

The VMEC non-axisymmetric MHD equilibrium code can compute free-boundary equilibria. Since VMEC assumes that magnetic fields within the plasma form closed and nested flux surfaces, the plasma-vacuum interface is a flux surface, and the total magnetic field there has no normal component. VMEC imposes this condition of zero normal field using the potential formulation of Merkel, and solves a Neumann problem for the magnetic potential in the exterior region. This boundary condition necessarily admits the possibility of a surface current on the interface. While this surface current may be small in MHD equilibrium, it is readily computed in terms of the magnetic potentials in both the interior and exterior regions, evaluated on the surface. If only the external magnetic potential is known (as in VMEC), then the surface current can be computed from the discontinuity of the tangential field across the interface. Examples of the surface current for VMEC equilibria will be shown for a zero-pressure stellarator equilibrium. Field-line following of the vacuum magnetic field shows magnetic islands within the plasma region.

Reconstruction of Energy Surfaces from Friction Force Microscopy Measurements with the Jarzynski Equality

NASA Astrophysics Data System (ADS)

Berkovich, Ronen; Klafter, Joseph; Urbakh, Michael

Free energy is one of the most fundamental thermodynamic functions, determining relative phase stability and serving as a generating function for other thermodynamic quantities. The calculation of free energies is a challenging enterprise. In equilibrium statistical mechanics, the free energy is related to the canonical partition function. The partition function itself involves integrations over all degrees of freedom in the system and, in most cases, cannot be easily calculated directly. In 1997, Jarzynski proved a remarkable equality that allows computing the equilibrium free-energy difference between two states from the probability distribution of the nonequilibrium work done on the system to switch between the two states. The Jarzynski equality provides a powerful free-energy difference estimator from a set of irreversible experiments. This method is closely related to free-energy perturbation approach, which is also a computational technique for estimating free-energy differences. The ability to map potential profiles and topologies is of major significance to areas as diverse as biological recognition and nanoscale friction. This capability has been demonstrated for frictional studies where a force between the tip of the scanning force microscope and the surface is probed. The surface free-energy corrugation produces a detectable friction forces. Thus, friction force microscopy (FFM) should be able to discriminate between energetically different areas on the probed surface. Here, we apply the Jarzynski equality for the analysis of FFM measurements and thus obtain a variation of the free energy along a surface.

Keto-enol tautomerism of (E)-2-[(3,4-dimethylphenylimino)methyl]-4-nitrophenol: Synthesis, X-ray, FT-IR, UV-Vis, NMR and quantum chemical characterizations

NASA Astrophysics Data System (ADS)

Özek Yıldırım, Arzu; Yıldırım, M. Hakkı; Albayrak Kaştaş, Çiǧdem

2017-01-01

(E)-2-((3,4-dimethylphenylimino)methyl)-4-nitrophenol, which is a new Schiff base compound, was synthesized and characterized by experimental and computational methods. Molecular geometry, harmonic oscillator model of aromaticity (HOMA) indices, intra- and inter-molecular interactions in the crystal structure were determined by using single crystal X-ray diffraction technique. The optimized structures, which are obtained by Gaussian and Slater type orbitals, were compared to experimental structures to determine how much correlation is found between the experimental and the calculated properties. Intramolecular and hyperconjugative interactions of bonds have been found by Natural Bond Orbital analysis. The experimental infrared spectrum of the compound has been analyzed in detail by the calculated infrared spectra and Potential Energy Distribution analysis. To find out about the correlation between the solvent polarity and the enol-keto equilibrium, experimental UV-Visible spectra of the compound were obtained in benzene, CHCl3, EtOH and DMSO solvents. In these solvents, the UV-Vis spectra and relaxed potential energy surface scan (PES) calculations have been performed to get more insight into the equilibrium dynamics. Solvent effects in UV-Vis and PES calculations have been taken into account by using Polarizable Continuum Modelling method. 1H and 13C NMR spectra of the compound (in DMSO) were analyzed. The computational study of nonlinear optical properties shows that the compound can be used for the development of nonlinear optical materials.

Toroidal figures of equilibrium from a second-order accurate, accelerated SCF method with subgrid approach

NASA Astrophysics Data System (ADS)

Huré, J.-M.; Hersant, F.

2017-02-01

We compute the structure of a self-gravitating torus with polytropic equation of state (EOS) rotating in an imposed centrifugal potential. The Poisson solver is based on isotropic multigrid with optimal covering factor (fluid section-to-grid area ratio). We work at second order in the grid resolution for both finite difference and quadrature schemes. For soft EOS (I.e. polytropic index n ≥ 1), the underlying second order is naturally recovered for boundary values and any other integrated quantity sensitive to the mass density (mass, angular momentum, volume, virial parameter, etc.), I.e. errors vary with the number N of nodes per direction as ˜1/N2. This is, however, not observed for purely geometrical quantities (surface area, meridional section area, volume), unless a subgrid approach is considered (I.e. boundary detection). Equilibrium sequences are also much better described, especially close to critical rotation. Yet another technical effort is required for hard EOS (n < 1), due to infinite mass density gradients at the fluid surface. We fix the problem by using kernel splitting. Finally, we propose an accelerated version of the self-consistent field (SCF) algorithm based on a node-by-node pre-conditioning of the mass density at each step. The computing time is reduced by a factor of 2 typically, regardless of the polytropic index. There is a priori no obstacle to applying these results and techniques to ellipsoidal configurations and even to 3D configurations.

Computer codes for the evaluation of thermodynamic and transport properties for equilibrium air to 30000 K

NASA Technical Reports Server (NTRS)

Thompson, Richard A.; Lee, Kam-Pui; Gupta, Roop N.

1991-01-01

The computer codes developed here provide self-consistent thermodynamic and transport properties for equilibrium air for temperatures from 500 to 30000 K over a temperature range of 10 (exp -4) to 10 (exp -2) atm. These properties are computed through the use of temperature dependent curve fits for discrete values of pressure. Interpolation is employed for intermediate values of pressure. The curve fits are based on mixture values calculated from an 11-species air model. Individual species properties used in the mixture relations are obtained from a recent study by the present authors. A review and discussion of the sources and accuracy of the curve fitted data used herein are given in NASA RP 1260.

Numerical solution of Space Shuttle Orbiter flow field including real gas effects

NASA Technical Reports Server (NTRS)

Prabhu, D. K.; Tannehill, J. C.

1984-01-01

The hypersonic, laminar flow around the Space Shuttle Orbiter has been computed for both an ideal gas (gamma = 1.2) and equilibrium air using a real-gas, parabolized Navier-Stokes code. This code employs a generalized coordinate transformation; hence, it places no restrictions on the orientation of the solution surfaces. The initial solution in the nose region was computed using a 3-D, real-gas, time-dependent Navier-Stokes code. The thermodynamic and transport properties of equilibrium air were obtained from either approximate curve fits or a table look-up procedure. Numerical results are presented for flight conditions corresponding to the STS-3 trajectory. The computed surface pressures and convective heating rates are compared with data from the STS-3 flight.

Essays on variational approximation techniques for stochastic optimization problems

NASA Astrophysics Data System (ADS)

Deride Silva, Julio A.

This dissertation presents five essays on approximation and modeling techniques, based on variational analysis, applied to stochastic optimization problems. It is divided into two parts, where the first is devoted to equilibrium problems and maxinf optimization, and the second corresponds to two essays in statistics and uncertainty modeling. Stochastic optimization lies at the core of this research as we were interested in relevant equilibrium applications that contain an uncertain component, and the design of a solution strategy. In addition, every stochastic optimization problem relies heavily on the underlying probability distribution that models the uncertainty. We studied these distributions, in particular, their design process and theoretical properties such as their convergence. Finally, the last aspect of stochastic optimization that we covered is the scenario creation problem, in which we described a procedure based on a probabilistic model to create scenarios for the applied problem of power estimation of renewable energies. In the first part, Equilibrium problems and maxinf optimization, we considered three Walrasian equilibrium problems: from economics, we studied a stochastic general equilibrium problem in a pure exchange economy, described in Chapter 3, and a stochastic general equilibrium with financial contracts, in Chapter 4; finally from engineering, we studied an infrastructure planning problem in Chapter 5. We stated these problems as belonging to the maxinf optimization class and, in each instance, we provided an approximation scheme based on the notion of lopsided convergence and non-concave duality. This strategy is the foundation of the augmented Walrasian algorithm, whose convergence is guaranteed by lopsided convergence, that was implemented computationally, obtaining numerical results for relevant examples. The second part, Essays about statistics and uncertainty modeling, contains two essays covering a convergence problem for a sequence of estimators, and a problem for creating probabilistic scenarios on renewable energies estimation. In Chapter 7 we re-visited one of the "folk theorems" in statistics, where a family of Bayes estimators under 0-1 loss functions is claimed to converge to the maximum a posteriori estimator. This assertion is studied under the scope of the hypo-convergence theory, and the density functions are included in the class of upper semicontinuous functions. We conclude this chapter with an example in which the convergence does not hold true, and we provided sufficient conditions that guarantee convergence. The last chapter, Chapter 8, addresses the important topic of creating probabilistic scenarios for solar power generation. Scenarios are a fundamental input for the stochastic optimization problem of energy dispatch, especially when incorporating renewables. We proposed a model designed to capture the constraints induced by physical characteristics of the variables based on the application of an epi-spline density estimation along with a copula estimation, in order to account for partial correlations between variables.

A finite difference scheme for the equilibrium equations of elastic bodies

NASA Technical Reports Server (NTRS)

Phillips, T. N.; Rose, M. E.

1984-01-01

A compact difference scheme is described for treating the first-order system of partial differential equations which describe the equilibrium equations of an elastic body. An algebraic simplification enables the solution to be obtained by standard direct or iterative techniques.

Reviews.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1988

1988-01-01

Reviews three computer software packages for Apple II computers. Includes "Simulation of Hemoglobin Function,""Solution Equilibrium Problems," and "Thin-Layer Chromatography." Contains ratings of ease of use, subject matter content, pedagogic value, and student reaction according to two separate reviewers for each…

Run-Reversal Equilibrium for Clinical Trial Randomization

PubMed Central

Grant, William C.

2015-01-01

In this paper, we describe a new restricted randomization method called run-reversal equilibrium (RRE), which is a Nash equilibrium of a game where (1) the clinical trial statistician chooses a sequence of medical treatments, and (2) clinical investigators make treatment predictions. RRE randomization counteracts how each investigator could observe treatment histories in order to forecast upcoming treatments. Computation of a run-reversal equilibrium reflects how the treatment history at a particular site is imperfectly correlated with the treatment imbalance for the overall trial. An attractive feature of RRE randomization is that treatment imbalance follows a random walk at each site, while treatment balance is tightly constrained and regularly restored for the overall trial. Less predictable and therefore more scientifically valid experiments can be facilitated by run-reversal equilibrium for multi-site clinical trials. PMID:26079608

Experimental determination of thermodynamic equilibrium in biocatalytic transamination.

PubMed

Tufvesson, Pär; Jensen, Jacob S; Kroutil, Wolfgang; Woodley, John M

2012-08-01

The equilibrium constant is a critical parameter for making rational design choices in biocatalytic transamination for the synthesis of chiral amines. However, very few reports are available in the scientific literature determining the equilibrium constant (K) for the transamination of ketones. Various methods for determining (or estimating) equilibrium have previously been suggested, both experimental as well as computational (based on group contribution methods). However, none of these were found suitable for determining the equilibrium constant for the transamination of ketones. Therefore, in this communication we suggest a simple experimental methodology which we hope will stimulate more accurate determination of thermodynamic equilibria when reporting the results of transaminase-catalyzed reactions in order to increase understanding of the relationship between substrate and product molecular structure on reaction thermodynamics. Copyright © 2012 Wiley Periodicals, Inc.

Direct Determination of the Equilibrium Unbinding Potential Profile for a Short DNA Duplex from Force Spectroscopy Data

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

Noy, A

2004-05-04

Modern force microscopy techniques allow researchers to use mechanical forces to probe interactions between biomolecules. However, such measurements often happen in non-equilibrium regime, which precludes straightforward extraction of the equilibrium energy information. Here we use the work averaging method based on Jarzynski equality to reconstruct the equilibrium interaction potential from the unbinding of a complementary 14-mer DNA duplex from the results of non-equilibrium single-molecule measurements. The reconstructed potential reproduces most of the features of the DNA stretching transition, previously observed only in equilibrium stretching of long DNA sequences. We also compare the reconstructed potential with the thermodynamic parameters of DNAmore » duplex unbinding and show that the reconstruction accurately predicts duplex melting enthalpy.« less

Does the nervous system use equilibrium-point control to guide single and multiple joint movements?

PubMed

Bizzi, E; Hogan, N; Mussa-Ivaldi, F A; Giszter, S

1992-12-01

The hypothesis that the central nervous system (CNS) generates movement as a shift of the limb's equilibrium posture has been corroborated experimentally in studies involving single- and multijoint motions. Posture may be controlled through the choice of muscle length-tension curve that set agonist-antagonist torque-angle curves determining an equilibrium position for the limb and the stiffness about the joints. Arm trajectories seem to be generated through a control signal defining a series of equilibrium postures. The equilibrium-point hypothesis drastically simplifies the requisite computations for multijoint movements and mechanical interactions with complex dynamic objects in the environment. Because the neuromuscular system is springlike, the instantaneous difference between the arm's actual position and the equilibrium position specified by the neural activity can generate the requisite torques, avoiding the complex "inverse dynamic" problem of computing the torques at the joints. The hypothesis provides a simple, unified description of posture and movement as well as contact control task performance, in which the limb must exert force stably and do work on objects in the environment. The latter is a surprisingly difficult problem, as robotic experience has shown. The prior evidence for the hypothesis came mainly from psychophysical and behavioral experiments. Our recent work has shown that microstimulation of the frog spinal cord's premotoneural network produces leg movements to various positions in the frog's motor space. The hypothesis can now be investigated in the neurophysiological machinery of the spinal cord.

Improving the Efficiency of Non-equilibrium Sampling in the Aqueous Environment via Implicit-Solvent Simulations.

PubMed

Liu, Hui; Chen, Fu; Sun, Huiyong; Li, Dan; Hou, Tingjun

2017-04-11

By means of estimators based on non-equilibrium work, equilibrium free energy differences or potentials of mean force (PMFs) of a system of interest can be computed from biased molecular dynamics (MD) simulations. The approach, however, is often plagued by slow conformational sampling and poor convergence, especially when the solvent effects are taken into account. Here, as a possible way to alleviate the problem, several widely used implicit-solvent models, which are derived from the analytic generalized Born (GB) equation and implemented in the AMBER suite of programs, were employed in free energy calculations based on non-equilibrium work and evaluated for their abilities to emulate explicit water. As a test case, pulling MD simulations were carried out on an alanine polypeptide with different solvent models and protocols, followed by comparisons of the reconstructed PMF profiles along the unfolding coordinate. The results show that when employing the non-equilibrium work method, sampling with an implicit-solvent model is several times faster and, more importantly, converges more rapidly than that with explicit water due to reduction of dissipation. Among the assessed GB models, the Neck variants outperform the OBC and HCT variants in terms of accuracy, whereas their computational costs are comparable. In addition, for the best-performing models, the impact of the solvent-accessible surface area (SASA) dependent nonpolar solvation term was also examined. The present study highlights the advantages of implicit-solvent models for non-equilibrium sampling.

Measurement of the Surface Dilatational Viscosity of an Insoluble Surfactant Monolayer at the Air/Water Interface Using a Pendant Drop Apparatus

NASA Technical Reports Server (NTRS)

Lorenzo, Jose; Couzis, Alex; Maldarelli, Charles; Singh, Bhim S. (Technical Monitor)

2000-01-01

When a fluid interface with surfactants is at rest, the interfacial stress is isotropic (as given by the equilibrium interfacial tension), and is described by the equation of state which relates the surface tension to the surfactant surface concentration. When surfactants are subjected to shear and dilatational flows, flow induced interaction of the surfactants; can create interfacial stresses apart from the equilibrium surface tension. The simplest relationship between surface strain rate and surface stress is the Boussinesq-Scriven constitutive equation completely characterized by three coefficients: equilibrium interfacial tension, surface shear viscosity, and surface dilatational viscosity Equilibrium interfacial tension and surface shear viscosity measurements are very well established. On the other hand, surface dilatational viscosity measurements are difficult because a flow which change the surface area also changes the surfactant surface concentration creating changes in the equilibrium interfacial tension that must be also taken into account. Surface dilatational viscosity measurements of existing techniques differ by five orders of magnitude and use spatially damped surface waves and rapidly expanding bubbles. In this presentation we introduce a new technique for measuring the surface dilatational viscosity by contracting an aqueous pendant drop attached to a needle tip and having and insoluble surfactant monolayer at the air-water interface. The isotropic total tension on the surface consists of the equilibrium surface tension and the tension due to the dilation. Compression rates are undertaken slow enough so that bulk hydrodynamic stresses are small compared to the surface tension force. Under these conditions we show that the total tension is uniform along the surface and that the Young-Laplace equation governs the drop shape with the equilibrium surface tension replaced by the constant surface isotropic stress. We illustrate this technique using DPPC as the insoluble surfacant monolayer and measured for it a surface dilatational viscosity in the LE phase that is 20 surface poise.

Using the Computer in Evolution Studies

ERIC Educational Resources Information Center

Mariner, James L.

1973-01-01

Describes a high school biology exercise in which a computer greatly reduces time spent on calculations. Genetic equilibrium demonstrated by the Hardy-Weinberg principle and the subsequent effects of violating any of its premises are more readily understood when frequencies of alleles through many generations are calculated by the computer. (JR)

Quantum Statistical Mechanics on a Quantum Computer

NASA Astrophysics Data System (ADS)

Raedt, H. D.; Hams, A. H.; Michielsen, K.; Miyashita, S.; Saito, K.

We describe a quantum algorithm to compute the density of states and thermal equilibrium properties of quantum many-body systems. We present results obtained by running this algorithm on a software implementation of a 21-qubit quantum computer for the case of an antiferromagnetic Heisenberg model on triangular lattices of different size.

Chemistry of vaporization of refractory materials

NASA Technical Reports Server (NTRS)

Gilles, P. W.

1975-01-01

A discussion is given of the principles of physical chemistry important in vaporization studies, notably the concepts of equilibrium, phase behavior, thermodynamics, solid solution, and kinetics. The important factors influencing equilibrium vaporization phenomena are discussed and illustrated. A proper course of a vaporization study consisting of 9 stages is proposed. The important experimental techniques of Knudsen effusion, Langmuir vaporization and mass spectrometry are discussed. The principles, the factors, the course of a study and the experimental techniques and procedures are illustrated by recent work on the Ti-O system.

Control of stochastic sensitivity in a stabilization problem for gas discharge system

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

Bashkirtseva, Irina

2015-11-30

We consider a nonlinear dynamic stochastic system with control. A problem of stochastic sensitivity synthesis of the equilibrium is studied. A mathematical technique of the solution of this problem is discussed. This technique is applied to the problem of the stabilization of the operating mode for the stochastic gas discharge system. We construct a feedback regulator that reduces the stochastic sensitivity of the equilibrium, suppresses large-amplitude oscillations, and provides a proper operation of this engineering device.

Unique equilibrium states for Bonatti–Viana diffeomorphisms

NASA Astrophysics Data System (ADS)

Climenhaga, Vaughn; Fisher, Todd; Thompson, Daniel J.

2018-06-01

We show that the robustly transitive diffeomorphisms constructed by Bonatti and Viana have unique equilibrium states for natural classes of potentials. In particular, we characterize the SRB measure as the unique equilibrium state for a suitable geometric potential. The techniques developed are applicable to a wide class of DA diffeomorphisms, and persist under C 1 perturbations of the map. These results are an application of general machinery developed by the first and last named authors.

Equilibrium sampling of environmental pollutants in fish: comparison with lipid-normalized concentrations and homogenization effects on chemical activity.

PubMed

Jahnke, Annika; Mayer, Philipp; Adolfsson-Erici, Margaretha; McLachlan, Michael S

2011-07-01

Equilibrium sampling of organic pollutants into the silicone polydimethylsiloxane (PDMS) has recently been applied in biological tissues including fish. Pollutant concentrations in PDMS can then be multiplied with lipid/PDMS distribution coefficients (D(Lipid,PDMS) ) to obtain concentrations in fish lipids. In the present study, PDMS thin films were used for equilibrium sampling of polychlorinated biphenyls (PCBs) in intact tissue of two eels and one salmon. A classical exhaustive extraction technique to determine lipid-normalized PCB concentrations, which assigns the body burden of the chemical to the lipid fraction of the fish, was additionally applied. Lipid-based PCB concentrations obtained by equilibrium sampling were 85 to 106% (Norwegian Atlantic salmon), 108 to 128% (Baltic Sea eel), and 51 to 83% (Finnish lake eel) of those determined using total extraction. This supports the validity of the equilibrium sampling technique, while at the same time confirming that the fugacity capacity of these lipid-rich tissues for PCBs was dominated by the lipid fraction. Equilibrium sampling was also applied to homogenates of the same fish tissues. The PCB concentrations in the PDMS were 1.2 to 2.0 times higher in the homogenates (statistically significant in 18 of 21 cases, p < 0.05), indicating that homogenization increased the chemical activity of the PCBs and decreased the fugacity capacity of the tissue. This observation has implications for equilibrium sampling and partition coefficients determined using tissue homogenates. Copyright © 2011 SETAC.

An analysis of artificial viscosity effects on reacting flows using a spectral multi-domain technique

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.; Streett, C. L.; Hussaini, M. Y.

1987-01-01

Standard techniques used to model chemically-reacting flows require an artificial viscosity for stability in the presence of strong shocks. The resulting shock is smeared over at least three computational cells, so that the thickness of the shock is dictated by the structure of the overall mesh and not the shock physics. A gas passing through a strong shock is thrown into a nonequilibrium state and subsequently relaxes down over some finite distance to an equilibrium end state. The artificial smearing of the shock envelops this relaxation zone which causes the chemical kinetics of the flow to be altered. A method is presented which can investigate these issues by following the chemical kinetics and flow kinetics of a gas passing through a fully resolved shock wave at hypersonic Mach numbers. A nonequilibrium chemistry model for air is incorporated into a spectral multidomain Navier-Stokes solution method. Since no artificial viscosity is needed for stability of the multidomain technique, the precise effect of this artifice on the chemical kinetics and relevant flow features can be determined.

A New Technique for Measuring Concentration Dependence of Self and Collective Diffusivity by using a Single Sample

NASA Astrophysics Data System (ADS)

Sirorattanakul, Krittanon; Shen, Chong; Ou-Yang, Daniel

Diffusivity governs the dynamics of interacting particles suspended in a solvent. At high particle concentration, the interactions between particles become non-negligible, making the values of self and collective diffusivity diverge and concentration-dependent. Conventional methods for measuring this dependency, such as forced Rayleigh scattering, fluorescence correlation spectroscopy (FCS), and dynamic light scattering (DLS) require preparation of multiple samples. We present a new technique to measure this dependency by using only a single sample. Dielectrophoresis (DEP) is used to create concentration gradient in the solution. Across this concentration distribution, we use FCS to measure the concentration-dependent self diffusivity. Then, we switch off DEP to allow the particles to diffuse back to equilibrium. We obtain the time series of concentration distribution from fluorescence microscopy and use them to determine the concentration-dependent collective diffusivity. We compare the experimental results with computer simulations to verify the validity of this technique. Time and spatial resolution limits of FCS and imaging are also analyzed to estimate the limitation of the proposed technique. NSF DMR-0923299, Lehigh College of Arts and Sciences Undergraduate Research Grant, Lehigh Department of Physics, Emulsion Polymers Institute.

Prediction of Temperatures of Austenite Equilibrium Transformations in Steels During Thermomechanical Processing

NASA Astrophysics Data System (ADS)

Samadian, Pedram; Parsa, Mohammad Habibi; Ahmadabadi, M. Nili; Mirzadeh, Hamed

2014-10-01

Knowledge about the transformation temperatures is crucial in processing of steels especially in thermomechanical processes because microstructures and mechanical properties after processing are closely related to the extent and type of transformations. The experimental determination of critical temperatures is costly, and therefore, it is preferred to predict them by mathematical methods. In the current work, new thermodynamically based models were developed for computing the Ae3 and Acm temperatures in the equilibrium cooling conditions when austenite is deformed at elevated temperatures. The main advantage of the proposed models is their capability to predict the temperatures of austenite equilibrium transformations in steels with total alloying elements (Mn + Si + Ni + Cr + Mo + Cu) less than 5 wt.% and Si less than 1 wt.% under the deformation conditions just by using the chemical potential of constituents, without the need for determining the total Gibbs free energy of steel which requires many experiments and computations.

Calculation of open and closed system elastic coefficients for multicomponent solids

NASA Astrophysics Data System (ADS)

Mishin, Y.

2015-06-01

Thermodynamic equilibrium in multicomponent solids subject to mechanical stresses is a complex nonlinear problem whose exact solution requires extensive computations. A few decades ago, Larché and Cahn proposed a linearized solution of the mechanochemical equilibrium problem by introducing the concept of open system elastic coefficients [Acta Metall. 21, 1051 (1973), 10.1016/0001-6160(73)90021-7]. Using the Ni-Al solid solution as a model system, we demonstrate that open system elastic coefficients can be readily computed by semigrand canonical Monte Carlo simulations in conjunction with the shape fluctuation approach. Such coefficients can be derived from a single simulation run, together with other thermodynamic properties needed for prediction of compositional fields in solid solutions containing defects. The proposed calculation approach enables streamlined solutions of mechanochemical equilibrium problems in complex alloys. Second order corrections to the linear theory are extended to multicomponent systems.

Computer codes for thermal analysis of a solid rocket motor nozzle

NASA Technical Reports Server (NTRS)

Chauhan, Rajinder Singh

1988-01-01

A number of computer codes are available for performing thermal analysis of solid rocket motor nozzles. Aerotherm Chemical Equilibrium (ACE) computer program can be used to perform one-dimensional gas expansion to determine the state of the gas at each location of a nozzle. The ACE outputs can be used as input to a computer program called Momentum/Energy Integral Technique (MEIT) for predicting boundary layer development development, shear, and heating on the surface of the nozzle. The output from MEIT can be used as input to another computer program called Aerotherm Charring Material Thermal Response and Ablation Program (CMA). This program is used to calculate oblation or decomposition response of the nozzle material. A code called Failure Analysis Nonlinear Thermal and Structural Integrated Code (FANTASTIC) is also likely to be used for performing thermal analysis of solid rocket motor nozzles after the program is duly verified. A part of the verification work on FANTASTIC was done by using one and two dimension heat transfer examples with known answers. An attempt was made to prepare input for performing thermal analysis of the CCT nozzle using the FANTASTIC computer code. The CCT nozzle problem will first be solved by using ACE, MEIT, and CMA. The same problem will then be solved using FANTASTIC. These results will then be compared for verification of FANTASTIC.

All-atom calculation of protein free-energy profiles

NASA Astrophysics Data System (ADS)

Orioli, S.; Ianeselli, A.; Spagnolli, G.; Faccioli, P.

2017-10-01

The Bias Functional (BF) approach is a variational method which enables one to efficiently generate ensembles of reactive trajectories for complex biomolecular transitions, using ordinary computer clusters. For example, this scheme was applied to simulate in atomistic detail the folding of proteins consisting of several hundreds of amino acids and with experimental folding time of several minutes. A drawback of the BF approach is that it produces trajectories which do not satisfy microscopic reversibility. Consequently, this method cannot be used to directly compute equilibrium observables, such as free energy landscapes or equilibrium constants. In this work, we develop a statistical analysis which permits us to compute the potential of mean-force (PMF) along an arbitrary collective coordinate, by exploiting the information contained in the reactive trajectories calculated with the BF approach. We assess the accuracy and computational efficiency of this scheme by comparing its results with the PMF obtained for a small protein by means of plain molecular dynamics.

A general equilibrium model of a production economy with asset markets

NASA Astrophysics Data System (ADS)

Raberto, Marco; Teglio, Andrea; Cincotti, Silvano

2006-10-01

In this paper, a general equilibrium model of a monetary production economy is presented. The model is characterized by three classes of agents: a representative firm, heterogeneous households, and the government. Two markets (i.e., a labour market and a goods market, are considered) and two assets are traded in exchange of money, namely, government bonds and equities. Households provide the labour force and decide on consumption and savings, whereas the firm provides consumption goods and demands labour. The government receives taxes from households and pays interests on debt. The Walrasian equilibrium is derived analytically. The dynamics through quantity constrained equilibria out from the Walrasian equilibrium is also studied by means of computer simulations.

Quantum Stochastic Trajectories: The Fokker-Planck-Bohm Equation Driven by the Reduced Density Matrix.

PubMed

Avanzini, Francesco; Moro, Giorgio J

2018-03-15

The quantum molecular trajectory is the deterministic trajectory, arising from the Bohm theory, that describes the instantaneous positions of the nuclei of molecules by assuring the agreement with the predictions of quantum mechanics. Therefore, it provides the suitable framework for representing the geometry and the motions of molecules without neglecting their quantum nature. However, the quantum molecular trajectory is extremely demanding from the computational point of view, and this strongly limits its applications. To overcome such a drawback, we derive a stochastic representation of the quantum molecular trajectory, through projection operator techniques, for the degrees of freedom of an open quantum system. The resulting Fokker-Planck operator is parametrically dependent upon the reduced density matrix of the open system. Because of the pilot role played by the reduced density matrix, this stochastic approach is able to represent accurately the main features of the open system motions both at equilibrium and out of equilibrium with the environment. To verify this procedure, the predictions of the stochastic and deterministic representation are compared for a model system of six interacting harmonic oscillators, where one oscillator is taken as the open quantum system of interest. The undeniable advantage of the stochastic approach is that of providing a simplified and self-contained representation of the dynamics of the open system coordinates. Furthermore, it can be employed to study the out of equilibrium dynamics and the relaxation of quantum molecular motions during photoinduced processes, like photoinduced conformational changes and proton transfers.

An implicit scheme with memory reduction technique for steady state solutions of DVBE in all flow regimes

NASA Astrophysics Data System (ADS)

Yang, L. M.; Shu, C.; Yang, W. M.; Wu, J.

2018-04-01

High consumption of memory and computational effort is the major barrier to prevent the widespread use of the discrete velocity method (DVM) in the simulation of flows in all flow regimes. To overcome this drawback, an implicit DVM with a memory reduction technique for solving a steady discrete velocity Boltzmann equation (DVBE) is presented in this work. In the method, the distribution functions in the whole discrete velocity space do not need to be stored, and they are calculated from the macroscopic flow variables. As a result, its memory requirement is in the same order as the conventional Euler/Navier-Stokes solver. In the meantime, it is more efficient than the explicit DVM for the simulation of various flows. To make the method efficient for solving flow problems in all flow regimes, a prediction step is introduced to estimate the local equilibrium state of the DVBE. In the prediction step, the distribution function at the cell interface is calculated by the local solution of DVBE. For the flow simulation, when the cell size is less than the mean free path, the prediction step has almost no effect on the solution. However, when the cell size is much larger than the mean free path, the prediction step dominates the solution so as to provide reasonable results in such a flow regime. In addition, to further improve the computational efficiency of the developed scheme in the continuum flow regime, the implicit technique is also introduced into the prediction step. Numerical results showed that the proposed implicit scheme can provide reasonable results in all flow regimes and increase significantly the computational efficiency in the continuum flow regime as compared with the existing DVM solvers.

Sensitivity of equilibrium profile reconstruction to motional Stark effect measurements

NASA Astrophysics Data System (ADS)

Batha, S. H.; Levinton, F. M.; Hirshman, S. P.; Bell, M. G.; Wieland, R. M.

1996-09-01

The magnetic-field pitch-angle profile, gamma p(R) identical to tan-1(Bpol/Btor), is measured on TFTR using a motional Stark effect (MSE) polarimeter. Measured pitch angle profiles, along with kinetic profiles and external magnetic measurements, are used to compute a self-consistent equilibrium using the free-boundary variational moments equilibrium code VMEC. Uncertainties in the q profile due to uncertainties in gamma P(R), magnetic measurements and kinetic measurements are found to be small. Subsequent uncertainties in the VMEC-calculated current density and shear profiles are also small

Biomechanical stability analysis of the lambda-model controlling one joint.

PubMed

Lan, L; Zhu, K Y

2007-06-01

Computer modeling and control of the human motor system might be helpful for understanding the mechanism of human motor system and for the diagnosis and treatment of neuromuscular disorders. In this paper, a brief view of the equilibrium point hypothesis for human motor system modeling is given, and the lambda-model derived from this hypothesis is studied. The stability of the lambda-model based on equilibrium and Jacobian matrix is investigated. The results obtained in this paper suggest that the lambda-model is stable and has a unique equilibrium point under certain conditions.

Non-linear quantum-classical scheme to simulate non-equilibrium strongly correlated fermionic many-body dynamics

PubMed Central

Kreula, J. M.; Clark, S. R.; Jaksch, D.

2016-01-01

We propose a non-linear, hybrid quantum-classical scheme for simulating non-equilibrium dynamics of strongly correlated fermions described by the Hubbard model in a Bethe lattice in the thermodynamic limit. Our scheme implements non-equilibrium dynamical mean field theory (DMFT) and uses a digital quantum simulator to solve a quantum impurity problem whose parameters are iterated to self-consistency via a classically computed feedback loop where quantum gate errors can be partly accounted for. We analyse the performance of the scheme in an example case. PMID:27609673

Application of Equilibrium Partitioning Theory to Soil PAH Contamination (External Review Draft)

EPA Science Inventory

In March 2004, ORD's Ecological Risk Assessment Support Center (ERASC) received a request from the Ecological Risk Assessment Forum (ERAF) to provide insight into the issue of whether equilibrium partitioning (EqP) techniques can be used to predict the toxicity of polycyclic arom...

Problem Solving and Chemical Equilibrium: Successful versus Unsuccessful Performance.

ERIC Educational Resources Information Center

Camacho, Moises; Good, Ron

1989-01-01

Describes the problem-solving behaviors of experts and novices engaged in solving seven chemical equilibrium problems. Lists 27 behavioral tendencies of successful and unsuccessful problem solvers. Discusses several implications for a problem solving theory, think-aloud techniques, adequacy of the chemistry domain, and chemistry instruction.…

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

Fath, L., E-mail: lukas.fath@kit.edu; Hochbruck, M., E-mail: marlis.hochbruck@kit.edu; Singh, C.V., E-mail: chandraveer.singh@utoronto.ca

Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementationmore » in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.« less

Microgravity Diode Laser Spectroscopy Measurements in a Reacting Vortex Ring

NASA Technical Reports Server (NTRS)

Chen, Shin-Juh; Dahm, Werner J. A.; Silver, Joel A.; Piltch, Nancy D.; VanderWal, R. (Technical Monitor)

2001-01-01

The technique of Diode Laser Spectroscopy (DLS) with wavelength modulation is utilized to measure the concentration of methane in reacting vortex rings under microgravity conditions. From the measured concentration of methane, other major species such as water, carbon dioxide, nitrogen, and oxygen can be easily computed under the assumption of equilibrium chemistry with an iterative method called ITAC (Iterative Temperature with Assumed Chemistry). The conserved scalar approach in modelling the coupling between fluid dynamics and combustion is utilized to represent the unknown variables in terms of the mixture fraction and scalar dissipation rate in conjunction with ITAC. Post-processing of the DLS and the method used to compute the species concentration are discussed. From the flame luminosity results, ring circulation appears to increase the fuel consumption rate inside the reacting vortex ring and the flame height for cases with similar fuel volumes but different ring circulations. The concentrations of methane, water, and carbon dioxide agree well with available results from numerical simulations.

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

PubMed Central

Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth

2016-01-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts. PMID:27124275

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

PubMed

Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2016-04-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

Digital-model simulation of the glacial-outwash aquifer, Otter Creek-Dry Creek basin, Cortland County, New York

USGS Publications Warehouse

Cosner, O.J.; Harsh, J.F.

1978-01-01

The city of Cortland, New York, and surrounding areas obtain water from the highly productive glacial-outwash aquifer underlying the Otter Creek-Dry Creek basin. Pumpage from the aquifer in 1976 was approximately 6.3 million gallons per day and is expected to increase as a result of population growth and urbanization. A digital ground-water model that uses a finite-difference approximation technique to solve partial differential equations of flow through a porous medium was used to simulate the movement of water within the aquifer. The model was calibrated to equilibrium conditions by comparing water levels measured in the aquifer in March 1976 with those computed by the model. Then, from the simulated water-level surface for March, a transient-condition run was made to simulate the surface as measured in September 1976. Computed water levels presented as contours are generally in close agreement with potentiometric-surface maps prepared from field measurements of March and September 1976. (Woodard-USGS)

Solute effects on edge dislocation pinning in complex alpha-Fe alloys

NASA Astrophysics Data System (ADS)

Pascuet, M. I.; Martínez, E.; Monnet, G.; Malerba, L.

2017-10-01

Reactor pressure vessel steels are well-known to harden and embrittle under neutron irradiation, mainly because of the formation of obstacles to the motion of dislocations, in particular, precipitates and clusters composed of Cu, Ni, Mn, Si and P. In this paper, we employ two complementary atomistic modelling techniques to study the heterogeneous precipitation and segregation of these elements and their effects on the edge dislocations in BCC iron. We use a special and highly computationally efficient Monte Carlo algorithm in a constrained semi-grand canonical ensemble to compute the equilibrium configurations for solute clusters around the dislocation core. Next, we use standard molecular dynamics to predict and analyze the effect of this segregation on the dislocation mobility. Consistently with expectations our results confirm that the required stress for dislocation unpinning from the precipitates formed on top of it is quite large. The identification of the precipitate resistance allows a quantitative treatment of atomistic results, enabling scale transition towards larger scale simulations, such as dislocation dynamics or phase field.

Inverse dynamic substructuring using the direct hybrid assembly in the frequency domain

NASA Astrophysics Data System (ADS)

D'Ambrogio, Walter; Fregolent, Annalisa

2014-04-01

The paper deals with the identification of the dynamic behaviour of a structural subsystem, starting from the known dynamic behaviour of both the coupled system and the remaining part of the structural system (residual subsystem). This topic is also known as decoupling problem, subsystem subtraction or inverse dynamic substructuring. Whenever it is necessary to combine numerical models (e.g. FEM) and test models (e.g. FRFs), one speaks of experimental dynamic substructuring. Substructure decoupling techniques can be classified as inverse coupling or direct decoupling techniques. In inverse coupling, the equations describing the coupling problem are rearranged to isolate the unknown substructure instead of the coupled structure. On the contrary, direct decoupling consists in adding to the coupled system a fictitious subsystem that is the negative of the residual subsystem. Starting from a reduced version of the 3-field formulation (dynamic equilibrium using FRFs, compatibility and equilibrium of interface forces), a direct hybrid assembly is developed by requiring that both compatibility and equilibrium conditions are satisfied exactly, either at coupling DoFs only, or at additional internal DoFs of the residual subsystem. Equilibrium and compatibility DoFs might not be the same: this generates the so-called non-collocated approach. The technique is applied using experimental data from an assembled system made by a plate and a rigid mass.

Performance Modeling of an Experimental Laser Propelled Lightcraft

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Chen, Yen-Sen; Liu, Jiwen; Myrabo, Leik N.; Mead, Franklin B., Jr.

2000-01-01

A computational plasma aerodynamics model is developed to study the performance of an experimental laser propelled lightcraft. The computational methodology is based on a time-accurate, three-dimensional, finite-difference, chemically reacting, unstructured grid, pressure- based formulation. The underlying physics are added and tested systematically using a building-block approach. The physics modeled include non-equilibn'um thermodynamics, non-equilibrium air-plasma finite-rate kinetics, specular ray tracing, laser beam energy absorption and equi refraction by plasma, non-equilibrium plasma radiation, and plasma resonance. A series of transient computations are performed at several laser pulse energy levels and the simulated physics are discussed and compared with those of tests and literature. The predicted coupling coefficients for the lightcraft compared reasonably well with those of tests conducted on a pendulum apparatus.

Buckling of pressure-loaded, long, shear deformable, cylindrical laminated shells

NASA Astrophysics Data System (ADS)

Anastasiadis, John S.; Simitses, George J.

A higher-order shell theory was developed (kinematic relations, constitutive relations, equilibrium equations and boundary conditions), which includes initial geometric imperfections and transverse shear effects for a laminated cylindrical shell under the action of pressure, axial compression and in-plane shear. Through the perturbation technique, buckling equations are derived for the corresponding 'perfect geometry' symmetric laminated configuration. Critical pressures are computed for very long cylinders for several stacking sequences, several radius-to-total-thickness ratios, three lamina materials (boron/epoxy, graphite/epoxy, and Kevlar/epoxy), and three shell theories: classical, first-order shear deformable and higher- (third-)order shear deformable. The results provide valuable information concerning the applicability (accurate prediction of buckling pressures) of the various shell theories.

Study of solid rocket motor for space shuttle booster, volume 2, book 5, appendices E thru H

NASA Technical Reports Server (NTRS)

1972-01-01

Preliminary parametric studies were performed to establish size, weight and packaging arrangements for aerodynamic decelerator devices that could be used for recovery of the expended solid propellant rocket motors used in the launch phase of the Space Shuttle System. Computations were made using standard engineering analysis techniques. Terminal stage parachutes were sized to provide equilibrium descent velocities for water entry that are presently thought to be acceptable without developing loads that could exceed the boosters structural integrity. The performance characteristics of the aerodynamic parachute decelerator devices considered are based on analysis and prior test results for similar configurations and are assumed to be maintained at the scale requirements of the present problem.

Synthesis of Silane and Silicon in a Non-equilibrium Plasma Jet

NASA Technical Reports Server (NTRS)

Calcote, H. F.

1978-01-01

The original objective of this program was to determine the feasibility of high volume, low-cost production of high purity silane or solar cell grade silicon using a non equilibrium plasma jet. The emphasis was changed near the end of the program to determine the feasibility of preparing photovoltaic amorphous silicon films directly using this method. The non equilibrium plasma jet should be further evaluated as a technique for producing high efficiency photovoltaic amorphous silicon films.

BGK-MD, Version 1.0

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

Haack, Jeffrey; Shohet, Gil

2016-12-02

The software implements a heterogeneous multiscale method (HMM), which involves solving a classical molecular dynamics (MD) problem and then computes the entropy production in order to compute the relaxation times towards equilibrium for use in a Bhatnagar-Gross-Krook (BGK) solver.

Equilibrium Reconstruction on the Large Helical Device

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

Samuel A. Lazerson, D. Gates, D. Monticello, H. Neilson, N. Pomphrey, A. Reiman S. Sakakibara, and Y. Suzuki

Equilibrium reconstruction is commonly applied to axisymmetric toroidal devices. Recent advances in computational power and equilibrium codes have allowed for reconstructions of three-dimensional fields in stellarators and heliotrons. We present the first reconstructions of finite beta discharges in the Large Helical Device (LHD). The plasma boundary and magnetic axis are constrained by the pressure profile from Thomson scattering. This results in a calculation of plasma beta without a-priori assumptions of the equipartition of energy between species. Saddle loop arrays place additional constraints on the equilibrium. These reconstruction utilize STELLOPT, which calls VMEC. The VMEC equilibrium code assumes good nested fluxmore » surfaces. Reconstructed magnetic fields are fed into the PIES code which relaxes this constraint allowing for the examination of the effect of islands and stochastic regions on the magnetic measurements.« less

Oxygen transport properties estimation by DSMC-CT simulations

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

Bruno, Domenico; Frezzotti, Aldo; Ghiroldi, Gian Pietro

Coupling DSMC simulations with classical trajectories calculations is emerging as a powerful tool to improve predictive capabilities of computational rarefied gas dynamics. The considerable increase of computational effort outlined in the early application of the method (Koura,1997) can be compensated by running simulations on massively parallel computers. In particular, GPU acceleration has been found quite effective in reducing computing time (Ferrigni,2012; Norman et al.,2013) of DSMC-CT simulations. The aim of the present work is to study rarefied Oxygen flows by modeling binary collisions through an accurate potential energy surface, obtained by molecular beams scattering (Aquilanti, et al.,1999). The accuracy ofmore » the method is assessed by calculating molecular Oxygen shear viscosity and heat conductivity following three different DSMC-CT simulation methods. In the first one, transport properties are obtained from DSMC-CT simulations of spontaneous fluctuation of an equilibrium state (Bruno et al, Phys. Fluids, 23, 093104, 2011). In the second method, the collision trajectory calculation is incorporated in a Monte Carlo integration procedure to evaluate the Taxman’s expressions for the transport properties of polyatomic gases (Taxman,1959). In the third, non-equilibrium zero and one-dimensional rarefied gas dynamic simulations are adopted and the transport properties are computed from the non-equilibrium fluxes of momentum and energy. The three methods provide close values of the transport properties, their estimated statistical error not exceeding 3%. The experimental values are slightly underestimated, the percentage deviation being, again, few percent.« less

Continuous analog of multiplicative algebraic reconstruction technique for computed tomography

NASA Astrophysics Data System (ADS)

Tateishi, Kiyoko; Yamaguchi, Yusaku; Abou Al-Ola, Omar M.; Kojima, Takeshi; Yoshinaga, Tetsuya

2016-03-01

We propose a hybrid dynamical system as a continuous analog to the block-iterative multiplicative algebraic reconstruction technique (BI-MART), which is a well-known iterative image reconstruction algorithm for computed tomography. The hybrid system is described by a switched nonlinear system with a piecewise smooth vector field or differential equation and, for consistent inverse problems, the convergence of non-negatively constrained solutions to a globally stable equilibrium is guaranteed by the Lyapunov theorem. Namely, we can prove theoretically that a weighted Kullback-Leibler divergence measure can be a common Lyapunov function for the switched system. We show that discretizing the differential equation by using the first-order approximation (Euler's method) based on the geometric multiplicative calculus leads to the same iterative formula of the BI-MART with the scaling parameter as a time-step of numerical discretization. The present paper is the first to reveal that a kind of iterative image reconstruction algorithm is constructed by the discretization of a continuous-time dynamical system for solving tomographic inverse problems. Iterative algorithms with not only the Euler method but also the Runge-Kutta methods of lower-orders applied for discretizing the continuous-time system can be used for image reconstruction. A numerical example showing the characteristics of the discretized iterative methods is presented.

Accelerated path integral methods for atomistic simulations at ultra-low temperatures

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

Uhl, Felix, E-mail: felix.uhl@rub.de; Marx, Dominik; Ceriotti, Michele

2016-08-07

Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated pathmore » integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH{sub 5}{sup +}. We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH{sub 4} to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state.« less

Teaching Chemical Equilibrium with the Jigsaw Technique

ERIC Educational Resources Information Center

Doymus, Kemal

2008-01-01

This study investigates the effect of cooperative learning (jigsaw) versus individual learning methods on students' understanding of chemical equilibrium in a first-year general chemistry course. This study was carried out in two different classes in the department of primary science education during the 2005-2006 academic year. One of the classes…

A New Application for Radioimmunoassay: Measurement of Thermodynamic Constants.

ERIC Educational Resources Information Center

Angstadt, Carol N.; And Others

1983-01-01

Describes a laboratory experiment in which an equilibrium radioimmunoassay (RIA) is used to estimate thermodynamic parameters such as equilibrium constants. The experiment is simple and inexpensive, and it introduces a technique that is important in the clinical chemistry and research laboratory. Background information, procedures, and results are…

Incorporation of a Chemical Equilibrium Equation of State into LOCI-Chem

NASA Technical Reports Server (NTRS)

Cox, Carey F.

2005-01-01

Renewed interest in development of advanced high-speed transport, reentry vehicles and propulsion systems has led to a resurgence of research into high speed aerodynamics. As this flow regime is typically dominated by hot reacting gaseous flow, efficient models for the characteristic chemical activity are necessary for accurate and cost effective analysis and design of aerodynamic vehicles that transit this regime. The LOCI-Chem code recently developed by Ed Luke at Mississippi State University for NASA/MSFC and used by NASA/MSFC and SSC represents an important step in providing an accurate, efficient computational tool for the simulation of reacting flows through the use of finite-rate kinetics [3]. Finite rate chemistry however, requires the solution of an additional N-1 species mass conservation equations with source terms involving reaction kinetics that are not fully understood. In the equilibrium limit, where the reaction rates approach infinity, these equations become very stiff. Through the use of the assumption of local chemical equilibrium the set of governing equations is reduced back to the usual gas dynamic equations, and thus requires less computation, while still allowing for the inclusion of reacting flow phenomenology. The incorporation of a chemical equilibrium equation of state module into the LOCI-Chem code was the primary objective of the current research. The major goals of the project were: (1) the development of a chemical equilibrium composition solver, and (2) the incorporation of chemical equilibrium solver into LOCI-Chem. Due to time and resource constraints, code optimization was not considered unless it was important to the proper functioning of the code.

The Effect of Cooperative Learning Approach Based on Conceptual Change Condition on Students' Understanding of Chemical Equilibrium Concepts

ERIC Educational Resources Information Center

Bilgin, Ibrahim; Geban, Omer

2006-01-01

The purpose of this study is to investigate the effects of the cooperative learning approach based on conceptual change conditions over traditional instruction on 10th grade students' conceptual understanding and achievement of computational problems related to chemical equilibrium concepts. The subjects of this study consisted of 87 tenth grade…

Cournot competition between a non-profit firm and a for-profit firm with uncertainty

NASA Astrophysics Data System (ADS)

Ferreira, Fernanda A.

2010-03-01

In this paper, we consider a Cournot competition between a nonprofit firm and a for-profit firm in a homogeneous goods market, with uncertain demand. Given an asymmetric tax schedule, we compute explicitly the Bayesian-Nash equilibrium. Furthermore, we analyze the effects of the tax rate and the degree of altruistic preference on market equilibrium outcomes.

Stresses in non-equilibrium fluids: Exact formulation and coarse-grained theory.

PubMed

Krüger, Matthias; Solon, Alexandre; Démery, Vincent; Rohwer, Christian M; Dean, David S

2018-02-28

Starting from the stochastic equation for the density operator, we formulate the exact (instantaneous) stress tensor for interacting Brownian particles and show that its average value agrees with expressions derived previously. We analyze the relation between the stress tensor and forces due to external potentials and observe that, out of equilibrium, particle currents give rise to extra forces. Next, we derive the stress tensor for a Landau-Ginzburg theory in generic, non-equilibrium situations, finding an expression analogous to that of the exact microscopic stress tensor, and discuss the computation of out-of-equilibrium (classical) Casimir forces. Subsequently, we give a general form for the stress tensor which is valid for a large variety of energy functionals and which reproduces the two mentioned cases. We then use these relations to study the spatio-temporal correlations of the stress tensor in a Brownian fluid, which we compute to leading order in the interaction potential strength. We observe that, after integration over time, the spatial correlations generally decay as power laws in space. These are expected to be of importance for driven confined systems. We also show that divergence-free parts of the stress tensor do not contribute to the Green-Kubo relation for the viscosity.

Stresses in non-equilibrium fluids: Exact formulation and coarse-grained theory

NASA Astrophysics Data System (ADS)

Krüger, Matthias; Solon, Alexandre; Démery, Vincent; Rohwer, Christian M.; Dean, David S.

2018-02-01

Starting from the stochastic equation for the density operator, we formulate the exact (instantaneous) stress tensor for interacting Brownian particles and show that its average value agrees with expressions derived previously. We analyze the relation between the stress tensor and forces due to external potentials and observe that, out of equilibrium, particle currents give rise to extra forces. Next, we derive the stress tensor for a Landau-Ginzburg theory in generic, non-equilibrium situations, finding an expression analogous to that of the exact microscopic stress tensor, and discuss the computation of out-of-equilibrium (classical) Casimir forces. Subsequently, we give a general form for the stress tensor which is valid for a large variety of energy functionals and which reproduces the two mentioned cases. We then use these relations to study the spatio-temporal correlations of the stress tensor in a Brownian fluid, which we compute to leading order in the interaction potential strength. We observe that, after integration over time, the spatial correlations generally decay as power laws in space. These are expected to be of importance for driven confined systems. We also show that divergence-free parts of the stress tensor do not contribute to the Green-Kubo relation for the viscosity.

Radiation calculation in non-equilibrium shock layer

NASA Astrophysics Data System (ADS)

Dubois, Joanne

2005-05-01

The purpose of the work was to investigate confidence in radiation predictions on an entry probe body in high temperature conditions taking the Huygens probe as an example. Existing engineering flowfield codes for shock tube and blunt body simulations were used and updated when necessary to compute species molar fractions and flow field parameters. An interface to the PARADE radiation code allowed radiative emission estimates to the body surface to be made. A validation of the radiative models in equilibrium conditions was first made with published data and by comparison with shock tube test case data from the IUSTI TCM2 facility with Titan like atmosphere test gas. Further verifications were made in non-equilibrium with published computations. These comparisons were initially made using a Boltzmann assumption for the electronic states of CN. An attempt was also made to use pseudo species for the individual electronic states of CN. Assumptions made in this analysis are described and a further comparison with shock tube data undertaken. Several CN radiation datasets have been used, and while improvements to the modelling tools have been made, it seems that considerable uncertainty remains in the modelling of the non-equilibrium emission using simple engineering methods.

Bioproducts and environmental quality: Biofuels, greenhouse gases, and water quality

NASA Astrophysics Data System (ADS)

Ren, Xiaolin

Promoting bio-based products is one oft-proposed solution to reduce GHG emissions because the feedstocks capture carbon, offsetting at least partially the carbon discharges resulting from use of the products. However, several life cycle analyses point out that while biofuels may emit less life cycle net carbon emissions than fossil fuels, they may exacerbate other parts of biogeochemical cycles, notably nutrient loads in the aquatic environment. In three essays, this dissertation explores the tradeoff between GHG emissions and nitrogen leaching associated with biofuel production using general equilibrium models. The first essay develops a theoretical general equilibrium model to calculate the second-best GHG tax with the existence of a nitrogen leaching distortion. The results indicate that the second-best GHG tax could be higher or lower than the first-best tax rates depending largely on the elasticity of substitution between fossil fuel and biofuel. The second and third essays employ computable general equilibrium models to further explore the tradeoff between GHG emissions and nitrogen leaching. The computable general equilibrium models also incorporate multiple biofuel pathways, i.e., biofuels made from different feedstocks using different processes, to identify the cost-effective combinations of biofuel pathways under different policies, and the corresponding economic and environmental impacts.

Control and instanton trajectories for random transitions in turbulent flows

NASA Astrophysics Data System (ADS)

Bouchet, Freddy; Laurie, Jason; Zaboronski, Oleg

2011-12-01

Many turbulent systems exhibit random switches between qualitatively different attractors. The transition between these bistable states is often an extremely rare event, that can not be computed through DNS, due to complexity limitations. We present results for the calculation of instanton trajectories (a control problem) between non-equilibrium stationary states (attractors) in the 2D stochastic Navier-Stokes equations. By representing the transition probability between two states using a path integral formulation, we can compute the most probable trajectory (instanton) joining two non-equilibrium stationary states. Technically, this is equivalent to the minimization of an action, which can be related to a fluid mechanics control problem.

CET93 and CETPC: An interim updated version of the NASA Lewis computer program for calculating complex chemical equilibria with applications

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Reno, Martin A.; Gordon, Sanford

1994-01-01

The NASA Lewis chemical equilibrium program with applications continues to be improved and updated. The latest version is CET93. This code, with smaller arrays, has been compiled for use on an IBM or IBM-compatible personal computer and is called CETPC. This report is intended to be primarily a users manual for CET93 and CETPC. It does not repeat the more complete documentation of earlier reports on the equilibrium program. Most of the discussion covers input and output files, two new options (ONLY and comments), example problems, and implementation of CETPC.

PARVMEC: An Efficient, Scalable Implementation of the Variational Moments Equilibrium Code

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

Seal, Sudip K; Hirshman, Steven Paul; Wingen, Andreas

The ability to sustain magnetically confined plasma in a state of stable equilibrium is crucial for optimal and cost-effective operations of fusion devices like tokamaks and stellarators. The Variational Moments Equilibrium Code (VMEC) is the de-facto serial application used by fusion scientists to compute magnetohydrodynamics (MHD) equilibria and study the physics of three dimensional plasmas in confined configurations. Modern fusion energy experiments have larger system scales with more interactive experimental workflows, both demanding faster analysis turnaround times on computational workloads that are stressing the capabilities of sequential VMEC. In this paper, we present PARVMEC, an efficient, parallel version of itsmore » sequential counterpart, capable of scaling to thousands of processors on distributed memory machines. PARVMEC is a non-linear code, with multiple numerical physics modules, each with its own computational complexity. A detailed speedup analysis supported by scaling results on 1,024 cores of a Cray XC30 supercomputer is presented. Depending on the mode of PARVMEC execution, speedup improvements of one to two orders of magnitude are reported. PARVMEC equips fusion scientists for the first time with a state-of-theart capability for rapid, high fidelity analyses of magnetically confined plasmas at unprecedented scales.« less

The QSE-Reduced Nuclear Reaction Network for Silicon Burning

NASA Astrophysics Data System (ADS)

Hix, W. Raphael; Parete-Koon, Suzanne T.; Freiburghaus, Christian; Thielemann, Friedrich-Karl

2007-09-01

Iron and neighboring nuclei are formed in massive stars shortly before core collapse and during their supernova outbursts, as well as during thermonuclear supernovae. Complete and incomplete silicon burning are responsible for the production of a wide range of nuclei with atomic mass numbers from 28 to 64. Because of the large number of nuclei involved, accurate modeling of silicon burning is computationally expensive. However, examination of the physics of silicon burning has revealed that the nuclear evolution is dominated by large groups of nuclei in mutual equilibrium. We present a new hybrid equilibrium-network scheme which takes advantage of this quasi-equilibrium in order to reduce the number of independent variables calculated. This allows accurate prediction of the nuclear abundance evolution, deleptonization, and energy generation at a greatly reduced computational cost when compared to a conventional nuclear reaction network. During silicon burning, the resultant QSE-reduced network is approximately an order of magnitude faster than the full network it replaces and requires the tracking of less than a third as many abundance variables, without significant loss of accuracy. These reductions in computational cost and the number of species evolved make QSE-reduced networks well suited for inclusion within hydrodynamic simulations, particularly in multidimensional applications.

Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces.

PubMed

Spezia, Riccardo; Martínez-Nuñez, Emilio; Vazquez, Saulo; Hase, William L

2017-04-28

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Author(s).

Comparison of Themodynamic and Transport Property Models for Computing Equilibrium High Enthalpy Flows

NASA Astrophysics Data System (ADS)

Ramasahayam, Veda Krishna Vyas; Diwakar, Anant; Bodi, Kowsik

2017-11-01

To study the flow of high temperature air in vibrational and chemical equilibrium, accurate models for thermodynamic state and transport phenomena are required. In the present work, the performance of a state equation model and two mixing rules for determining equilibrium air thermodynamic and transport properties are compared with that of curve fits. The thermodynamic state model considers 11 species which computes flow chemistry by an iterative process and the mixing rules considered for viscosity are Wilke and Armaly-Sutton. The curve fits of Srinivasan, which are based on Grabau type transition functions, are chosen for comparison. A two-dimensional Navier-Stokes solver is developed to simulate high enthalpy flows with numerical fluxes computed by AUSM+-up. The accuracy of state equation model and curve fits for thermodynamic properties is determined using hypersonic inviscid flow over a circular cylinder. The performance of mixing rules and curve fits for viscosity are compared using hypersonic laminar boundary layer prediction on a flat plate. It is observed that steady state solutions from state equation model and curve fits match with each other. Though curve fits are significantly faster the state equation model is more general and can be adapted to any flow composition.

Single-molecule techniques in biophysics: a review of the progress in methods and applications.

PubMed

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J M; Leake, Mark C

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Single-molecule techniques in biophysics: a review of the progress in methods and applications

NASA Astrophysics Data System (ADS)

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J. M.; Leake, Mark C.

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in ‘force spectroscopy’ techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Quantum Kinetics and the Zeno Ansatz: Sterile Neutrino Dark Matter in the Early Universe

NASA Astrophysics Data System (ADS)

Dvornikov, Olexiy V.

We solved the quantum kinetic equations for the evolution of neutrino states in the early universe. Starting at high temperatures, we evolve neutrino states to observe the resonant conversion of active-to-sterile neutrinos in a lepton asymmetric (more neutrinos than anti-neutrinos) universe. We find that at high temperatures, the high neutrino scattering and oscillation rates enforce a local equilibrium that balances the growth of coherence at the oscillation rate and the damping of coherence through scattering. This equilibrium, which we call a "quantum kinetic equilibrium," appears to approximately hold throughout the neutrino evolution, from the initial conditions through resonances that may be non adiabatic. Using this quantum kinetic equilibrium informs a proper choice of the initial conditions of the neutrino state and the relaxation process that occurs to this equilibrium when the initial conditions (as are typically chosen in the literature) are not coincident with the equilibrium values. We also discuss how to use this equilibrium to reduce the computational expense of solving the full quantum kinetic equations for neutrino states evolving in the early universe.

Generalized non-equilibrium vertex correction method in coherent medium theory for quantum transport simulation of disordered nanoelectronics

NASA Astrophysics Data System (ADS)

Yan, Jiawei; Ke, Youqi

In realistic nanoelectronics, disordered impurities/defects are inevitable and play important roles in electron transport. However, due to the lack of effective quantum transport method, the important effects of disorders remain poorly understood. Here, we report a generalized non-equilibrium vertex correction (NVC) method with coherent potential approximation to treat the disorder effects in quantum transport simulation. With this generalized NVC method, any averaged product of two single-particle Green's functions can be obtained by solving a set of simple linear equations. As a result, the averaged non-equilibrium density matrix and various important transport properties, including averaged current, disordered induced current fluctuation and the averaged shot noise, can all be efficiently computed in a unified scheme. Moreover, a generalized form of conditionally averaged non-equilibrium Green's function is derived to incorporate with density functional theory to enable first-principles simulation. We prove the non-equilibrium coherent potential equals the non-equilibrium vertex correction. Our approach provides a unified, efficient and self-consistent method for simulating non-equilibrium quantum transport through disorder nanoelectronics. Shanghaitech start-up fund.

A stabilized element-based finite volume method for poroelastic problems

NASA Astrophysics Data System (ADS)

Honório, Hermínio T.; Maliska, Clovis R.; Ferronato, Massimiliano; Janna, Carlo

2018-07-01

The coupled equations of Biot's poroelasticity, consisting of stress equilibrium and fluid mass balance in deforming porous media, are numerically solved. The governing partial differential equations are discretized by an Element-based Finite Volume Method (EbFVM), which can be used in three dimensional unstructured grids composed of elements of different types. One of the difficulties for solving these equations is the numerical pressure instability that can arise when undrained conditions take place. In this paper, a stabilization technique is developed to overcome this problem by employing an interpolation function for displacements that considers also the pressure gradient effect. The interpolation function is obtained by the so-called Physical Influence Scheme (PIS), typically employed for solving incompressible fluid flows governed by the Navier-Stokes equations. Classical problems with analytical solutions, as well as three-dimensional realistic cases are addressed. The results reveal that the proposed stabilization technique is able to eliminate the spurious pressure instabilities arising under undrained conditions at a low computational cost.

Estimation of Regional Evapotranspiration Using Remotely Sensed Land Surface Temperature. Part 2: Application of Equilibrium Evaporation Model to Estimate Evapotranspiration by Remote Sensing Technique. [Japan

NASA Technical Reports Server (NTRS)

Kotoda, K.; Nakagawa, S.; Kai, K.; Yoshino, M. M.; Takeda, K.; Seki, K.

1985-01-01

In a humid region like Japan, it seems that the radiation term in the energy balance equation plays a more important role for evapotranspiration then does the vapor pressure difference between the surface and lower atmospheric boundary layer. A Priestley-Taylor type equation (equilibrium evaporation model) is used to estimate evapotranspiration. Net radiation, soil heat flux, and surface temperature data are obtained. Only temperature data obtained by remotely sensed techniques are used.

Equilibrium Shapes of Large Trans-Neptunian Objects

NASA Astrophysics Data System (ADS)

Rambaux, Nicolas; Baguet, Daniel; Chambat, Frederic; Castillo-Rogez, Julie C.

2017-11-01

The large trans-Neptunian objects (TNO) with radii larger than 400 km are thought to be in hydrostatic equilibrium. Their shapes can provide clues regarding their internal structures that would reveal information on their formation and evolution. In this paper, we explore the equilibrium figures of five TNOs, and we show that the difference between the equilibrium figures of homogeneous and heterogeneous interior models can reach several kilometers for fast rotating and low density bodies. Such a difference could be measurable by ground-based techniques. This demonstrates the importance of developing the shape up to second and third order when modeling the shapes of large and rapid rotators.

Computational understanding of Li-ion batteries

NASA Astrophysics Data System (ADS)

Urban, Alexander; Seo, Dong-Hwa; Ceder, Gerbrand

2016-03-01

Over the last two decades, computational methods have made tremendous advances, and today many key properties of lithium-ion batteries can be accurately predicted by first principles calculations. For this reason, computations have become a cornerstone of battery-related research by providing insight into fundamental processes that are not otherwise accessible, such as ionic diffusion mechanisms and electronic structure effects, as well as a quantitative comparison with experimental results. The aim of this review is to provide an overview of state-of-the-art ab initio approaches for the modelling of battery materials. We consider techniques for the computation of equilibrium cell voltages, 0-Kelvin and finite-temperature voltage profiles, ionic mobility and thermal and electrolyte stability. The strengths and weaknesses of different electronic structure methods, such as DFT+U and hybrid functionals, are discussed in the context of voltage and phase diagram predictions, and we review the merits of lattice models for the evaluation of finite-temperature thermodynamics and kinetics. With such a complete set of methods at hand, first principles calculations of ordered, crystalline solids, i.e., of most electrode materials and solid electrolytes, have become reliable and quantitative. However, the description of molecular materials and disordered or amorphous phases remains an important challenge. We highlight recent exciting progress in this area, especially regarding the modelling of organic electrolytes and solid-electrolyte interfaces.

Nicholas Metropolis Award for Outstanding Doctoral Thesis Work in Computational Physics Talk: Understanding Nano-scale Electronic Systems via Large-scale Computation

NASA Astrophysics Data System (ADS)

Cao, Chao

2009-03-01

Nano-scale physical phenomena and processes, especially those in electronics, have drawn great attention in the past decade. Experiments have shown that electronic and transport properties of functionalized carbon nanotubes are sensitive to adsorption of gas molecules such as H2, NO2, and NH3. Similar measurements have also been performed to study adsorption of proteins on other semiconductor nano-wires. These experiments suggest that nano-scale systems can be useful for making future chemical and biological sensors. Aiming to understand the physical mechanisms underlying and governing property changes at nano-scale, we start off by investigating, via first-principles method, the electronic structure of Pd-CNT before and after hydrogen adsorption, and continue with coherent electronic transport using non-equilibrium Green’s function techniques combined with density functional theory. Once our results are fully analyzed they can be used to interpret and understand experimental data, with a few difficult issues to be addressed. Finally, we discuss a newly developed multi-scale computing architecture, OPAL, that coordinates simultaneous execution of multiple codes. Inspired by the capabilities of this computing framework, we present a scenario of future modeling and simulation of multi-scale, multi-physical processes.

Investigation of island formation due to RMPs in DIII-D plasmas with the SIESTA resistive MHD equilibrium code

NASA Astrophysics Data System (ADS)

Hirshman, S. P.; Shafer, M. W.; Seal, S. K.; Canik, J. M.

2016-04-01

> The SIESTA magnetohydrodynamic (MHD) equilibrium code has been used to compute a sequence of ideally stable equilibria resulting from numerical variation of the helical resonant magnetic perturbation (RMP) applied to an axisymmetric DIII-D plasma equilibrium. Increasing the perturbation strength at the dominant , resonant surface leads to lower MHD energies and increases in the equilibrium island widths at the (and sidebands) surfaces, in agreement with theoretical expectations. Island overlap at large perturbation strengths leads to stochastic magnetic fields which correlate well with the experimentally inferred field structure. The magnitude and spatial phase (around the dominant rational surfaces) of the resonant (shielding) component of the parallel current are shown to change qualitatively with the magnetic island topology.

Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II

NASA Astrophysics Data System (ADS)

Nemtseva, Elena V.; Lashchuk, Olesya O.; Gerasimova, Marina A.; Melnik, Tatiana N.; Nagibina, Galina S.; Melnik, Bogdan S.

2018-01-01

In most cases, intermediate states of multistage folding proteins are not ‘visible’ under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II.

PubMed

Nemtseva, Elena V; Lashchuk, Olesya O; Gerasimova, Marina A; Melnik, Tatiana N; Nagibina, Galina S; Melnik, Bogdan S

2017-12-21

In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

Equilibrium Speciation of Select Lanthanides in the Presence of Acidic Ligands in Homo- and Heterogeneous Solutions

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

Robinson, Troy A

2011-08-01

This dissertation explores lanthanide speciation in liquid solution systems related to separation schemes involving the acidic ligands: bis(2-ethylhexyl) phosphoric acid (HDEHP), lactate, and 8-hydroxyquinoline. Equilibrium speciation of neodymium (Nd 3+), sodium (Na+), HDEHP, water, and lactate in the TALSPEAK liquid-liquid extraction system was explored under varied Nd 3+ loading of HDEHP in the organic phase and through extraction from aqueous HCl and lactate media. System speciation was probed through vapor pressure osmometry, visible and Fourier Transform Infrared (FTIR) spectroscopy, 22Na and 13C labeled lactate radiotracer distribution measurements, Karl Fischer titrations, and equilibrium pH measurements. Distribution of Nd 3+, Na +,more » lactate, and equilibrium pH were modeled using the SXLSQI software to obtain logKNd and logKNa extraction constants under selected conditions. Results showed that high Nd 3+ loading of the HDEHP led to Nd 3+ speciation that departs from the ion exchange mechanism and includes formation of highly aggregated, polynuclear [NdLactate(DEHP) 2] x; (with x > 1). By substituting lanthanum (La 3+) for Nd 3+ in this system, NMR scoping experiments using 23Na, 31P nuclei and 13C labeled lactate were performed. Results indicated that this technique is sensitive to changes in system speciation, and that further experiments are warranted. In a homogeneous system representing the TALSPEAK aqueous phase, Lactate protonation behavior at various temperatures was characterized using a combination of potentiometric titration and modeling with the Hyperquad computer program. The temperature dependent deprotonation behavior of lactate showed little change with temperature at 2.0 M NaCl ionic strength. Cloud point extraction is a non-traditional separation technique that starts with a homogeneous phase that becomes heterogeneous by the micellization of surfactants through the increase of temperature. To better understand the behavior of europium (Eu 3+) and 8-hydroxyquinoline under cloud point extraction conditions, potentiometric and spectrophotometric titrations coupled with modeling with Hyperquad and SQUAD computer programs were performed to assess europium (Eu 3+) and 8-hydroxyquinoline speciation. Experiments in both water and a 1wt% Triton X-114/water mixed solvent were compared to understand the effect of Triton X-114 on the system speciation. Results indicated that increased solvation of 8-hydroxyquinoline by the mixed solvent lead to more stable complexes involving 8-hydroxyquinoline than in water, whereas competition between hydroxide and Triton X-114 for Eu 3+ led to lower stability hydrolysis complexes in the mixed solvent than in water. Lanthanide speciation is challenging due to the trivalent oxidation state that leads to multiple ligand complexes, including some mixed complexes. The complexity of the system demands well-designed and precise experiments that capture the nuances of the chemistry. This work increased the understanding of lanthanide speciation in the explored systems, but more work is required to produce a comprehensive understanding of the speciation involved.« less

Coupling of PIES 3-D Equilibrium Code and NIFS Bootstrap Code with Applications to the Computation of Stellarator Equilibria

NASA Astrophysics Data System (ADS)

Monticello, D. A.; Reiman, A. H.; Watanabe, K. Y.; Nakajima, N.; Okamoto, M.

1997-11-01

The existence of bootstrap currents in both tokamaks and stellarators was confirmed, experimentally, more than ten years ago. Such currents can have significant effects on the equilibrium and stability of these MHD devices. In addition, stellarators, with the notable exception of W7-X, are predicted to have such large bootstrap currents that reliable equilibrium calculations require the self-consistent evaluation of bootstrap currents. Modeling of discharges which contain islands requires an algorithm that does not assume good surfaces. Only one of the two 3-D equilibrium codes that exist, PIES( Reiman, A. H., Greenside, H. S., Compt. Phys. Commun. 43), (1986)., can easily be modified to handle bootstrap current. Here we report on the coupling of the PIES 3-D equilibrium code and NIFS bootstrap code(Watanabe, K., et al., Nuclear Fusion 35) (1995), 335.

Chemical Equilibrium, Unit 2: Le Chatelier's Principle. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

ERIC Educational Resources Information Center

Jameson, A. Keith

Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on Le Chatelier's principle includes objectives, prerequisites, pretest, instructions for executing the computer program, and…

Multiscale Simulation of Microbe Structure and Dynamics

PubMed Central

Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.

2012-01-01

A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin. PMID:21802438

Stability and bifurcation analysis on a ratio-dependent predator-prey model with time delay

NASA Astrophysics Data System (ADS)

Xu, Rui; Gan, Qintao; Ma, Zhien

2009-08-01

A ratio-dependent predator-prey model with time delay due to the gestation of the predator is investigated. By analyzing the corresponding characteristic equations, the local stability of a positive equilibrium and a semi-trivial boundary equilibrium is discussed, respectively. Further, it is proved that the system undergoes a Hopf bifurcation at the positive equilibrium. Using the normal form theory and the center manifold reduction, explicit formulae are derived to determine the direction of bifurcations and the stability and other properties of bifurcating periodic solutions. By means of an iteration technique, sufficient conditions are obtained for the global attractiveness of the positive equilibrium. By comparison arguments, the global stability of the semi-trivial equilibrium is also addressed. Numerical simulations are carried out to illustrate the main results.

A Harris-Todaro Agent-Based Model to Rural-Urban Migration

NASA Astrophysics Data System (ADS)

Espíndola, Aquino L.; Silveira, Jaylson J.; Penna, T. J. P.

2006-09-01

The Harris-Todaro model of the rural-urban migration process is revisited under an agent-based approach. The migration of the workers is interpreted as a process of social learning by imitation, formalized by a computational model. By simulating this model, we observe a transitional dynamics with continuous growth of the urban fraction of overall population toward an equilibrium. Such an equilibrium is characterized by stabilization of rural-urban expected wages differential (generalized Harris-Todaro equilibrium condition), urban concentration and urban unemployment. These classic results obtained originally by Harris and Todaro are emergent properties of our model.

Algorithm For Hypersonic Flow In Chemical Equilibrium

NASA Technical Reports Server (NTRS)

Palmer, Grant

1989-01-01

Implicit, finite-difference, shock-capturing algorithm calculates inviscid, hypersonic flows in chemical equilibrium. Implicit formulation chosen because overcomes limitation on mathematical stability encountered in explicit formulations. For dynamical portion of problem, Euler equations written in conservation-law form in Cartesian coordinate system for two-dimensional or axisymmetric flow. For chemical portion of problem, equilibrium state of gas at each point in computational grid determined by minimizing local Gibbs free energy, subject to local conservation of molecules, atoms, ions, and total enthalpy. Major advantage: resulting algorithm naturally stable and captures strong shocks without help of artificial-dissipation terms to damp out spurious numerical oscillations.

Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins.

PubMed

Abdizadeh, H; Atilgan, A R; Atilgan, C; Dedeoglu, B

2017-11-15

With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.

Optimal control strategy for a novel computer virus propagation model on scale-free networks

NASA Astrophysics Data System (ADS)

Zhang, Chunming; Huang, Haitao

2016-06-01

This paper aims to study the combined impact of reinstalling system and network topology on the spread of computer viruses over the Internet. Based on scale-free network, this paper proposes a novel computer viruses propagation model-SLBOSmodel. A systematic analysis of this new model shows that the virus-free equilibrium is globally asymptotically stable when its spreading threshold is less than one; nevertheless, it is proved that the viral equilibrium is permanent if the spreading threshold is greater than one. Then, the impacts of different model parameters on spreading threshold are analyzed. Next, an optimally controlled SLBOS epidemic model on complex networks is also studied. We prove that there is an optimal control existing for the control problem. Some numerical simulations are finally given to illustrate the main results.

A study of reacting free and ducted hydrogen/air jets

NASA Technical Reports Server (NTRS)

Beach, H. L., Jr.

1975-01-01

The mixing and reaction of a supersonic jet of hydrogen in coaxial free and ducted high temperature test gases were investigated. The importance of chemical kinetics on computed results, and the utilization of free-jet theoretical approaches to compute enclosed flow fields were studied. Measured pitot pressure profiles were correlated by use of a parabolic mixing analysis employing an eddy viscosity model. All computations, including free, ducted, reacting, and nonreacting cases, use the same value of the empirical constant in the viscosity model. Equilibrium and finite rate chemistry models were utilized. The finite rate assumption allowed prediction of observed ignition delay, but the equilibrium model gave the best correlations downstream from the ignition location. Ducted calculations were made with finite rate chemistry; correlations were, in general, as good as the free-jet results until problems with the boundary conditions were encountered.

MBSSAS: A code for the computation of margules parameters and equilibrium relations in binary solid-solution aqueous-solution systems

USGS Publications Warehouse

Glynn, P.D.

1991-01-01

The computer code MBSSAS uses two-parameter Margules-type excess-free-energy of mixing equations to calculate thermodynamic equilibrium, pure-phase saturation, and stoichiometric saturation states in binary solid-solution aqueous-solution (SSAS) systems. Lippmann phase diagrams, Roozeboom diagrams, and distribution-coefficient diagrams can be constructed from the output data files, and also can be displayed by MBSSAS (on IBM-PC compatible computers). MBSSAS also will calculate accessory information, such as the location of miscibility gaps, spinodal gaps, critical-mixing points, alyotropic extrema, Henry's law solid-phase activity coefficients, and limiting distribution coefficients. Alternatively, MBSSAS can use such information (instead of the Margules, Guggenheim, or Thompson and Waldbaum excess-free-energy parameters) to calculate the appropriate excess-free-energy of mixing equation for any given SSAS system. ?? 1991.

Computation of thermodynamic equilibrium in systems under stress

NASA Astrophysics Data System (ADS)

Vrijmoed, Johannes C.; Podladchikov, Yuri Y.

2016-04-01

Metamorphic reactions may be partly controlled by the local stress distribution as suggested by observations of phase assemblages around garnet inclusions related to an amphibolite shear zone in granulite of the Bergen Arcs in Norway. A particular example presented in fig. 14 of Mukai et al. [1] is discussed here. A garnet crystal embedded in a plagioclase matrix is replaced on the left side by a high pressure intergrowth of kyanite and quartz and on the right side by chlorite-amphibole. This texture apparently represents disequilibrium. In this case, the minerals adapt to the low pressure ambient conditions only where fluids were present. Alternatively, here we compute that this particular low pressure and high pressure assemblage around a stressed rigid inclusion such as garnet can coexist in equilibrium. To do the computations we developed the Thermolab software package. The core of the software package consists of Matlab functions that generate Gibbs energy of minerals and melts from the Holland and Powell database [2] and aqueous species from the SUPCRT92 database [3]. Most up to date solid solutions are included in a general formulation. The user provides a Matlab script to do the desired calculations using the core functions. Gibbs energy of all minerals, solutions and species are benchmarked versus THERMOCALC, PerpleX [4] and SUPCRT92 and are reproduced within round off computer error. Multi-component phase diagrams have been calculated using Gibbs minimization to benchmark with THERMOCALC and Perple_X. The Matlab script to compute equilibrium in a stressed system needs only two modifications of the standard phase diagram script. Firstly, Gibbs energy of phases considered in the calculation is generated for multiple values of thermodynamic pressure. Secondly, for the Gibbs minimization the proportion of the system at each particular thermodynamic pressure needs to be constrained. The user decides which part of the stress tensor is input as thermodynamic pressure. To compute a case of high and low pressure around a stressed inclusion we first did a Finite Element Method calculation of a rigid inclusion in a viscous matrix under simple shear. From the computed stress distribution we took the local pressure (mean stress) in each grid point of the FEM calculation. This was used as input thermodynamic pressure in the Gibbs minimization and the result showed it is possible to have an equilibrium situation in which chlorite-amphibole is stable in the low pressure domain and kyanite in the high pressure domain of the stress field around the inclusion. Interestingly, the calculation predicts the redistribution of fluid from an average content of fluid in the system. The fluid in equilibrium tends to accumulate in the low pressure areas whereas it leaves the high pressure areas dry. Transport of fluid components occurs not necessarily by fluid flow, but may happen for example by diffusion. We conclude that an apparent disequilibrium texture may be explained by equilibrium under pressure variations, and apparent fluid addition by redistribution of fluid controlled by the local stress distribution. [1] Mukai et al. (2014), Journal of Petrology, 55 (8), p. 1457-1477. [2] Holland and Powell (1998), Journal of Metamorphic Geology, 16, p. 309-343 [3] Johnson et al. (1992), Computers & Geosciences, 18 (7), p. 899-947 [4] Connolly (2005), Earth and Planetary Science Letters, 236, p. 524-541

Using Think-Aloud Protocols to Investigate Secondary School Chemistry Teachers' Misconceptions about Chemical Equilibrium

ERIC Educational Resources Information Center

Cheung, Derek

2009-01-01

Secondary school chemistry teachers' understanding of chemical equilibrium was investigated through interviews using the think-aloud technique. The interviews were conducted with twelve volunteer chemistry teachers in Hong Kong. Their teaching experience ranged from 3 to 18 years. They were asked to predict what would happen to the equilibrium…

A CRDS approach to gas phase equilibrium constants: the case of N 2O 4 ↔ 2NO 2 at 283 K

NASA Astrophysics Data System (ADS)

Tuchler, Matthew F.; Schmidt, Kierstin L.; Morgan, Mackenzie

2005-01-01

We report a general technique for determining the gas phase equilibrium constant, KP, of the A ↔ 2C system using cavity ringdown spectroscopy (CRDS). Working at a constant temperature, the absorption of one of the equilibrium species is measured at two different total pressures. KP is determined from the total pressures of the equilibrium mixture and the ratio of the absorptions. Theoretical limits on sensitivity of this technique are described as a function of experimental conditions. We present results from the reaction N 2O 4 ↔ 2NO 2 measured at T = 283 K. KP measured in this experiment, 21 (±5) Torr, is found to be lower than that recommended by the NASA Panel for Data Evaluation, 32 Torr. [S.P. Sander, A.R. Ravishankara, D.M. Golden, C.E. Kolb, M.J. Kurylo, R.E. Huie, V.L. Orkin, M.J. Molina, G.K. Moortgat, B.J. Finlayson-Pitts, Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies. Evaluation No. 14; Jet Propulsion Laboratory, Pasadena, CA, 2003].

Computational Thermochemistry of Jet Fuels and Rocket Propellants

NASA Technical Reports Server (NTRS)

Crawford, T. Daniel

2002-01-01

The design of new high-energy density molecules as candidates for jet and rocket fuels is an important goal of modern chemical thermodynamics. The NASA Glenn Research Center is home to a database of thermodynamic data for over 2000 compounds related to this goal, in the form of least-squares fits of heat capacities, enthalpies, and entropies as functions of temperature over the range of 300 - 6000 K. The chemical equilibrium with applications (CEA) program written and maintained by researchers at NASA Glenn over the last fifty years, makes use of this database for modeling the performance of potential rocket propellants. During its long history, the NASA Glenn database has been developed based on experimental results and data published in the scientific literature such as the standard JANAF tables. The recent development of efficient computational techniques based on quantum chemical methods provides an alternative source of information for expansion of such databases. For example, it is now possible to model dissociation or combustion reactions of small molecules to high accuracy using techniques such as coupled cluster theory or density functional theory. Unfortunately, the current applicability of reliable computational models is limited to relatively small molecules containing only around a dozen (non-hydrogen) atoms. We propose to extend the applicability of coupled cluster theory- often referred to as the 'gold standard' of quantum chemical methods- to molecules containing 30-50 non-hydrogen atoms. The centerpiece of this work is the concept of local correlation, in which the description of the electron interactions- known as electron correlation effects- are reduced to only their most important localized components. Such an advance has the potential to greatly expand the current reach of computational thermochemistry and thus to have a significant impact on the theoretical study of jet and rocket propellants.

Reviewing Some Crucial Concepts of Gibbs Energy in Chemical Equilibrium Using a Computer-Assisted, Guided-Problem-Solving Approach

ERIC Educational Resources Information Center

Borge, Javier

2015-01-01

G, G°, [delta][subscript r]G, [delta][subscript r]G°, [delta]G, and [delta]G° are essential quantities to master the chemical equilibrium. Although the number of publications devoted to explaining these items is extremely high, it seems that they do not produce the desired effect because some articles and textbooks are still being written with…

Using computer algebra and SMT-solvers to analyze a mathematical model of cholera propagation

NASA Astrophysics Data System (ADS)

Trujillo Arredondo, Mariana

2014-06-01

We analyze a mathematical model for the transmission of cholera. The model is already defined and involves variables such as the pathogen agent, which in this case is the bacterium Vibrio cholera, and the human population. The human population is divided into three classes: susceptible, infectious and removed. Using Computer Algebra, specifically Maple we obtain two equilibrium states: the disease free state and the endemic state. Using Maple it is possible to prove that the disease free state is locally asymptotically stable if and only if R0 < 1. Using Maple it is possible to prove that the endemic equilibrium state is locally stable when it exists, it is to say when R0 > 1. Using the package Red-Log of the Computer algebra system Reduce and the SMT-Solver Z3Py it is possible to obtain numerical conditions for the model. The formula for the basic reproductive number makes a synthesis with all epidemic parameters in the model. Also it is possible to make numerical simulations which are very illustrative about the epidemic patters that are expected to be observed in real situations. We claim that these kinds of software are very useful in the analysis of epidemic models given that the symbolic computation provides algebraic formulas for the basic reproductive number and such algebraic formulas are very useful to derive control measures. For other side, computer algebra software is a powerful tool to make the stability analysis for epidemic models given that the all steps in the stability analysis can be made automatically: finding the equilibrium points, computing the jacobian, computing the characteristic polynomial for the jacobian, and applying the Routh-Hurwitz theorem to the characteristic polynomial. Finally, using SMT-Solvers is possible to make automatically checks of satisfiability, validity and quantifiers elimination being these computations very useful to analyse complicated epidemic models.

Development of an automated experimental setup for the study of ionic-exchange kinetics. Application to the ionic adsorption, equilibrium attainment and dissolution of apatite compounds.

PubMed

Thomann, J M; Gasser, P; Bres, E F; Voegel, J C; Gramain, P

1990-02-01

An ion-selective electrode and microcomputer-based experimental setup for the study of ionic-exchange kinetics between a powdered solid and the solution is described. The equipment is composed of easily available commercial devices and a data acquisition and regularization computer program is presented. The system, especially developed to investigate the ionic adsorption, equilibrium attainment and dissolution of hard mineralized tissues, provides good reliable results by taking into account the volume changes of the reacting solution and the electrode behaviour under different experimental conditions, and by avoiding carbonation of the solution. A second computer program, using the regularized data and the experimental parameters, calculates the quantities of protons consumed and calcium released in the case of equilibrium attainment and dissolution of apatite-like compounds. Finally, typical examples of ion-exchange and dissolution kinetics under constant pH of enamel and synthetic hydroxyapatite are examined.

Transport and equilibrium in field-reversed mirrors

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

Boyd, J.K.

Two plasma models relevant to compact torus research have been developed to study transport and equilibrium in field reversed mirrors. In the first model for small Larmor radius and large collision frequency, the plasma is described as an adiabatic hydromagnetic fluid. In the second model for large Larmor radius and small collision frequency, a kinetic theory description has been developed. Various aspects of the two models have been studied in five computer codes ADB, AV, NEO, OHK, RES. The ADB code computes two dimensional equilibrium and one dimensional transport in a flux coordinate. The AV code calculates orbit average integralsmore » in a harmonic oscillator potential. The NEO code follows particle trajectories in a Hill's vortex magnetic field to study stochasticity, invariants of the motion, and orbit average formulas. The OHK code displays analytic psi(r), B/sub Z/(r), phi(r), E/sub r/(r) formulas developed for the kinetic theory description. The RES code calculates resonance curves to consider overlap regions relevant to stochastic orbit behavior.« less

How important is thermodynamics for identifying elementary flux modes?

PubMed Central

Peres, Sabine; Jolicœur, Mario; Moulin, Cécile

2017-01-01

We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations. The method is compared with the method based on a binary distinction between reversible and irreversible reactions. When all reactions are reversible, adding the constraints based on equilibrium constants reduces the number of elementary flux modes (EFMs) by a factor of two. Declaring in advance some reactions as irreversible, based on reliable biochemical expertise, can in general reduce the number of EFMs by a greater factor. But, even in this case, computing tEFMs can rule out some EFMs which are biochemically irrelevant. We applied our method to two published models described with binary distinction: the monosaccharide metabolism and the central carbon metabolism of Chinese hamster ovary cells. The results show that the binary distinction is in good agreement with biochemical observations. Moreover, the suppression of the EFMs that are not consistent with the equilibrium constants appears to be biologically relevant. PMID:28222104

SU-G-IeP2-11: Measurement of Equilibrium Doses in Computed Tomography: Comparative Study of Ionization and Solid-State Dosimeters

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

Matsubara, K; Kobayashi, A; Koshida, K

Purpose: This study aimed to compare equilibrium doses in computed tomography (CT) obtained from ionization and solid-state dosimeters based on the approach presented in the American Association of Physicists in Medicine Report No. 111. The equilibrium doses were also compared with the CT dose index (CTDI) using a 10-cm pencil-type ionization chamber. Methods: A 0.6-cm{sup 3} ionization chamber (10X6-0.6CT) and a solid-state detector (CT Dose Profiler [CTDP]) were calibrated using 80–130 kVp X-ray beams (44.5–55.8 keV of effective energy) from a radiography X-ray machine against a reference ionization dosimeter. Three 16- or 32-cm diameter polymethyl methacrylate (PMMA) phantoms were assembledmore » consecutively on the CT table to obtain equilibrium doses. The 10X6-0.6CT and CTDP were each placed at the center and peripheral holes (12, 3, 6, and 9 o’clock) of the z-center. Central and mean peripheral equilibrium doses were obtained by scanning with longitudinal translation for a length less than the entire phantom length. CTDIs were also obtained with a 10-cm pencil-type ionization chamber (10X6-0.6CT) by scanning a 16- or 32-cm diameter PMMA phantom with one rotation of the X-ray tube. Results: The difference of calibration coefficients between 80 and 130 kVp was 21.1% for the CTDP and 0.7% for the 10X6-0.6CT. The equilibrium doses were higher than the CTDI. Especially at the peripheral positions and 80 kVp, the 10X6-0.6CT showed higher equilibrium doses than CTDP. However, the relation between the equilibrium dose for the 10X6-0.6CT and the CTDP differed depending on the phantom size, scanner type, measurement position, and selected acquisition parameters. Conclusion: The use of a 10-cm pencil-type ionization chamber causes underestimation of the equilibrium dose. The CTDP has a higher energy dependency than the 10X6-0.6CT. The obtained equilibrium doses are different between the 10X6-0.6CT and the CTDP depending on various conditions. This study was supported by JSPS KAKENHI Grant Number 15K09887.« less

Computer programs for axial flow compressor design

NASA Technical Reports Server (NTRS)

Carmody, R. H.; Creveling, H. F.

1969-01-01

Four computer programs examine effects of design parameters and indicate areas for research of multistage axial flow compressors. The programs provide information on velocity diagrams and stage-by-stage performance calculation, radial equilibrium of flow, radial distribution of total pressure, and off-design performance calculation.

The automated design of materials far from equilibrium

NASA Astrophysics Data System (ADS)

Miskin, Marc Z.

Automated design is emerging as a powerful concept in materials science. By combining computer algorithms, simulations, and experimental data, new techniques are being developed that start with high level functional requirements and identify the ideal materials that achieve them. This represents a radically different picture of how materials become functional in which technological demand drives material discovery, rather than the other way around. At the frontiers of this field, materials systems previously considered too complicated can start to be controlled and understood. Particularly promising are materials far from equilibrium. Material robustness, high strength, self-healing and memory are properties displayed by several materials systems that are intrinsically out of equilibrium. These and other properties could be revolutionary, provided they can first be controlled. This thesis conceptualizes and implements a framework for designing materials that are far from equilibrium. We show how, even in the absence of a complete physical theory, design from the top down is possible and lends itself to producing physical insight. As a prototype system, we work with granular materials: collections of athermal, macroscopic identical objects, since these materials function both as an essential component of industrial processes as well as a model system for many non-equilibrium states of matter. We show that by placing granular materials in the context of design, benefits emerge simultaneously for fundamental and applied interests. As first steps, we use our framework to design granular aggregates with extreme properties like high stiffness, and softness. We demonstrate control over nonlinear effects by producing exotic aggregates that stiffen under compression. Expanding on our framework, we conceptualize new ways of thinking about material design when automatic discovery is possible. We show how to build rules that link particle shapes to arbitrary granular packing density. We examine how the results of a design process are contingent upon operating conditions by studying which shapes dissipate energy fastest in a granular gas. We even move to create optimization algorithms for the expressed purpose of material design, by integrating them with statistical mechanics. In all of these cases, we show that turning to machines puts a fresh perspective on materials far from equilibrium. By matching forms to functions, complexities become possibilities, motifs emerge that describe new physics, and the door opens to rational design.

ms2: A molecular simulation tool for thermodynamic properties

NASA Astrophysics Data System (ADS)

Deublein, Stephan; Eckl, Bernhard; Stoll, Jürgen; Lishchuk, Sergey V.; Guevara-Carrion, Gabriela; Glass, Colin W.; Merker, Thorsten; Bernreuther, Martin; Hasse, Hans; Vrabec, Jadran

2011-11-01

This work presents the molecular simulation program ms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules. ms2 features the two main molecular simulation techniques, molecular dynamics (MD) and Monte-Carlo. It supports the calculation of vapor-liquid equilibria of pure fluids and multi-component mixtures described by rigid molecular models on the basis of the grand equilibrium method. Furthermore, it is capable of sampling various classical ensembles and yields numerous thermodynamic properties. To evaluate the chemical potential, Widom's test molecule method and gradual insertion are implemented. Transport properties are determined by equilibrium MD simulations following the Green-Kubo formalism. ms2 is designed to meet the requirements of academia and industry, particularly achieving short response times and straightforward handling. It is written in Fortran90 and optimized for a fast execution on a broad range of computer architectures, spanning from single processor PCs over PC-clusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable to different computing platforms. Feature tools facilitate the interaction with the code and the interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work. Program summaryProgram title:ms2 Catalogue identifier: AEJF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Special Licence supplied by the authors No. of lines in distributed program, including test data, etc.: 82 794 No. of bytes in distributed program, including test data, etc.: 793 705 Distribution format: tar.gz Programming language: Fortran90 Computer: The simulation tool ms2 is usable on a wide variety of platforms, from single processor machines over PC-clusters and vector computers to vector-parallel architectures. (Tested with Fortran compilers: gfortran, Intel, PathScale, Portland Group and Sun Studio.) Operating system: Unix/Linux, Windows Has the code been vectorized or parallelized?: Yes. Message Passing Interface (MPI) protocol Scalability. Excellent scalability up to 16 processors for molecular dynamics and >512 processors for Monte-Carlo simulations. RAM:ms2 runs on single processors with 512 MB RAM. The memory demand rises with increasing number of processors used per node and increasing number of molecules. Classification: 7.7, 7.9, 12 External routines: Message Passing Interface (MPI) Nature of problem: Calculation of application oriented thermodynamic properties for rigid electro-neutral molecules: vapor-liquid equilibria, thermal and caloric data as well as transport properties of pure fluids and multi-component mixtures. Solution method: Molecular dynamics, Monte-Carlo, various classical ensembles, grand equilibrium method, Green-Kubo formalism. Restrictions: No. The system size is user-defined. Typical problems addressed by ms2 can be solved by simulating systems containing typically 2000 molecules or less. Unusual features: Feature tools are available for creating input files, analyzing simulation results and visualizing molecular trajectories. Additional comments: Sample makefiles for multiple operation platforms are provided. Documentation is provided with the installation package and is available at http://www.ms-2.de. Running time: The running time of ms2 depends on the problem set, the system size and the number of processes used in the simulation. Running four processes on a "Nehalem" processor, simulations calculating VLE data take between two and twelve hours, calculating transport properties between six and 24 hours.

Measurement of myocardial extracellular volume fraction by using equilibrium contrast-enhanced CT: validation against histologic findings.

PubMed

Bandula, Steve; White, Steven K; Flett, Andrew S; Lawrence, David; Pugliese, Francesca; Ashworth, Michael T; Punwani, Shonit; Taylor, Stuart A; Moon, James C

2013-11-01

To develop and validate equilibrium contrast material-enhanced computed tomography (CT) to measure myocardial extracellular volume (ECV) fraction by using a histologic reference standard and to compare equilibrium CT with equilibrium contrast-enhanced magnetic resonance (MR) imaging. A local ethics committee approved the study, and all subjects gave fully informed written consent. An equilibrium CT protocol was developed using iohexol at 300 mg of iodine per milliliter (bolus of 1 mg per kilogram of body weight administered at a rate of 3 mL/sec, followed immediately by an infusion of 1.88 mL/kg per hour with CT imaging before and at 25 minutes after injection of bolus of contrast agent) and ECV within the myocardial septum measured using both equilibrium CT and equilibrium MR imaging in patients with severe aortic stenosis. Biopsy samples of the myocardial septum collected during valve replacement surgery were used for histologic quantification of extracellular fibrosis with picrosirius red staining. Equilibrium CT- and equilibrium MR imaging-derived ECV measurements were compared with histologically quantified fibrosis by using Pearson correlation. Agreement between equilibrium CT and equilibrium MR imaging was assessed by using Bland-Altman comparison. Twenty-three patients (16 male, seven female; mean age, 70.8 years; standard deviation, 8.3) were recruited. The mean percentage of histologic fibrosis was 18% (intersubject range, 5%-40%). There was a significant correlation between both equilibrium CT- and equilibrium MR imaging-derived ECV and percentage of histologic fibrosis (r = 0.71 [P < .001] and r = 0.84 [P < .0001], respectively). Equilibrium CT-derived ECV was significantly correlated to equilibrium MR imaging-derived ECV (r = 0.73). ECV measured by using equilibrium CT in patients with aortic stenosis correlates with histologic quantification of myocardial fibrosis and with ECV derived by using equilibrium MR imaging. RSNA, 2013

Modeling Secondary Organic Aerosols over Europe: Impact of Activity Coefficients and Viscosity

NASA Astrophysics Data System (ADS)

Kim, Y.; Sartelet, K.; Couvidat, F.

2014-12-01

Semi-volatile organic species (SVOC) can condense on suspended particulate materials (PM) in the atmosphere. The modeling of condensation/evaporation of SVOC often assumes that gas-phase and particle-phase concentrations are at equilibrium. However, recent studies show that secondary organic aerosols (SOA) may not be accurately represented by an equilibrium approach between the gas and particle phases, because organic aerosols in the particle phase may be very viscous. The condensation in the viscous liquid phase is limited by the diffusion from the surface of PM to its core. Using a surrogate approach to represent SVOC, depending on the user's choice, the secondary organic aerosol processor (SOAP) may assume equilibrium or model dynamically the condensation/evaporation between the gas and particle phases to take into account the viscosity of organic aerosols. The model is implemented in the three-dimensional chemistry-transport model of POLYPHEMUS. In SOAP, activity coefficients for organic mixtures can be computed using UNIFAC for short-range interactions between molecules and AIOMFAC to also take into account the effect of inorganic species on activity coefficients. Simulations over Europe are performed and POLYPHEMUS/SOAP is compared to POLYPHEMUS/H2O, which was previously used to model SOA using the equilibrium approach with activity coefficients from UNIFAC. Impacts of the dynamic approach on modeling SOA over Europe are evaluated. The concentrations of SOA using the dynamic approach are compared with those using the equilibrium approach. The increase of computational cost is also evaluated.

DREAM3D simulations of inner-belt dynamics

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

Cunningham, Gregory Scott

2015-05-26

A 1973 paper by Lyons and Thorne explains the two-belt structure for electrons in the inner magnetosphere as a balance between inward radial diffusion and loss to the atmosphere, where the loss to the atmosphere is enabled by pitch-angle scattering from Coulomb and wave-particle interactions. In the 1973 paper, equilibrium solutions to a decoupled set of 1D radial diffusion equations, one for each value of the first invariant of motion, μ, were computed to produce the equilibrium two-belt structure. Each 1D radial diffusion equation incorporated an L-and μ-dependent `lifetime' due to the Coulomb and wave-particle interactions. This decoupling of themore » problem is appropriate under the assumption that radial diffusion is slow in comparison to pitch-angle scattering. However, for some values of μ and L the lifetime associated with pitch-angle scattering is comparable to the timescale associated with radial diffusion, suggesting that the true equilibrium solutions might reflect `coupled modes' involving pitch-angle scattering and radial diffusion and thus requiring a 3D diffusion model. In the work we show here, we have computed the equilibrium solutions using our 3D diffusion model, DREAM3D, that allows for such coupling. We find that the 3D equilibrium solutions are quite similar to the solutions shown in the 1973 paper when we use the same physical models for radial diffusion and pitch-angle scattering from hiss. However, we show that the equilibrium solutions are quite sensitive to various aspects of the physics model employed in the 1973 paper that can be improved, suggesting that additional work needs to be done to understand the two-belt structure.« less

The Secondary Organic Aerosol Processor (SOAP v1.0) model: a unified model with different ranges of complexity based on the molecular surrogate approach

NASA Astrophysics Data System (ADS)

Couvidat, F.; Sartelet, K.

2014-01-01

The Secondary Organic Aerosol Processor (SOAP v1.0) model is presented. This model is designed to be modular with different user options depending on the computing time and the complexity required by the user. This model is based on the molecular surrogate approach, in which each surrogate compound is associated with a molecular structure to estimate some properties and parameters (hygroscopicity, absorption on the aqueous phase of particles, activity coefficients, phase separation). Each surrogate can be hydrophilic (condenses only on the aqueous phase of particles), hydrophobic (condenses only on the organic phase of particles) or both (condenses on both the aqueous and the organic phases of particles). Activity coefficients are computed with the UNIFAC thermodynamic model for short-range interactions and with the AIOMFAC parameterization for medium and long-range interactions between electrolytes and organic compounds. Phase separation is determined by Gibbs energy minimization. The user can choose between an equilibrium and a dynamic representation of the organic aerosol. In the equilibrium representation, compounds in the particle phase are assumed to be at equilibrium with the gas phase. However, recent studies show that the organic aerosol (OA) is not at equilibrium with the gas phase because the organic phase could be semi-solid (very viscous liquid phase). The condensation or evaporation of organic compounds could then be limited by the diffusion in the organic phase due to the high viscosity. A dynamic representation of secondary organic aerosols (SOA) is used with OA divided into layers, the first layer at the center of the particle (slowly reaches equilibrium) and the final layer near the interface with the gas phase (quickly reaches equilibrium).

Communication: Microphase equilibrium and assembly dynamics.

PubMed

Zhuang, Yuan; Charbonneau, Patrick

2017-09-07

Despite many attempts, ordered equilibrium microphases have yet to be obtained in experimental colloidal suspensions. The recent computation of the equilibrium phase diagram of a microscopic, particle-based microphase former [Zhuang et al., Phys. Rev. Lett. 116, 098301 (2016)] has nonetheless found such mesoscale assemblies to be thermodynamically stable. Here, we consider their equilibrium and assembly dynamics. At intermediate densities above the order-disorder transition, we identify four different dynamical regimes and the structural changes that underlie the dynamical crossovers from one disordered regime to the next. Below the order-disorder transition, we also find that periodic lamellae are the most dynamically accessible of the periodic microphases. Our analysis thus offers a comprehensive view of the dynamics of disordered microphases and a route to the assembly of periodic microphases in a putative well-controlled, experimental system.

A finite element method to compute three-dimensional equilibrium configurations of fluid membranes: Optimal parameterization, variational formulation and applications

NASA Astrophysics Data System (ADS)

Rangarajan, Ramsharan; Gao, Huajian

2015-09-01

We introduce a finite element method to compute equilibrium configurations of fluid membranes, identified as stationary points of a curvature-dependent bending energy functional under certain geometric constraints. The reparameterization symmetries in the problem pose a challenge in designing parametric finite element methods, and existing methods commonly resort to Lagrange multipliers or penalty parameters. In contrast, we exploit these symmetries by representing solution surfaces as normal offsets of given reference surfaces and entirely bypass the need for artificial constraints. We then resort to a Galerkin finite element method to compute discrete C1 approximations of the normal offset coordinate. The variational framework presented is suitable for computing deformations of three-dimensional membranes subject to a broad range of external interactions. We provide a systematic algorithm for computing large deformations, wherein solutions at subsequent load steps are identified as perturbations of previously computed ones. We discuss the numerical implementation of the method in detail and demonstrate its optimal convergence properties using examples. We discuss applications of the method to studying adhesive interactions of fluid membranes with rigid substrates and to investigate the influence of membrane tension in tether formation.

Shot Noise in a Quantum Dot with the Finite Coulomb Interaction

NASA Astrophysics Data System (ADS)

Cao, Xian-Sheng

2011-09-01

We study the shot noise in a quantum dot which coupled to metallic leads using the equation of motion of nonequilibrium Green's function technique at Kondo temperature T K . We compute the out of equilibrium density of states, the current and the shot noise. We find that the value of shot noise in the finite coulomb interaction case is smaller than one at Kondo temperature T K when variation of ɛ d values of the QD energy in the absence of the external magnetic field. We also find that the values of S(0)/ V are almost insusceptible to U when eV d under 2, while the values of S(0)/ V appear slightly branch off when the value of eV d approach to 6.

Characterization of urania vaporization with transpiration coupled thermogravimetry

DOE PAGES

McMurray, J. W.

2015-12-05

Determining equilibrium vapor pressures of materials is made easier by transpiration measurements. However, the traditional technique involves condensing the volatiles entrained in a carrier gas outside of the hot measurement zone. One potential problem is deposition en route to a cooled collector. Thermogravimetric analysis (TGA) can be used to measure in situ mass loss due to vaporization and therefore obviate the need to analyze the entire gas train due to premature plating of vapor species. Therefore, a transpiration coupled TGA technique was used to determine equilibrium pressures of UO3 gas over fluorite structure UO2+x and U3O8 at T = (1573more » and 1773) K. Moreover, we compared to calculations from models and databases in the open literature. Our study gives clarity to the thermochemical data for UO3 gas and validates the mass loss transpiration method using thermogravimetry for determining equilibrium vapor pressures of non-stoichiometric oxides.« less

An implicit flux-split algorithm to calculate hypersonic flowfields in chemical equilibrium

NASA Technical Reports Server (NTRS)

Palmer, Grant

1987-01-01

An implicit, finite-difference, shock-capturing algorithm that calculates inviscid, hypersonic flows in chemical equilibrium is presented. The flux vectors and flux Jacobians are differenced using a first-order, flux-split technique. The equilibrium composition of the gas is determined by minimizing the Gibbs free energy at every node point. The code is validated by comparing results over an axisymmetric hemisphere against previously published results. The algorithm is also applied to more practical configurations. The accuracy, stability, and versatility of the algorithm have been promising.

IRREVERSIBLE PROCESSES IN A PLASMA

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

Balescu, R.

1959-04-01

ABS>The characteristic divergences caused by long-range phenomena in gases can be eliminated in equilibrium situations by partial summations of terms individually divergent but whose sum converges. It is shown how the recently developed diagram technique enables treatment of non-equilibrium cases by a rigorous asymptotic method. The general ideas underlying the approach are briefly indicated. (T.R. H.)

STUDYING THE EFFECTS OF CALCIUM AND MAGNESIUM ON SIZE-DISTRIBUTED NITRATE AND AMMONIUM WITH EQUISOLV II. (R823186)

EPA Science Inventory

Abstract

A chemical equilibrium code was improved and used to show that calcium and magnesium have a large yet different effect on the aerosol size distribution in different regions of Los Angeles. In the code, a new technique of solving individual equilibrium equation...

A Graphical Simulation of Vapor-Liquid Equilibrium for Use as an Undergraduate Laboratory Experiment and to Demonstrate the Concept of Mathematical Modeling.

ERIC Educational Resources Information Center

Whitman, David L.; Terry, Ronald E.

1985-01-01

Demonstrating petroleum engineering concepts in undergraduate laboratories often requires expensive and time-consuming experiments. To eliminate these problems, a graphical simulation technique was developed for junior-level laboratories which illustrate vapor-liquid equilibrium and the use of mathematical modeling. A description of this…

An Application of Variational Theory to an Integrated Walrasian Model of Exchange, Consumption and Production

NASA Astrophysics Data System (ADS)

Donato, M. B.; Milasi, M.; Vitanza, C.

2010-09-01

An existence result of a Walrasian equilibrium for an integrated model of exchange, consumption and production is obtained. The equilibrium model is characterized in terms of a suitable generalized quasi-variational inequality; so the existence result comes from an original technique which takes into account tools of convex and set-valued analysis.

An Interactive Computer Program for Simulating the Effects of Olivine Fractionation from Basaltic and Ultrabasic Liquids.

ERIC Educational Resources Information Center

Pearce, Thomas H.

1983-01-01

Describes interactive computer program (listing available from author) which simulates olivine fractionation from basaltic/ultrabasic liquid. The menu-driven nature of the program (for Apple II microcomputer) allows students to select ideal Rayleigh fractionation or equilibrium crystallization. (JN)

Convergence to equilibrium of renormalised solutions to nonlinear chemical reaction–diffusion systems

NASA Astrophysics Data System (ADS)

Fellner, Klemens; Tang, Bao Quoc

2018-06-01

The convergence to equilibrium for renormalised solutions to nonlinear reaction-diffusion systems is studied. The considered reaction-diffusion systems arise from chemical reaction networks with mass action kinetics and satisfy the complex balanced condition. By applying the so-called entropy method, we show that if the system does not have boundary equilibria, i.e. equilibrium states lying on the boundary of R_+^N, then any renormalised solution converges exponentially to the complex balanced equilibrium with a rate, which can be computed explicitly up to a finite-dimensional inequality. This inequality is proven via a contradiction argument and thus not explicitly. An explicit method of proof, however, is provided for a specific application modelling a reversible enzyme reaction by exploiting the specific structure of the conservation laws. Our approach is also useful to study the trend to equilibrium for systems possessing boundary equilibria. More precisely, to show the convergence to equilibrium for systems with boundary equilibria, we establish a sufficient condition in terms of a modified finite-dimensional inequality along trajectories of the system. By assuming this condition, which roughly means that the system produces too much entropy to stay close to a boundary equilibrium for infinite time, the entropy method shows exponential convergence to equilibrium for renormalised solutions to complex balanced systems with boundary equilibria.

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

Siol, Sebastian; Holder, Aaron; Ortiz, Brenden R.

Here, the controlled decomposition of metastable alloys is an attractive route to form nanostructured thermoelectric materials with reduced thermal conductivity. The ternary SnTe–MnTe and SnTe–SnSe heterostructural alloys have been demonstrated as promising materials for thermoelectric applications. In this work, the quaternary Sn 1–yMnyTe 1–xSe x phase space serves as a relevant model system to explore how a combination of computational and combinatorial-growth methods can be used to study equilibrium and non-equilibrium solubility limits. Results from first principle calculations indicate low equilibrium solubility for x,y < 0.05 that are in good agreement with results obtained from bulk equilibrium synthesis experiments andmore » predict significantly higher spinodal limits. An experimental screening using sputtered combinatorial thin film sample libraries showed a remarkable increase in non-equilibrium solubility for x,y > 0.2. These theoretical and experimental results were used to guide the bulk synthesis of metastable alloys. The ability to reproduce the non-equilibrium solubility levels in bulk materials indicates that such theoretical calculations and combinatorial growth can inform bulk synthetic routes. Further, the large difference between equilibrium and non-equilibrium solubility limits in Sn 1–yMn yTe 1–xSe x indicates these metastable alloys are attractive in terms of nano-precipitate formation for potential thermoelectric applications.« less

Bertrand and Cournot oligopolies when rivals' costs are unknown

NASA Astrophysics Data System (ADS)

Ferreira, Fernanda A.; Ferreira, Flávio

2010-10-01

We study Bertrand and Cournot oligopoly models with incomplete information about rivals' costs, where the uncertainty is given by a uniform distribution. We compute the Bayesian-Nash equilibrium of both games, the ex-ante expected profits and the ex-post profits of each firm. We see that, in the price competition, even though only one firm produces in equilibrium, all firms have a positive ex-ante expected profit.

A note on AB INITIO semiconductor band structures

NASA Astrophysics Data System (ADS)

Fiorentini, Vincenzo

1992-09-01

We point out that only the internal features of the DFT ab initio theoretical picture of a crystal should be used in a consistent ab initio calculation of the band structure. As a consequence, we show that ground-state band structure calculations should be performed for the system in equilibrium at zero pressure, i.e. at the computed equilibrium cell volume ω th. Examples of consequences of this attitude are considered.

Multibody Parachute Flight Simulations for Planetary Entry Trajectories Using "Equilibrium Points"

NASA Technical Reports Server (NTRS)

Raiszadeh, Ben

2003-01-01

A method has been developed to reduce numerical stiffness and computer CPU requirements of high fidelity multibody flight simulations involving parachutes for planetary entry trajectories. Typical parachute entry configurations consist of entry bodies suspended from a parachute, connected by flexible lines. To accurately calculate line forces and moments, the simulations need to keep track of the point where the flexible lines meet (confluence point). In previous multibody parachute flight simulations, the confluence point has been modeled as a point mass. Using a point mass for the confluence point tends to make the simulation numerically stiff, because its mass is typically much less that than the main rigid body masses. One solution for stiff differential equations is to use a very small integration time step. However, this results in large computer CPU requirements. In the method described in the paper, the need for using a mass as the confluence point has been eliminated. Instead, the confluence point is modeled using an "equilibrium point". This point is calculated at every integration step as the point at which sum of all line forces is zero (static equilibrium). The use of this "equilibrium point" has the advantage of both reducing the numerical stiffness of the simulations, and eliminating the dynamical equations associated with vibration of a lumped mass on a high-tension string.

Applicability of Markets to Global Scheduling in Grids: Critical Examination of General Equilibrium Theory and Market Folklore

NASA Technical Reports Server (NTRS)

Nakai, Junko; VanDerWijngaart, Rob F.

2003-01-01

Markets are often considered superior to other global scheduling mechanisms for distributed computing systems. This claim is supported by: a casual observation from our every-day life that markets successfully equilibrate supply and demand, and the features of markets which originate in the general equilibrium theory, e.g., efficiency and the lack of necessity of 2 central controller. This paper describes why such beliefs in markets are not warranted. It does so by examining the general equilibrium theory, in terms of scope, abstraction, and interpretation. Not only does the general equilibrium theory fail to provide a satisfactory explanation of actual economies, including a computing-resource economy, it also falls short of supplying theoretical foundations for commonly held views of market desirability. This paper also points out that the argument for the desirability of markets involves circular reasoning and that the desirability can be established only vis-a-vis a scheduling goal. Finally, recasting the conclusion of Arrow's Impossibility Theorem as that for global scheduling, we conclude that there exists no market-based scheduler that is rational (in the sense defined in microeconomic theory), takes into account utility of more than one user, and yet yields a Pareto-optimal outcome for arbitrary user utility functions.

Properties of thermal air plasma with admixing of copper and carbon

NASA Astrophysics Data System (ADS)

Fesenko, S.; Veklich, A.; Boretskij, V.; Cressault, Y.; Gleizes, A.; Teulet, Ph

2014-11-01

This paper deals with investigations of air plasma with admixing of copper and carbon. Model plasma source unit with real breaking arc was used for the simulation of real discharges, which can be occurred during sliding of Cu-C composite electrodes on copper wire at electromotive vehicles. The complex technique of plasma property studies is developed. From one hand, the radial profiles of temperature and electron density in plasma of electric arc discharge in air between Cu-C composite and copper electrodes in air flow were measured by optical spectroscopy techniques. From another hand, the radial profiles of electric conductivity of plasma mixture were calculated by solution of energy balance equation. It was assumed that the thermal conductivity of air plasma is not depending on copper or carbon vapor admixtures. The electron density is obtained from electric conductivity profiles by calculation in assumption of local thermodynamic equilibrium in plasma. Computed in such way radial profiles of electron density in plasma of electric arc discharge in air between copper electrodes were compared with experimentally measured profiles. It is concluded that developed techniques of plasma diagnostics can be reasonably used in investigations of thermal plasma with copper and carbon vapors.

Pressure gradients fail to predict diffusio-osmosis

NASA Astrophysics Data System (ADS)

Liu, Yawei; Ganti, Raman; Frenkel, Daan

2018-05-01

We present numerical simulations of diffusio-osmotic flow, i.e. the fluid flow generated by a concentration gradient along a solid-fluid interface. In our study, we compare a number of distinct approaches that have been proposed for computing such flows and compare them with a reference calculation based on direct, non-equilibrium molecular dynamics simulations. As alternatives, we consider schemes that compute diffusio-osmotic flow from the gradient of the chemical potentials of the constituent species and from the gradient of the component of the pressure tensor parallel to the interface. We find that the approach based on treating chemical potential gradients as external forces acting on various species agrees with the direct simulations, thereby supporting the approach of Marbach et al (2017 J. Chem. Phys. 146 194701). In contrast, an approach based on computing the gradients of the microscopic pressure tensor does not reproduce the direct non-equilibrium results.

A study of some non-equilibrium driven models and their contribution to the understanding of molecular motors

NASA Astrophysics Data System (ADS)

Mazilu, Irina; Gonzalez, Joshua

2008-03-01

From the point of view of a physicist, a bio-molecular motor represents an interesting non-equilibrium system and it is directly amenable to an analysis using standard methods of non-equilibrium statistical physics. We conduct a rigorous Monte Carlo study of three different driven lattice gas models that retain the basic behavior of three types of cytoskeletal molecular motors. Our models incorporate novel features such as realistic dynamics rules and complex motor-motor interactions. We are interested to have a deeper understanding of how various parameters influence the macroscopic behavior of these systems, what is the density profile and if the system undergoes a phase transition. On the analytical front, we computed the steady-state probability distributions exactly for the one of the models using the matrix method that was established in 1993 by B. Derrida et al. We also explored the possibilities offered by the ``Bethe ansatz'' method by mapping some well studied spin models into asymmetric simple exclusion models (already analyzed using computer simulations), and to use the results obtained for the spin models in finding an exact solution for our problem. We have exhaustive computational studies of the kinesin and dynein molecular motor models that prove to be very useful in checking our analytical work.

Nonequilibrium Supersonic Freestream Studied Using Coherent Anti-Stokes Raman Spectroscopy

NASA Technical Reports Server (NTRS)

Cutler, Andrew D.; Cantu, Luca M.; Gallo, Emanuela C. A.; Baurle, Rob; Danehy, Paul M.; Rockwell, Robert; Goyne, Christopher; McDaniel, Jim

2015-01-01

Measurements were conducted at the University of Virginia Supersonic Combustion Facility of the flow in a constant-area duct downstream of a Mach 2 nozzle. The airflow was heated to approximately 1200 K in the facility heater upstream of the nozzle. Dual-pump coherent anti-Stokes Raman spectroscopy was used to measure the rotational and vibrational temperatures of N2 and O2 at two planes in the duct. The expectation was that the vibrational temperature would be in equilibrium, because most scramjet facilities are vitiated air facilities and are in vibrational equilibrium. However, with a flow of clean air, the vibrational temperature of N2 along a streamline remains approximately constant between the measurement plane and the facility heater, the vibrational temperature of O2 in the duct is about 1000 K, and the rotational temperature is consistent with the isentropic flow. The measurements of N2 vibrational temperature enabled cross-stream nonuniformities in the temperature exiting the facility heater to be documented. The measurements are in agreement with computational fluid dynamics models employing separate lumped vibrational and translational/rotational temperatures. Measurements and computations are also reported for a few percent steam addition to the air. The effect of the steam is to bring the flow to thermal equilibrium, also in agreement with the computational fluid dynamics.

Computational and theoretical modeling of pH and flow effects on the early-stage non-equilibrium self-assembly of optoelectronic peptides

NASA Astrophysics Data System (ADS)

Mansbach, Rachael; Ferguson, Andrew

Self-assembling π-conjugated peptides are attractive candidates for the fabrication of bioelectronic materials possessing optoelectronic properties due to electron delocalization over the conjugated peptide groups. We present a computational and theoretical study of an experimentally-realized optoelectronic peptide that displays triggerable assembly in low pH to resolve the microscopic effects of flow and pH on the non-equilibrium morphology and kinetics of assembly. Using a combination of molecular dynamics simulations and hydrodynamic modeling, we quantify the time and length scales at which convective flows employed in directed assembly compete with microscopic diffusion to influence assembly. We also show that there is a critical pH below which aggregation proceeds irreversibly, and quantify the relationship between pH, charge density, and aggregate size. Our work provides new fundamental understanding of pH and flow of non-equilibrium π-conjugated peptide assembly, and lays the groundwork for the rational manipulation of environmental conditions and peptide chemistry to control assembly and the attendant emergent optoelectronic properties. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Award # DE-SC0011847, and by the Computational Science and Engineering Fellowship from the University of Illinois at Urbana-Champaign.

Dissociation and Internal Excitation of Molecular Nitrogen Due to N + N2 Collisions Using Direct Molecular Simulation

NASA Technical Reports Server (NTRS)

Grover, Maninder S.; Schwartzentruber, Thomas E.; Jaffe, Richard L.

2017-01-01

In this work we present a molecular level study of N2+N collisions, focusing on excitation of internal energy modes and non-equilibrium dissociation. The computation technique used here is the direct molecular simulation (DMS) method and the molecular interactions have been modeled using an ab-initio potential energy surface (PES) developed at NASA's Ames Research Center. We carried out vibrational excitation calculations between 5000K and 30000K and found that the characteristic vibrational excitation time for the N + N2 process was an order of magnitude lower than that predicted by the Millikan and White correlation. It is observed that during vibrational excitation the high energy tail of the vibrational energy distribution gets over populated first and the lower energy levels get populated as the system evolves. It is found that the non-equilibrium dissociation rate coefficients for the N + N2 process are larger than those for the N2 + N2 process. This is attributed to the non-equilibrium vibrational energy distributions for the N + N2 process being less depleted than that for the N2 +N2 process. For an isothermal simulation we find that the probability of dissociation goes as 1/T(sub tr) for molecules with internal energy (epsilon(sub int)) less than approximately 9.9eV, while for molecules with epsilon (sub int) greater than 9.9eV the dissociation probability was weakly dependent on translational temperature of the system. We compared non-equilibrium dissociation rate coefficients and characteristic vibrational excitation times obtained by using the ab-initio PES developed at NASA's Ames Research Center to those obtained by using an ab-initio PES developed at the University of Minnesota. Good agreement was found between the macroscopic properties and molecular level description of the system obtained by using the two PESs.

Numerical simulation of hypersonic inlet flows with equilibrium or finite rate chemistry

NASA Technical Reports Server (NTRS)

Yu, Sheng-Tao; Hsieh, Kwang-Chung; Shuen, Jian-Shun; Mcbride, Bonnie J.

1988-01-01

An efficient numerical program incorporated with comprehensive high temperature gas property models has been developed to simulate hypersonic inlet flows. The computer program employs an implicit lower-upper time marching scheme to solve the two-dimensional Navier-Stokes equations with variable thermodynamic and transport properties. Both finite-rate and local-equilibrium approaches are adopted in the chemical reaction model for dissociation and ionization of the inlet air. In the finite rate approach, eleven species equations coupled with fluid dynamic equations are solved simultaneously. In the local-equilibrium approach, instead of solving species equations, an efficient chemical equilibrium package has been developed and incorporated into the flow code to obtain chemical compositions directly. Gas properties for the reaction products species are calculated by methods of statistical mechanics and fit to a polynomial form for C(p). In the present study, since the chemical reaction time is comparable to the flow residence time, the local-equilibrium model underpredicts the temperature in the shock layer. Significant differences of predicted chemical compositions in shock layer between finite rate and local-equilibrium approaches have been observed.

Teaching an Old Dog an Old Trick: FREE-FIX and Free-Boundary Axisymmetric MHD Equilibrium

NASA Astrophysics Data System (ADS)

Guazzotto, Luca

2015-11-01

A common task in plasma physics research is the calculation of an axisymmetric equilibrium for tokamak modeling. The main unknown of the problem is the magnetic poloidal flux ψ. The easiest approach is to assign the shape of the plasma and only solve the equilibrium problem in the plasma / closed-field-lines region (the ``fixed-boundary approach''). Often, one may also need the vacuum fields, i.e. the equilibrium in the open-field-lines region, requiring either coil currents or ψ on some closed curve outside the plasma to be assigned (the ``free-boundary approach''). Going from one approach to the other is a textbook problem, involving the calculation of Green's functions and surface integrals in the plasma. However, no tools are readily available to perform this task. Here we present a code (FREE-FIX) to compute a boundary condition for a free-boundary equilibrium given only the corresponding fixed-boundary equilibrium. An improvement to the standard solution method, allowing for much faster calculations, is presented. Applications are discussed. PPPL fund 245139 and DOE grant G00009102.

Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

PubMed Central

KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

2014-01-01

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

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.

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling.

PubMed

Kane, Patrick; Zollman, Kevin J S

2015-01-01

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the "hybrid equilibrium," to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith's Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory.

Blurring out hydrogen: The dynamical structure of teflic acid

NASA Astrophysics Data System (ADS)

Herbers, S.; Obenchain, D. A.; Kraus, P.; Wachsmuth, D.; Grabow, J.-U.

2018-05-01

The microwave spectra of 10 teflic acid isotopologues were recorded in the frequency range of 3-25 GHz using supersonic jet-expansion Fourier transform microwave spectroscopy. Despite being asymmetric in its equilibrium structure, the delocalization of the hydrogen atom leads to a symmetric top vibrational ground state structure. In this work, we present the zero point structure obtained from the experimental rotational constants and an approach to determine the semi-experimental equilibrium structure aided by ab initio data. The Te-O bond length determined in the equilibrium structure is accurate to the picometer and can be used as a benchmark for computational methods treating relativistic effects.

Molecular simulations of diffusion in electrolytes

NASA Astrophysics Data System (ADS)

Wheeler, Dean Richard

This work demonstrates new methodologies for simulating multicomponent diffusion in concentrated solutions using molecular dynamics (MD). Experimental diffusion data for concentrated multicomponent solutions are often lacking, as are accurate methods of predicting diffusion for nonideal solutions. MD can be a viable means of understanding and predicting multicomponent diffusion. While there have been several prior reports of MD simulations of mutual diffusion, no satisfactory expressions for simulating Stefan-Maxwell diffusivities for an arbitrary number of species exist. The approaches developed here allow for the computation of a full diffusion matrix for any number of species in both nonequilibrium and equilibrium MD ensembles. Our nonequilibrium approach is based on the application of constant external fields to drive species diffusion. Our equilibrium approach uses a newly developed Green-Kubo formula for Stefan-Maxwell diffusivities. In addition, as part of this work, we demonstrate a widely applicable means of increasing the computational efficiency of the Ewald sum, a technique for handling long-range Coulombic interactions in simulations. The theoretical development is applicable to any solution which can be simulated using MD; nevertheless, our primary interest is in electrochemical applications. To this end, the methods are tested by simulations of aqueous salt solutions and lithium-battery electrolytes. KCl and NaCl aqueous solutions were simulated over the concentration range 1 to 4 molal. Intermolecular-potential models were parameterized for these transport-based simulations. This work is the first to simulate all three independent diffusion coefficients for aqueous NaCl and KCl solutions. The results show that the nonequilibrium and equilibrium methods are consistent with each other, and in moderate agreement with experiment. We simulate lithium-battery electrolytes containing LiPF6 in propylene carbonate and mixed ethylene carbonate-dimethyl carbonate solvents. As with the aqueous-solution work, potential parameters were generated for these molecules. These nonaqueous electrolytes demonstrate rich transport behavior, which the simulations are able to reproduce qualitatively. In a mixed-solvent simulation we regress all six independent transport coefficients. The simulations show that strong ion pairing is responsible for the increase in viscosity and maximum in conductivity as ion concentrations are increased.

Combustion Gas Properties I-ASTM Jet a Fuel and Dry Air

NASA Technical Reports Server (NTRS)

Jones, R. E.; Trout, A. M.; Wear, J. D.; Mcbride, B. J.

1984-01-01

A series of computations was made to produce the equilibrium temperature and gas composition for ASTM jet A fuel and dry air. The computed tables and figures provide combustion gas property data for pressures from 0.5 to 50 atmospheres and equivalence ratios from 0 to 2.0.

A Computer-Aided Exercise for Checking Novices' Understanding of Market Equilibrium Changes.

ERIC Educational Resources Information Center

Katz, Arnold

1999-01-01

Describes a computer-aided supplement to the introductory microeconomics course that enhances students' understanding with simulation-based tools for reviewing what they have learned from lectures and conventional textbooks about comparing market equilibria. Includes a discussion of students' learning progressions and retention after using the…

The quasi-equilibrium response of MOS structures: Quasi-static factor

NASA Astrophysics Data System (ADS)

Okeke, M.; Balland, B.

1984-07-01

The dynamic response of a MOS structure driven into a non-equilibrium behaviour by a voltage ramp is presented. In contrast to Khun's quasi-static technique it is shown that any ramp-driven MOS structure has some degree of non-equilibrium. A quasi staticity factor μAK which serves as a measure of the degree of quasi-equilibrium, has been introduced for the first time. The mathematical model presented in the paper allows a better explanation of the experimental recordings. It is shown that this model could be used to analyse the various features of the response of the structure and that such physical parameters as the generation-rate, trap activation energy, and the effective capture constants could be obtained.

Perturbation analysis for patch occupancy dynamics

USGS Publications Warehouse

Martin, Julien; Nichols, James D.; McIntyre, Carol L.; Ferraz, Goncalo; Hines, James E.

2009-01-01

Perturbation analysis is a powerful tool to study population and community dynamics. This article describes expressions for sensitivity metrics reflecting changes in equilibrium occupancy resulting from small changes in the vital rates of patch occupancy dynamics (i.e., probabilities of local patch colonization and extinction). We illustrate our approach with a case study of occupancy dynamics of Golden Eagle (Aquila chrysaetos) nesting territories. Examination of the hypothesis of system equilibrium suggests that the system satisfies equilibrium conditions. Estimates of vital rates obtained using patch occupancy models are used to estimate equilibrium patch occupancy of eagles. We then compute estimates of sensitivity metrics and discuss their implications for eagle population ecology and management. Finally, we discuss the intuition underlying our sensitivity metrics and then provide examples of ecological questions that can be addressed using perturbation analyses. For instance, the sensitivity metrics lead to predictions about the relative importance of local colonization and local extinction probabilities in influencing equilibrium occupancy for rare and common species.

Integrated Force Method Solution to Indeterminate Structural Mechanics Problems

NASA Technical Reports Server (NTRS)

Patnaik, Surya N.; Hopkins, Dale A.; Halford, Gary R.

2004-01-01

Strength of materials problems have been classified into determinate and indeterminate problems. Determinate analysis primarily based on the equilibrium concept is well understood. Solutions of indeterminate problems required additional compatibility conditions, and its comprehension was not exclusive. A solution to indeterminate problem is generated by manipulating the equilibrium concept, either by rewriting in the displacement variables or through the cutting and closing gap technique of the redundant force method. Compatibility improvisation has made analysis cumbersome. The authors have researched and understood the compatibility theory. Solutions can be generated with equal emphasis on the equilibrium and compatibility concepts. This technique is called the Integrated Force Method (IFM). Forces are the primary unknowns of IFM. Displacements are back-calculated from forces. IFM equations are manipulated to obtain the Dual Integrated Force Method (IFMD). Displacement is the primary variable of IFMD and force is back-calculated. The subject is introduced through response variables: force, deformation, displacement; and underlying concepts: equilibrium equation, force deformation relation, deformation displacement relation, and compatibility condition. Mechanical load, temperature variation, and support settling are equally emphasized. The basic theory is discussed. A set of examples illustrate the new concepts. IFM and IFMD based finite element methods are introduced for simple problems.

Equilibrium-point control hypothesis examined by measured arm stiffness during multijoint movement.

PubMed

Gomi, H; Kawato

1996-04-05

For the last 20 years, it has been hypothesized that well-coordinated, multijoint movements are executed without complex computation by the brain, with the use of springlike muscle properties and peripheral neural feedback loops. However, it has been technically and conceptually difficult to examine this "equilibrium-point control" hypothesis directly in physiological or behavioral experiments. A high-performance manipulandum was developed and used here to measure human arm stiffness, the magnitude of which during multijoint movement is important for this hypothesis. Here, the equilibrium-point trajectory was estimated from the measured stiffness, the actual trajectory, and the generated torque. Its velocity profile differed from that of the actual trajectory. These results argue against the hypothesis that the brain sends as a motor command only an equilibrium-point trajectory similar to the actual trajectory.

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

Ivanov, A. A., E-mail: aai@a5.kiam.ru; Martynov, A. A., E-mail: martynov@a5.kiam.ru; Medvedev, S. Yu., E-mail: medvedev@a5.kiam.ru

In the MHD tokamak plasma theory, the plasma pressure is usually assumed to be isotropic. However, plasma heating by neutral beam injection and RF heating can lead to a strong anisotropy of plasma parameters and rotation of the plasma. The development of MHD equilibrium theory taking into account the plasma inertia and anisotropic pressure began a long time ago, but until now it has not been consistently applied in computational codes for engineering calculations of the plasma equilibrium and evolution in tokamak. This paper contains a detailed derivation of the axisymmetric plasma equilibrium equation in the most general form (withmore » arbitrary rotation and anisotropic pressure) and description of the specialized version of the SPIDER code. The original method of calculation of the equilibrium with an anisotropic pressure and a prescribed rotational transform profile is proposed. Examples of calculations and discussion of the results are also presented.« less

Investigation of island formation due to RMPs in DIII-D plasmas with the SIESTA resistive MHD equilibrium code

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

Hirshman, S. P.; Shafer, M. W.; Seal, S. K.

The SIESTA magnetohydrodynamic (MHD) equilibrium code has been used to compute a sequence of ideally stable equilibria resulting from numerical variation of the helical resonant magnetic perturbation (RMP) applied to an axisymmetric DIII-D plasma equilibrium. Increasing the perturbation strength at the dominant m=2, n=-1 , resonant surface leads to lower MHD energies and increases in the equilibrium island widths at the m=2 (and sidebands) surfaces, in agreement with theoretical expectations. Island overlap at large perturbation strengths leads to stochastic magnetic fields which correlate well with the experimentally inferred field structure. The magnitude and spatial phase (around the dominant rational surfaces)more » of the resonant (shielding) component of the parallel current are shown to change qualitatively with the magnetic island topology.« less

Investigation of island formation due to RMPs in DIII-D plasmas with the SIESTA resistive MHD equilibrium code

DOE PAGES

Hirshman, S. P.; Shafer, M. W.; Seal, S. K.; ...

2016-03-03

The SIESTA magnetohydrodynamic (MHD) equilibrium code has been used to compute a sequence of ideally stable equilibria resulting from numerical variation of the helical resonant magnetic perturbation (RMP) applied to an axisymmetric DIII-D plasma equilibrium. Increasing the perturbation strength at the dominant m=2, n=-1 , resonant surface leads to lower MHD energies and increases in the equilibrium island widths at the m=2 (and sidebands) surfaces, in agreement with theoretical expectations. Island overlap at large perturbation strengths leads to stochastic magnetic fields which correlate well with the experimentally inferred field structure. The magnitude and spatial phase (around the dominant rational surfaces)more » of the resonant (shielding) component of the parallel current are shown to change qualitatively with the magnetic island topology.« less

Dynamics of one-dimensional self-gravitating systems using Hermite-Legendre polynomials

NASA Astrophysics Data System (ADS)

Barnes, Eric I.; Ragan, Robert J.

2014-01-01

The current paradigm for understanding galaxy formation in the Universe depends on the existence of self-gravitating collisionless dark matter. Modelling such dark matter systems has been a major focus of astrophysicists, with much of that effort directed at computational techniques. Not surprisingly, a comprehensive understanding of the evolution of these self-gravitating systems still eludes us, since it involves the collective non-linear dynamics of many particle systems interacting via long-range forces described by the Vlasov equation. As a step towards developing a clearer picture of collisionless self-gravitating relaxation, we analyse the linearized dynamics of isolated one-dimensional systems near thermal equilibrium by expanding their phase-space distribution functions f(x, v) in terms of Hermite functions in the velocity variable, and Legendre functions involving the position variable. This approach produces a picture of phase-space evolution in terms of expansion coefficients, rather than spatial and velocity variables. We obtain equations of motion for the expansion coefficients for both test-particle distributions and self-gravitating linear perturbations of thermal equilibrium. N-body simulations of perturbed equilibria are performed and found to be in excellent agreement with the expansion coefficient approach over a time duration that depends on the size of the expansion series used.

Free energy and phase equilibria for the restricted primitive model of ionic fluids from Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Orkoulas, Gerassimos; Panagiotopoulos, Athanassios Z.

1994-07-01

In this work, we investigate the liquid-vapor phase transition of the restricted primitive model of ionic fluids. We show that at the low temperatures where the phase transition occurs, the system cannot be studied by conventional molecular simulation methods because convergence to equilibrium is slow. To accelerate convergence, we propose cluster Monte Carlo moves capable of moving more than one particle at a time. We then address the issue of charged particle transfers in grand canonical and Gibbs ensemble Monte Carlo simulations, for which we propose a biased particle insertion/destruction scheme capable of sampling short interparticle distances. We compute the chemical potential for the restricted primitive model as a function of temperature and density from grand canonical Monte Carlo simulations and the phase envelope from Gibbs Monte Carlo simulations. Our calculated phase coexistence curve is in agreement with recent results of Caillol obtained on the four-dimensional hypersphere and our own earlier Gibbs ensemble simulations with single-ion transfers, with the exception of the critical temperature, which is lower in the current calculations. Our best estimates for the critical parameters are T*c=0.053, ρ*c=0.025. We conclude with possible future applications of the biased techniques developed here for phase equilibrium calculations for ionic fluids.

Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

PubMed Central

Chng, Choon-Peng; Yang, Lee-Wei

2008-01-01

Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the absence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed. PMID:19812774

On the P 21/m and Pmmn pathways of the B1 B2 phase transition in NaCl: a quantum-mechanical study

NASA Astrophysics Data System (ADS)

Catti, Michele

2004-06-01

The monoclinic P 21/m and orthorhombic Pmmn (Watanabe et al' s-type) mechanisms of the high-pressure phase transition of NaCl between the B1 (rocksalt, Fm\\overline 3 m ) and B2 (CsCl-like, Pm\\overline 3 m ) cubic phases were investigated by ab initio DFT techniques with all-electron localized basis sets. Enthalpy profiles versus the order parameter were computed at constant pressures of 15, 26.3 (equilibrium) and 35 GPa for each pathway. The monoclinic path shows a lower activation enthalpy at the equilibrium pressure, but at different p values (hysteresis effects) the other mechanism becomes competitive. In the P 21/m case, sharp jumps of structural parameters are observed along the transformation coordinate, which can be explained by a mechanism based on discontinuous sliding of alternating pairs of (100) atomic layers. This accounts also for the predicted formation of a metastable intermediate Cmcm phase with TlI-like structure, similar to that observed experimentally at high pressure in AgCl, and the relations with the KOH structure are discussed, too. On the other hand, along the Pmmn pathway the structural parameters vary quite smoothly, indicating a continuous motion of neighbouring atomic planes within the constraint of the additional mirror symmetry.

A theory for protein dynamics: Global anisotropy and a normal mode approach to local complexity

NASA Astrophysics Data System (ADS)

Copperman, Jeremy; Romano, Pablo; Guenza, Marina

2014-03-01

We propose a novel Langevin equation description for the dynamics of biological macromolecules by projecting the solvent and all atomic degrees of freedom onto a set of coarse-grained sites at the single residue level. We utilize a multi-scale approach where molecular dynamic simulations are performed to obtain equilibrium structural correlations input to a modified Rouse-Zimm description which can be solved analytically. The normal mode solution provides a minimal basis set to account for important properties of biological polymers such as the anisotropic global structure, and internal motion on a complex free-energy surface. This multi-scale modeling method predicts the dynamics of both global rotational diffusion and constrained internal motion from the picosecond to the nanosecond regime, and is quantitative when compared to both simulation trajectory and NMR relaxation times. Utilizing non-equilibrium sampling techniques and an explicit treatment of the free-energy barriers in the mode coordinates, the model is extended to include biologically important fluctuations in the microsecond regime, such as bubble and fork formation in nucleic acids, and protein domain motion. This work supported by the NSF under the Graduate STEM Fellows in K-12 Education (GK-12) program, grant DGE-0742540 and NSF grant DMR-0804145, computational support from XSEDE and ACISS.

Computing the cross sections of nuclear reactions with nuclear clusters emission for proton energies between 30 MeV and 2.6 GeV

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

Korovin, Yu. A.; Maksimushkina, A. V., E-mail: AVMaksimushkina@mephi.ru; Frolova, T. A.

2016-12-15

The cross sections of nuclear reactions involving emission of clusters of light nuclei in proton collisions with a heavy-metal target are computed for incident-proton energies between 30 MeV and 2.6 GeV. The calculation relies on the ALICE/ASH and CASCADE/INPE computer codes. The parameters determining the pre-equilibrium cluster emission are varied in the computation.

Tracking Filament Evolution in the Low Solar Corona Using Remote Sensing and In Situ Observations

NASA Astrophysics Data System (ADS)

Kocher, Manan; Landi, Enrico; Lepri, Susan. T.

2018-06-01

In the present work, we analyze a filament eruption associated with an interplanetary coronal mass ejection that arrived at L1 on 2011 August 5. In multiwavelength Solar Dynamic Observatory/Advanced Imaging Assembly (AIA) images, three plasma parcels within the filament were tracked at high cadence along the solar corona. A novel absorption diagnostic technique was applied to the filament material traveling along the three chosen trajectories to compute the column density and temperature evolution in time. Kinematics of the filamentary material were estimated using STEREO/Extreme Ultraviolet Imager and STEREO/COR1 observations. The Michigan Ionization Code used inputs of these density, temperature, and speed profiles for the computation of ionization profiles of the filament plasma. Based on these measurements, we conclude that the core plasma was in near ionization equilibrium, and the ionization states were still evolving at the altitudes where they were visible in absorption in AIA images. Additionally, we report that the filament plasma was heterogeneous, and the filamentary material was continuously heated as it expanded in the low solar corona.

Experimental investigation of nozzle/plume aerodynamics at hypersonic speeds

NASA Technical Reports Server (NTRS)

Bogdanoff, David W.; Cambier, Jean-Luc; Papadopoulos, Perikles

1994-01-01

Much of the work involved the Ames 16-Inch Shock Tunnel facility. The facility was reactivated and upgraded, a data acquisition system was configured and upgraded several times, several facility calibrations were performed and test entries with a wedge model with hydrogen injection and a full scramjet combustor model, with hydrogen injection, were performed. Extensive CFD modeling of the flow in the facility was done. This includes modeling of the unsteady flow in the driver and driven tubes and steady flow modeling of the nozzle flow. Other modeling efforts include simulations of non-equilibrium flows and turbulence, plasmas, light gas guns and the use of non-ideal gas equations of state. New experimental techniques to improve the performance of gas guns, shock tubes and tunnels and scramjet combustors were conceived and studied computationally. Ways to improve scramjet engine performance using steady and pulsed detonation waves were also studied computationally. A number of studies were performed on the operation of the ram accelerator, including investigations of in-tube gasdynamic heating and the use of high explosives to raise the velocity capability of the device.

Quantum dynamical framework for Brownian heat engines

NASA Astrophysics Data System (ADS)

Agarwal, G. S.; Chaturvedi, S.

2013-07-01

We present a self-contained formalism modeled after the Brownian motion of a quantum harmonic oscillator for describing the performance of microscopic Brownian heat engines such as Carnot, Stirling, and Otto engines. Our theory, besides reproducing the standard thermodynamics results in the steady state, enables us to study the role dissipation plays in determining the efficiency of Brownian heat engines under actual laboratory conditions. In particular, we analyze in detail the dynamics associated with decoupling a system in equilibrium with one bath and recoupling it to another bath and obtain exact analytical results, which are shown to have significant ramifications on the efficiencies of engines involving such a step. We also develop a simple yet powerful technique for computing corrections to the steady state results arising from finite operation time and use it to arrive at the thermodynamic complementarity relations for various operating conditions and also to compute the efficiencies of the three engines cited above at maximum power. Some of the methods and exactly solvable models presented here are interesting in their own right and could find useful applications in other contexts as well.

Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

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

Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr

2013-11-07

Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality.more » By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.« less

High School Forum

ERIC Educational Resources Information Center

Herron, J. Dudley, Ed.

1977-01-01

Discusses uses of programmable pocket electronic calculators in the secondary level classroom. Uses discussed include: grading, laboratory, exercises, computing T-scores, and a quantitative approach to chemical equilibrium. (SL)

3D nozzle flow simulations including state-to-state kinetics calculation

NASA Astrophysics Data System (ADS)

Cutrone, L.; Tuttafesta, M.; Capitelli, M.; Schettino, A.; Pascazio, G.; Colonna, G.

2014-12-01

In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma. In this paper, we present an optimized methodology to approach plasma numerical simulation by state-to-state kinetics calculations in a fully 3D Navier-Stokes CFD solver. Numerical simulations of an expanding flow are presented aimed at comparing the behavior of state-to-state chemical kinetics models with respect to the macroscopic thermochemical non-equilibrium models that are usually used in the numerical computation of high temperature hypersonic flows. The comparison is focused both on the differences in the numerical results and on the computational effort associated with each approach.

Characterization and Computational Modeling of Minor Phases in Alloy LSHR

NASA Technical Reports Server (NTRS)

Jou, Herng-Jeng; Olson, Gregory; Gabb, Timothy; Garg, Anita; Miller, Derek

2012-01-01

The minor phases of powder metallurgy disk superalloy LSHR were studied. Samples were consistently heat treated at three different temperatures for long times to approach equilibrium. Additional heat treatments were also performed for shorter times, to assess minor phase kinetics in non-equilibrium conditions. Minor phases including MC carbides, M23C6 carbides, M3B2 borides, and sigma were identified. Their average sizes and total area fractions were determined. CALPHAD thermodynamics databases and PrecipiCalc(TradeMark), a computational precipitation modeling tool, were employed with Ni-base thermodynamics and diffusion databases to model and simulate the phase microstructural evolution observed in the experiments with an objective to identify the model limitations and the directions of model enhancement.

A homogenization-based quasi-discrete method for the fracture of heterogeneous materials

NASA Astrophysics Data System (ADS)

Berke, P. Z.; Peerlings, R. H. J.; Massart, T. J.; Geers, M. G. D.

2014-05-01

The understanding and the prediction of the failure behaviour of materials with pronounced microstructural effects is of crucial importance. This paper presents a novel computational methodology for the handling of fracture on the basis of the microscale behaviour. The basic principles presented here allow the incorporation of an adaptive discretization scheme of the structure as a function of the evolution of strain localization in the underlying microstructure. The proposed quasi-discrete methodology bridges two scales: the scale of the material microstructure, modelled with a continuum type description; and the structural scale, where a discrete description of the material is adopted. The damaging material at the structural scale is divided into unit volumes, called cells, which are represented as a discrete network of points. The scale transition is inspired by computational homogenization techniques; however it does not rely on classical averaging theorems. The structural discrete equilibrium problem is formulated in terms of the underlying fine scale computations. Particular boundary conditions are developed on the scale of the material microstructure to address damage localization problems. The performance of this quasi-discrete method with the enhanced boundary conditions is assessed using different computational test cases. The predictions of the quasi-discrete scheme agree well with reference solutions obtained through direct numerical simulations, both in terms of crack patterns and load versus displacement responses.

In Situ Study of Microstructure Evolution in Solidification of Hypereutectic Al-Si Alloys with Application of Thermal Analysis and Neutron Diffraction

NASA Astrophysics Data System (ADS)

Sediako, Dimitry G.; Kasprzak, Wojciech

2015-09-01

Understanding of the kinetics of solid-phase evolution in solidification of hypereutectic aluminum alloys is a key to control their as-cast microstructure and resultant mechanical properties, and in turn, to enhance the service characteristics of actual components. This study was performed to evaluate the solidification kinetics for three P-modified hypereutectic Al-19 pct Si alloys: namely, Al-Si binary alloy and with the subsequent addition of 2.8 pct Cu and 2.8 pct Cu + 0.7 pct Mg. Metallurgical evaluation included thermodynamic calculations of the solidification process using the FactSage™ 6.2 software package, as well as experimental thermal analysis, and in situ neutron diffraction. The study revealed kinetics of solid α-Al, solid Si, Al2Cu, and Mg2Si evolution, as well as the individual effects of Cu and Mg alloying additions on the solidification path of the Al-Si system. Various techniques applied in this study resulted in some discrepancies in the results. For example, the FactSage computations, in general, resulted in 281 K to 286 K (8 °C to 13 °C) higher Al-Si eutectic temperatures than the ones recorded in the thermal analysis, which are also ~278 K (~5 °C) higher than those observed in the in situ neutron diffraction. None of the techniques can provide a definite value for the solidus temperature, as this is affected by the chosen calculation path [283 K to 303 K (10 °C to 30 °C) higher for equilibrium solidification vs non-equilibrium] for the FactSage analysis; and further complicated by evolution of secondary Al-Cu and Mg-Si phases that commenced at the end of solidification. An explanation of the discrepancies observed and complications associated with every technique applied is offered in the paper.

Efficient Application of Continuous Fractional Component Monte Carlo in the Reaction Ensemble

PubMed Central

2017-01-01

A new formulation of the Reaction Ensemble Monte Carlo technique (RxMC) combined with the Continuous Fractional Component Monte Carlo method is presented. This method is denoted by serial Rx/CFC. The key ingredient is that fractional molecules of either reactants or reaction products are present and that chemical reactions always involve fractional molecules. Serial Rx/CFC has the following advantages compared to other approaches: (1) One directly obtains chemical potentials of all reactants and reaction products. Obtained chemical potentials can be used directly as an independent check to ensure that chemical equilibrium is achieved. (2) Independent biasing is applied to the fractional molecules of reactants and reaction products. Therefore, the efficiency of the algorithm is significantly increased, compared to the other approaches. (3) Changes in the maximum scaling parameter of intermolecular interactions can be chosen differently for reactants and reaction products. (4) The number of fractional molecules is reduced. As a proof of principle, our method is tested for Lennard-Jones systems at various pressures and for various chemical reactions. Excellent agreement was found both for average densities and equilibrium mixture compositions computed using serial Rx/CFC, RxMC/CFCMC previously introduced by Rosch and Maginn (Journal of Chemical Theory and Computation, 2011, 7, 269–279), and the conventional RxMC approach. The serial Rx/CFC approach is also tested for the reaction of ammonia synthesis at various temperatures and pressures. Excellent agreement was found between results obtained from serial Rx/CFC, experimental results from literature, and thermodynamic modeling using the Peng–Robinson equation of state. The efficiency of reaction trial moves is improved by a factor of 2 to 3 (depending on the system) compared to the RxMC/CFCMC formulation by Rosch and Maginn. PMID:28737933

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

PubMed Central

Whitney, Anna; Shakhnovich, Eugene I.

2015-01-01

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

Simulating the reactions of CO2 in aqueous monoethanolamine solution by reaction ensemble Monte Carlo using the continuous fractional component method.

PubMed

Balaji, Sayee Prasaad; Gangarapu, Satesh; Ramdin, Mahinder; Torres-Knoop, Ariana; Zuilhof, Han; Goetheer, Earl L V; Dubbeldam, David; Vlugt, Thijs J H

2015-06-09

Molecular simulations were used to compute the equilibrium concentrations of the different species in CO2/monoethanolamine solutions for different CO2 loadings. Simulations were performed in the Reaction Ensemble using the continuous fractional component Monte Carlo method at temperatures of 293, 333, and 353 K. The resulting computed equilibrium concentrations are in excellent agreement with experimental data. The effect of different reaction pathways was investigated. For a complete understanding of the equilibrium speciation, it is essential to take all elementary reactions into account because considering only the overall reaction of CO2 with MEA is insufficient. The effects of electrostatics and intermolecular van der Waals interactions were also studied, clearly showing that solvation of reactants and products is essential for the reaction. The Reaction Ensemble Monte Carlo using the continuous fractional component method opens the possibility of investigating the effects of the solvent on CO2 chemisorption by eliminating the need to study different reaction pathways and concentrate only on the thermodynamics of the system.

An Adaptive QSE-reduced Nuclear Reaction Network for Silicon Burning

NASA Astrophysics Data System (ADS)

Parete-Koon, Suzanne; Hix, William Raphael; Thielemann, Friedrich-Karl

2010-02-01

The nuclei of the ``iron peak'' are formed late in the evolution of massive stars and during supernovae. Silicon burning during these events is responsible for the production of a wide range of nuclei with atomic mass numbers from 28 to 64. The large number of nuclei involved make accurate modeling of silicon burning computationally expensive. Examination of the physics of silicon burning reveals that the nuclear evolution is dominated by large groups of nuclei in mutual equilibrium. We present an improvement on our hybrid equilibrium-network scheme that takes advantage of this quasi-equilibrium (QSE) to reduce the number of independent variables calculated. Because the membership and number of these groups vary as the temperature, density and electron faction change, achieving maximal efficiency requires dynamic adjustment of group number and membership. The resultant QSE-reduced network is up to 20 times faster than the full network it replaces without significant loss of accuracy. These reductions in computational cost and the number of species evolved make QSE-reduced networks well suited for inclusion within hydrodynamic simulations, particularly in multi-dimensional applications. )

The NATA code: Theory and analysis, volume 1. [user manuals (computer programming) - gas dynamics, wind tunnels

NASA Technical Reports Server (NTRS)

Bade, W. L.; Yos, J. M.

1975-01-01

A computer program for calculating quasi-one-dimensional gas flow in axisymmetric and two-dimensional nozzles and rectangular channels is presented. Flow is assumed to start from a state of thermochemical equilibrium at a high temperature in an upstream reservoir. The program provides solutions based on frozen chemistry, chemical equilibrium, and nonequilibrium flow with finite reaction rates. Electronic nonequilibrium effects can be included using a two-temperature model. An approximate laminar boundary layer calculation is given for the shear and heat flux on the nozzle wall. Boundary layer displacement effects on the inviscid flow are considered also. Chemical equilibrium and transport property calculations are provided by subroutines. The code contains precoded thermochemical, chemical kinetic, and transport cross section data for high-temperature air, CO2-N2-Ar mixtures, helium, and argon. It provides calculations of the stagnation conditions on axisymmetric or two-dimensional models, and of the conditions on the flat surface of a blunt wedge. The primary purpose of the code is to describe the flow conditions and test conditions in electric arc heated wind tunnels.

Extension of the quantum-kinetic model to lunar and Mars return physics

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

Liechty, D. S.; Lewis, M. J.

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high-mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. A recently introduced molecular-level chemistry model, the quantum-kinetic, or Q-K, model that predicts reaction rates for gases in thermal equilibrium and non-equilibrium using only kinetic theory and fundamental molecular properties, is extended in the current work to include electronic energy level transitions and reactions involving charged particles. Like the Q-K procedures for neutral species chemical reactions, these new models are phenomenological procedures that aimmore » to reproduce the reaction/transition rates but do not necessarily capture the exact physics. These engineering models are necessarily efficient due to the requirement to compute billions of simulated collisions in direct simulation Monte Carlo (DSMC) simulations. The new models are shown to generally agree within the spread of reported transition and reaction rates from the literature for near equilibrium conditions.« less

Using Computer-Based "Experiments" in the Analysis of Chemical Reaction Equilibria

ERIC Educational Resources Information Center

Li, Zhao; Corti, David S.

2018-01-01

The application of the Reaction Monte Carlo (RxMC) algorithm to standard textbook problems in chemical reaction equilibria is discussed. The RxMC method is a molecular simulation algorithm for studying the equilibrium properties of reactive systems, and therefore provides the opportunity to develop computer-based "experiments" for the…

Prediction of Combustion Gas Deposit Compositions

NASA Technical Reports Server (NTRS)

Kohl, F. J.; Mcbride, B. J.; Zeleznik, F. J.; Gordon, S.

1985-01-01

Demonstrated procedure used to predict accurately chemical compositions of complicated deposit mixtures. NASA Lewis Research Center's Computer Program for Calculation of Complex Chemical Equilibrium Compositions (CEC) used in conjunction with Computer Program for Calculation of Ideal Gas Thermodynamic Data (PAC) and resulting Thermodynamic Data Base (THDATA) to predict deposit compositions from metal or mineral-seeded combustion processes.

Exploring Lake Ecology in a Computer-Supported Learning Environment

ERIC Educational Resources Information Center

Ergazaki, Marida; Zogza, Vassiliki

2008-01-01

This study highlights the computer-mediated discursive activity of two dyads of first year educational sciences students, each collaboratively exploring several options for increasing the equilibrium size of a fish population in a lake. Our focus is on peers' attempts to come up with justified predictions about the adequacy of several options for…

Energy flow in non-equilibrium conformal field theory

NASA Astrophysics Data System (ADS)

Bernard, Denis; Doyon, Benjamin

2012-09-01

We study the energy current and its fluctuations in quantum gapless 1d systems far from equilibrium modeled by conformal field theory, where two separated halves are prepared at distinct temperatures and glued together at a point contact. We prove that these systems converge towards steady states, and give a general description of such non-equilibrium steady states in terms of quantum field theory data. We compute the large deviation function, also called the full counting statistics, of energy transfer through the contact. These are universal and satisfy fluctuation relations. We provide a simple representation of these quantum fluctuations in terms of classical Poisson processes whose intensities are proportional to Boltzmann weights.

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling

PubMed Central

Kane, Patrick; Zollman, Kevin J. S.

2015-01-01

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the “hybrid equilibrium,” to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith’s Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory. PMID:26348617

Simulant Gas Test Technique Feasibility

DTIC Science & Technology

1990-05-01

DY’NAMICS LABORATORY WRIGHT RESEARCH AND DEVELOPMENT CENTER AIR FORCE SYSTEMS COMMAND WRIGHT-PATTERSON AIR FORCE BASE, OHIO 45433-6553 NOTIr’ When...TERMS (Continue on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Hypersonic-test Air -chemistry Non-equilibrium-flow 0g...ABSTRACT (Continue on reverse if necessary and identify by block number) ’[lie Ulcertaillty engendered by non-equilibrium air effects on hypersonic

Paper spray mass spectrometry applied in the monitoring of a chemical system in dynamic chemical equilibrium: the redox process of methylene blue.

PubMed

de Paula, Camila Cristina Almeida; Valadares, Alberto; Jurisch, Marina; Piccin, Evandro; Augusti, Rodinei

2016-05-15

The monitoring of chemical systems in dynamic equilibrium is not an easy task. This is due to the high rate at which the system returns to equilibrium after being perturbed, which hampers the possibility of following the aftereffects of the disturbance. In this context, it is necessary to use a fast analytical technique that requires no (or minimal) sample preparation, and which is capable of monitoring the species constituting the system in equilibrium. Paper spray ionization mass spectrometry (PS-MS), a recently introduced ambient ionization technique, has such characteristics and hence was chosen for monitoring a model system: the redox process of methylene blue. The model system evaluated herein was composed of three cationic species of methylene blue (MB), which coexist in a dynamic redox system: (1) [MB](+) of m/z 284 (cationic MB); (2) [MB + H + e](+•) of m/z 285 (the protonated form of a transient species resulting from the reduction of [MB](+) ); (3) [MB + 2H + 2e](+) or [leuco-MB + H](+) of m/z 286 (the protonated leuco form of MB). Aliquots of a MB solution were collected before and after the addition of a reducing agent (metallic zinc) and directly analyzed by PS-MS for identification of the predominant cationic species at different conditions. The mass spectra revealed that before the addition of the reducing agent the ion of m/z 284 (cationic MB) is the unique species. Upon the addition of the reducing agent and acid, however, the solution continuously undergo discoloration while reduced species derived directly from cationic MB (m/z 285 and 286) are detected in the mass spectra with increasing intensities. Fragmentation patterns obtained for each ionic species, i.e. [MB](+) , [MB + H + e](+•) and [leuco-MB + H](+) , shown to be consistent with the proposed structures. The PS-MS technique proved to be suitable for an in situ and 'near' real-time analysis of the dynamic equilibrium involving the redox of MB in aqueous medium. The data clearly demonstrated how the redox equilibrium shifts depending on the disturbance caused to the system. Copyright © 2016 John Wiley & Sons, Ltd.

Experience in using a numerical scheme with artificial viscosity at solving the Riemann problem for a multi-fluid model of multiphase flow

NASA Astrophysics Data System (ADS)

Bulovich, S. V.; Smirnov, E. M.

2018-05-01

The paper covers application of the artificial viscosity technique to numerical simulation of unsteady one-dimensional multiphase compressible flows on the base of the multi-fluid approach. The system of the governing equations is written under assumption of the pressure equilibrium between the "fluids" (phases). No interfacial exchange is taken into account. A model for evaluation of the artificial viscosity coefficient that (i) assumes identity of this coefficient for all interpenetrating phases and (ii) uses the multiphase-mixture Wood equation for evaluation of a scale speed of sound has been suggested. Performance of the artificial viscosity technique has been evaluated via numerical solution of a model problem of pressure discontinuity breakdown in a three-fluid medium. It has been shown that a relatively simple numerical scheme, explicit and first-order, combined with the suggested artificial viscosity model, predicts a physically correct behavior of the moving shock and expansion waves, and a subsequent refinement of the computational grid results in a monotonic approaching to an asymptotic time-dependent solution, without non-physical oscillations.

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques

PubMed Central

Provasi, Davide; Artacho, Marta Camacho; Negri, Ana; Mobarec, Juan Carlos; Filizola, Marta

2011-01-01

Extensive experimental information supports the formation of ligand-specific conformations of G protein-coupled receptors (GPCRs) as a possible molecular basis for their functional selectivity for signaling pathways. Taking advantage of the recently published inactive and active crystal structures of GPCRs, we have implemented an all-atom computational strategy that combines different adaptive biasing techniques to identify ligand-specific conformations along pre-determined activation pathways. Using the prototypic GPCR β2-adrenergic receptor as a suitable test case for validation, we show that ligands with different efficacies (either inverse agonists, neutral antagonists, or agonists) modulate the free-energy landscape of the receptor by shifting the conformational equilibrium towards active or inactive conformations depending on their elicited physiological response. Notably, we provide for the first time a quantitative description of the thermodynamics of the receptor in an explicit atomistic environment, which accounts for the receptor basal activity and the stabilization of different active-like states by differently potent agonists. Structural inspection of these metastable states reveals unique conformations of the receptor that may have been difficult to retrieve experimentally. PMID:22022248

A global optimization perspective on molecular clusters.

PubMed

Marques, J M C; Pereira, F B; Llanio-Trujillo, J L; Abreu, P E; Albertí, M; Aguilar, A; Pirani, F; Bartolomei, M

2017-04-28

Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points. In particular, global optimization methods are of major importance to search for the low-energy structures of molecular aggregates. We review the application of global optimization techniques to several molecular clusters; some new results are also reported. Emphasis is given to evolutionary algorithms and their application in the study of the microsolvation of alkali-metal and Ca 2+ ions with various types of solvents.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Author(s).

A global optimization perspective on molecular clusters

PubMed Central

Pereira, F. B.; Llanio-Trujillo, J. L.; Abreu, P. E.; Albertí, M.; Aguilar, A.; Pirani, F.; Bartolomei, M.

2017-01-01

Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points. In particular, global optimization methods are of major importance to search for the low-energy structures of molecular aggregates. We review the application of global optimization techniques to several molecular clusters; some new results are also reported. Emphasis is given to evolutionary algorithms and their application in the study of the microsolvation of alkali-metal and Ca2+ ions with various types of solvents. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320902

Three dimensional PNS solutions of hypersonic internal flows with equilibrium chemistry

NASA Technical Reports Server (NTRS)

Liou, May-Fun

1989-01-01

An implicit procedure for solving parabolized Navier-Stokes equations under the assumption of a general equation of state for a gas in chemical equilibrium is given. A general and consistent approach for the evaluation of Jacobian matrices in the implicit operator avoids the use of unnecessary auxiliary quantities and approximations, and leads to a simple expression. Applications to two- and three-dimensional flow problems show efficiency in computer time and economy in storage.

Multistage Schemes with Multigrid for Euler and Navier-Strokes Equations: Components and Analysis

NASA Technical Reports Server (NTRS)

Swanson, R. C.; Turkel, Eli

1997-01-01

A class of explicit multistage time-stepping schemes with centered spatial differencing and multigrids are considered for the compressible Euler and Navier-Stokes equations. These schemes are the basis for a family of computer programs (flow codes with multigrid (FLOMG) series) currently used to solve a wide range of fluid dynamics problems, including internal and external flows. In this paper, the components of these multistage time-stepping schemes are defined, discussed, and in many cases analyzed to provide additional insight into their behavior. Special emphasis is given to numerical dissipation, stability of Runge-Kutta schemes, and the convergence acceleration techniques of multigrid and implicit residual smoothing. Both the Baldwin and Lomax algebraic equilibrium model and the Johnson and King one-half equation nonequilibrium model are used to establish turbulence closure. Implementation of these models is described.

Spillover, nonlinearity, and flexible structures

NASA Technical Reports Server (NTRS)

Bass, Robert W.; Zes, Dean

1991-01-01

Many systems whose evolution in time is governed by Partial Differential Equations (PDEs) are linearized around a known equilibrium before Computer Aided Control Engineering (CACE) is considered. In this case, there are infinitely many independent vibrational modes, and it is intuitively evident on physical grounds that infinitely many actuators would be needed in order to control all modes. A more precise, general formulation of this grave difficulty (spillover problem) is due to A.V. Balakrishnan. A possible route to circumvention of this difficulty lies in leaving the PDE in its original nonlinear form, and adding the essentially finite dimensional control action prior to linearization. One possibly applicable technique is the Liapunov Schmidt rigorous reduction of singular infinite dimensional implicit function problems to finite dimensional implicit function problems. Omitting details of Banach space rigor, the formalities of this approach are given.

Sodium sulfate: Vaporization thermodynamics and role in corrosive flames

NASA Technical Reports Server (NTRS)

Kohl, F. J.

1975-01-01

Gaseous species over liquid Na2SO4 were identified by the technique of molecular beam mass spectrometry. The heat and entropy of vaporization of the Na2SO4 molecule were measured directly. Comparisons of the experimental entropy with values calculated using various molecular parameters were used to estimate the molecular structure and vibrational frequencies. The thermodynamic properties of gaseous and condensed phase Na2SO4, along with additional pertinent species, were used in a computer program to calculate equilibrium flame compositions and temperatures for representative turbine engine and burner rig flames. Compositions were calculated at various fuel-to-oxidant ratios with additions of sulfur to the fuel and the components of sea salt to the intake air. Temperatures for condensation of Na2SO4 were obtained as a function of sulfur and sea salt concentrations.

Polynomial approximations of thermodynamic properties of arbitrary gas mixtures over wide pressure and density ranges

NASA Technical Reports Server (NTRS)

Allison, D. O.

1972-01-01

Computer programs for flow fields around planetary entry vehicles require real-gas equilibrium thermodynamic properties in a simple form which can be evaluated quickly. To fill this need, polynomial approximations were found for thermodynamic properties of air and model planetary atmospheres. A coefficient-averaging technique was used for curve fitting in lieu of the usual least-squares method. The polynomials consist of terms up to the ninth degree in each of two variables (essentially pressure and density) including all cross terms. Four of these polynomials can be joined to cover, for example, a range of about 1000 to 11000 K and 0.00001 to 1 atmosphere (1 atm = 1.0133 x 100,000 N/m sq) for a given thermodynamic property. Relative errors of less than 1 percent are found over most of the applicable range.

Media effects in modulating the conformational equilibrium of a model compound for tumor necrosis factor converting enzyme inhibition

NASA Astrophysics Data System (ADS)

Banchelli, Martina; Guardiani, Carlo; Sandberg, Robert B.; Menichetti, Stefano; Procacci, Piero; Caminati, Gabriella

2015-07-01

Small-molecule inhibitors of Tumor Necrosis Factor α Converting Enzyme (TACE) are a promising therapeutic tool for Rheumatoid Arthritis, Multiple Sclerosis and other autoimmune diseases. Here we report on an extensive chemical-physical analysis of the media effects in modulating the conformational landscape of MBET306, the common scaffold and a synthetic precursor of a family of recently discovered tartrate-based TACE inhibitors. The structural features of this molecule with potential pharmaceutical applications have been disclosed by interpreting extensive photophysical measurements in various solvents with the aid of enhanced sampling molecular dynamics simulations and time dependent density functional calculations. Using a combination of experimental and computational techniques, the paper provides a general protocol for studying the structure in solution of molecular systems characterized by the existence of conformational metastable states.

EQ3NR, a computer program for geochemical aqueous speciation-solubility calculations: Theoretical manual, user`s guide, and related documentation (Version 7.0); Part 3

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

Wolery, T.J.

1992-09-14

EQ3NR is an aqueous solution speciation-solubility modeling code. It is part of the EQ3/6 software package for geochemical modeling. It computes the thermodynamic state of an aqueous solution by determining the distribution of chemical species, including simple ions, ion pairs, and complexes, using standard state thermodynamic data and various equations which describe the thermodynamic activity coefficients of these species. The input to the code describes the aqueous solution in terms of analytical data, including total (analytical) concentrations of dissolved components and such other parameters as the pH, pHCl, Eh, pe, and oxygen fugacity. The input may also include a desiredmore » electrical balancing adjustment and various constraints which impose equilibrium with special pure minerals, solid solution end-member components (of specified mole fractions), and gases (of specified fugacities). The code evaluates the degree of disequilibrium in terms of the saturation index (SI = 1og Q/K) and the thermodynamic affinity (A = {minus}2.303 RT log Q/K) for various reactions, such as mineral dissolution or oxidation-reduction in the aqueous solution itself. Individual values of Eh, pe, oxygen fugacity, and Ah (redox affinity) are computed for aqueous redox couples. Equilibrium fugacities are computed for gas species. The code is highly flexible in dealing with various parameters as either model inputs or outputs. The user can specify modification or substitution of equilibrium constants at run time by using options on the input file.« less

Finite Beta Boundary Magnetic Fields of NCSX

NASA Astrophysics Data System (ADS)

Grossman, A.; Kaiser, T.; Mioduszewski, P.

2004-11-01

The magnetic field between the plasma surface and wall of the National Compact Stellarator (NCSX), which uses quasi-symmetry to combine the best features of the tokamak and stellarator in a configuration of low aspect ratio is mapped via field line tracing in a range of finite beta in which part of the rotational transform is generated by the bootstrap current. We adopt the methodology developed for W7-X, in which an equilibrium solution is computed by an inverse equilibrium solver based on an energy minimizing variational moments code, VMEC2000[1], which solves directly for the shape of the flux surfaces given the external coils and their currents as well as a bootstrap current provided by a separate transport calculation. The VMEC solution and the Biot-Savart vacuum fields are coupled to the magnetic field solver for finite-beta equilibrium (MFBE2001)[2] code to determine the magnetic field on a 3D grid over a computational domain. It is found that the edge plasma is more stellarator-like, with a complex 3D structure, and less like the ordered 2D symmetric structure of a tokamak. The field lines make a transition from ergodically covering a surface to ergodically covering a volume, as the distance from the last closed magnetic surface is increased. The results are compared with the PIES[3] calculations. [1] S.P. Hirshman et al. Comput. Phys. Commun. 43 (1986) 143. [2] E. Strumberger, et al. Nucl. Fusion 42 (2002) 827. [3] A.H. Reiman and H.S. Greenside, Comput. Phys. Commun. 43, 157 (1986).

Pharmaceutical industry and trade liberalization using computable general equilibrium model.

PubMed

Barouni, M; Ghaderi, H; Banouei, Aa

2012-01-01

Computable general equilibrium models are known as a powerful instrument in economic analyses and widely have been used in order to evaluate trade liberalization effects. The purpose of this study was to provide the impacts of trade openness on pharmaceutical industry using CGE model. Using a computable general equilibrium model in this study, the effects of decrease in tariffs as a symbol of trade liberalization on key variables of Iranian pharmaceutical products were studied. Simulation was performed via two scenarios in this study. The first scenario was the effect of decrease in tariffs of pharmaceutical products as 10, 30, 50, and 100 on key drug variables, and the second was the effect of decrease in other sectors except pharmaceutical products on vital and economic variables of pharmaceutical products. The required data were obtained and the model parameters were calibrated according to the social accounting matrix of Iran in 2006. The results associated with simulation demonstrated that the first scenario has increased import, export, drug supply to markets and household consumption, while import, export, supply of product to market, and household consumption of pharmaceutical products would averagely decrease in the second scenario. Ultimately, society welfare would improve in all scenarios. We presents and synthesizes the CGE model which could be used to analyze trade liberalization policy issue in developing countries (like Iran), and thus provides information that policymakers can use to improve the pharmacy economics.

Groundwater flux estimation in streams: A thermal equilibrium approach

USGS Publications Warehouse

Zhou, Yan; Fox, Garey A.; Miller, Ron B.; Mollenhauer, Robert; Brewer, Shannon K.

2018-01-01

Stream and groundwater interactions play an essential role in regulating flow, temperature, and water quality for stream ecosystems. Temperature gradients have been used to quantify vertical water movement in the streambed since the 1960s, but advancements in thermal methods are still possible. Seepage runs are a method commonly used to quantify exchange rates through a series of streamflow measurements but can be labor and time intensive. The objective of this study was to develop and evaluate a thermal equilibrium method as a technique for quantifying groundwater flux using monitored stream water temperature at a single point and readily available hydrological and atmospheric data. Our primary assumption was that stream water temperature at the monitored point was at thermal equilibrium with the combination of all heat transfer processes, including mixing with groundwater. By expanding the monitored stream point into a hypothetical, horizontal one-dimensional thermal modeling domain, we were able to simulate the thermal equilibrium achieved with known atmospheric variables at the point and quantify unknown groundwater flux by calibrating the model to the resulting temperature signature. Stream water temperatures were monitored at single points at nine streams in the Ozark Highland ecoregion and five reaches of the Kiamichi River to estimate groundwater fluxes using the thermal equilibrium method. When validated by comparison with seepage runs performed at the same time and reach, estimates from the two methods agreed with each other with an R2 of 0.94, a root mean squared error (RMSE) of 0.08 (m/d) and a Nash–Sutcliffe efficiency (NSE) of 0.93. In conclusion, the thermal equilibrium method was a suitable technique for quantifying groundwater flux with minimal cost and simple field installation given that suitable atmospheric and hydrological data were readily available.

Groundwater flux estimation in streams: A thermal equilibrium approach

NASA Astrophysics Data System (ADS)

Zhou, Yan; Fox, Garey A.; Miller, Ron B.; Mollenhauer, Robert; Brewer, Shannon

2018-06-01

Stream and groundwater interactions play an essential role in regulating flow, temperature, and water quality for stream ecosystems. Temperature gradients have been used to quantify vertical water movement in the streambed since the 1960s, but advancements in thermal methods are still possible. Seepage runs are a method commonly used to quantify exchange rates through a series of streamflow measurements but can be labor and time intensive. The objective of this study was to develop and evaluate a thermal equilibrium method as a technique for quantifying groundwater flux using monitored stream water temperature at a single point and readily available hydrological and atmospheric data. Our primary assumption was that stream water temperature at the monitored point was at thermal equilibrium with the combination of all heat transfer processes, including mixing with groundwater. By expanding the monitored stream point into a hypothetical, horizontal one-dimensional thermal modeling domain, we were able to simulate the thermal equilibrium achieved with known atmospheric variables at the point and quantify unknown groundwater flux by calibrating the model to the resulting temperature signature. Stream water temperatures were monitored at single points at nine streams in the Ozark Highland ecoregion and five reaches of the Kiamichi River to estimate groundwater fluxes using the thermal equilibrium method. When validated by comparison with seepage runs performed at the same time and reach, estimates from the two methods agreed with each other with an R2 of 0.94, a root mean squared error (RMSE) of 0.08 (m/d) and a Nash-Sutcliffe efficiency (NSE) of 0.93. In conclusion, the thermal equilibrium method was a suitable technique for quantifying groundwater flux with minimal cost and simple field installation given that suitable atmospheric and hydrological data were readily available.

Evaporation in Capillary Porous Media at the Perfect Piston-Like Invasion Limit: Evidence of Nonlocal Equilibrium Effects

NASA Astrophysics Data System (ADS)

Attari Moghaddam, Alireza; Prat, Marc; Tsotsas, Evangelos; Kharaghani, Abdolreza

2017-12-01

The classical continuum modeling of evaporation in capillary porous media is revisited from pore network simulations of the evaporation process. The computed moisture diffusivity is characterized by a minimum corresponding to the transition between liquid and vapor transport mechanisms confirming previous interpretations. Also the study suggests an explanation for the scattering generally observed in the moisture diffusivity obtained from experimental data. The pore network simulations indicate a noticeable nonlocal equilibrium effect leading to a new interpretation of the vapor pressure-saturation relationship classically introduced to obtain the one-equation continuum model of evaporation. The latter should not be understood as a desorption isotherm as classically considered but rather as a signature of a nonlocal equilibrium effect. The main outcome of this study is therefore that nonlocal equilibrium two-equation model must be considered for improving the continuum modeling of evaporation.

Phase and vacancy behaviour of hard "slanted" cubes

NASA Astrophysics Data System (ADS)

van Damme, R.; van der Meer, B.; van den Broeke, J. J.; Smallenburg, F.; Filion, L.

2017-09-01

We use computer simulations to study the phase behaviour for hard, right rhombic prisms as a function of the angle of their rhombic face (the "slant" angle). More specifically, using a combination of event-driven molecular dynamics simulations, Monte Carlo simulations, and free-energy calculations, we determine and characterize the equilibrium phases formed by these particles for various slant angles and densities. Surprisingly, we find that the equilibrium crystal structure for a large range of slant angles and densities is the simple cubic crystal—despite the fact that the particles do not have cubic symmetry. Moreover, we find that the equilibrium vacancy concentration in this simple cubic phase is extremely high and depends only on the packing fraction and not the particle shape. At higher densities, a rhombic crystal appears as the equilibrium phase. We summarize the phase behaviour of this system by drawing a phase diagram in the slant angle-packing fraction plane.

N-Methyl Inversion and Accurate Equilibrium Structures in Alkaloids: Pseudopelletierine.

PubMed

Vallejo-López, Montserrat; Écija, Patricia; Vogt, Natalja; Demaison, Jean; Lesarri, Alberto; Basterretxea, Francisco J; Cocinero, Emilio J

2017-11-21

A rotational spectroscopy investigation has resolved the conformational equilibrium and structural properties of the alkaloid pseudopelletierine. Two different conformers, which originate from inversion of the N-methyl group from an axial to an equatorial position, have been unambiguously identified in the gas phase, and nine independent isotopologues have been recorded by Fourier-transform microwave spectroscopy in a jet expansion. Both conformers share a chair-chair configuration of the two bridged six-membered rings. The conformational equilibrium is displaced towards the axial form, with a relative population in the supersonic jet of N axial /N equatorial ≈2/1. An accurate equilibrium structure has been determined by using the semiexperimental mixed-estimation method and alternatively computed by quantum-chemical methods up to the coupled-cluster level of theory. A comparison with the N-methyl inversion equilibria in related tropanes is also presented. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of segmental left ventricular wall motion by equilibrium gated radionuclide ventriculography.

PubMed

Van Nostrand, D; Janowitz, W R; Holmes, D R; Cohen, H A

1979-01-01

The ability of equilibrium gated radionuclide ventriculography to detect segmental left ventricular (LV) wall motion abnormalities was determined in 26 patients undergoing cardiac catheterization. Multiple gated studies obtained in 30 degrees right anterior oblique and 45 degrees left anterior oblique projections, played back in a movie format, were compared to the corresponding LV ventriculograms. The LV wall in the two projections was divided into eight segments. Each segment was graded as normal, hypokinetic, akinetic, dyskinetic, or indeterminate. Thirteen percent of the segments in the gated images were indeterminate; 24 out of 27 of these were proximal or distal inferior wall segments. There was exact agreement in 86% of the remaining segments. The sensitivity of the radionuclide technique for detecting normal versus any abnormal wall motion was 71%, with a specificity of 99%. Equilibrium gated ventriculography is an excellent noninvasive technique for evaluating segmental LV wall motion. It is least reliable in assessing the proximal inferior wall and interventricular septum.

Dynamic Analysis of a Reaction-Diffusion Rumor Propagation Model

NASA Astrophysics Data System (ADS)

Zhao, Hongyong; Zhu, Linhe

2016-06-01

The rapid development of the Internet, especially the emergence of the social networks, leads rumor propagation into a new media era. Rumor propagation in social networks has brought new challenges to network security and social stability. This paper, based on partial differential equations (PDEs), proposes a new SIS rumor propagation model by considering the effect of the communication between the different rumor infected users on rumor propagation. The stabilities of a nonrumor equilibrium point and a rumor-spreading equilibrium point are discussed by linearization technique and the upper and lower solutions method, and the existence of a traveling wave solution is established by the cross-iteration scheme accompanied by the technique of upper and lower solutions and Schauder’s fixed point theorem. Furthermore, we add the time delay to rumor propagation and deduce the conditions of Hopf bifurcation and stability switches for the rumor-spreading equilibrium point by taking the time delay as the bifurcation parameter. Finally, numerical simulations are performed to illustrate the theoretical results.

Numerical computation of viscous flow around bodies and wings moving at supersonic speeds

NASA Technical Reports Server (NTRS)

Tannehill, J. C.

1984-01-01

Research in aerodynamics is discussed. The development of equilibrium air curve fits; computation of hypersonic rarefield leading edge flows; computation of 2-D and 3-D blunt body laminar flows with an impinging shock; development of a two-dimensional or axisymmetric real gas blunt body code; a study of an over-relaxation procedure forthe MacCormack finite-difference scheme; computation of 2-D blunt body turbulent flows with an impinging shock; computation of supersonic viscous flow over delta wings at high angles of attack; and computation of the Space Shuttle Orbiter flowfield are discussed.

CET89 - CHEMICAL EQUILIBRIUM WITH TRANSPORT PROPERTIES, 1989

NASA Technical Reports Server (NTRS)

Mcbride, B.

1994-01-01

Scientists and engineers need chemical equilibrium composition data to calculate the theoretical thermodynamic properties of a chemical system. This information is essential in the design and analysis of equipment such as compressors, turbines, nozzles, engines, shock tubes, heat exchangers, and chemical processing equipment. The substantial amount of numerical computation required to obtain equilibrium compositions and transport properties for complex chemical systems led scientists at NASA's Lewis Research Center to develop CET89, a program designed to calculate the thermodynamic and transport properties of these systems. CET89 is a general program which will calculate chemical equilibrium compositions and mixture properties for any chemical system with available thermodynamic data. Generally, mixtures may include condensed and gaseous products. CET89 performs the following operations: it 1) obtains chemical equilibrium compositions for assigned thermodynamic states, 2) calculates dilute-gas transport properties of complex chemical mixtures, 3) obtains Chapman-Jouguet detonation properties for gaseous species, 4) calculates incident and reflected shock properties in terms of assigned velocities, and 5) calculates theoretical rocket performance for both equilibrium and frozen compositions during expansion. The rocket performance function allows the option of assuming either a finite area or an infinite area combustor. CET89 accommodates problems involving up to 24 reactants, 20 elements, and 600 products (400 of which may be condensed). The program includes a library of thermodynamic and transport properties in the form of least squares coefficients for possible reaction products. It includes thermodynamic data for over 1300 gaseous and condensed species and transport data for 151 gases. The subroutines UTHERM and UTRAN convert thermodynamic and transport data to unformatted form for faster processing. The program conforms to the FORTRAN 77 standard, except for some input in NAMELIST format. It requires about 423 KB memory, and is designed to be used on mainframe, workstation, and mini computers. Due to its memory requirements, this program does not readily lend itself to implementation on MS-DOS based machines.

Non-equilibrium hydrogen ionization in 2D simulations of the solar atmosphere

NASA Astrophysics Data System (ADS)

Leenaarts, J.; Carlsson, M.; Hansteen, V.; Rutten, R. J.

2007-10-01

Context: The ionization of hydrogen in the solar chromosphere and transition region does not obey LTE or instantaneous statistical equilibrium because the timescale is long compared with important hydrodynamical timescales, especially of magneto-acoustic shocks. Since the pressure, temperature, and electron density depend sensitively on hydrogen ionization, numerical simulation of the solar atmosphere requires non-equilibrium treatment of all pertinent hydrogen transitions. The same holds for any diagnostic application employing hydrogen lines. Aims: To demonstrate the importance and to quantify the effects of non-equilibrium hydrogen ionization, both on the dynamical structure of the solar atmosphere and on hydrogen line formation, in particular Hα. Methods: We implement an algorithm to compute non-equilibrium hydrogen ionization and its coupling into the MHD equations within an existing radiation MHD code, and perform a two-dimensional simulation of the solar atmosphere from the convection zone to the corona. Results: Analysis of the simulation results and comparison to a companion simulation assuming LTE shows that: a) non-equilibrium computation delivers much smaller variations of the chromospheric hydrogen ionization than for LTE. The ionization is smaller within shocks but subsequently remains high in the cool intershock phases. As a result, the chromospheric temperature variations are much larger than for LTE because in non-equilibrium, hydrogen ionization is a less effective internal energy buffer. The actual shock temperatures are therefore higher and the intershock temperatures lower. b) The chromospheric populations of the hydrogen n = 2 level, which governs the opacity of Hα, are coupled to the ion populations. They are set by the high temperature in shocks and subsequently remain high in the cool intershock phases. c) The temperature structure and the hydrogen level populations differ much between the chromosphere above photospheric magnetic elements and above quiet internetwork. d) The hydrogen n = 2 population and column density are persistently high in dynamic fibrils, suggesting that these obtain their visibility from being optically thick in Hα also at low temperature. Movie and Appendix A are only available in electronic form at http://www.aanda.org

HO-CHUNK: Radiation Transfer code

NASA Astrophysics Data System (ADS)

Whitney, Barbara A.; Wood, Kenneth; Bjorkman, J. E.; Cohen, Martin; Wolff, Michael J.

2017-11-01

HO-CHUNK calculates radiative equilibrium temperature solution, thermal and PAH/vsg emission, scattering and polarization in protostellar geometries. It is useful for computing spectral energy distributions (SEDs), polarization spectra, and images.

Dynamics of Equilibrium Points in a Uniformly Rotating Second-Order and Degree Gravitational Field

NASA Astrophysics Data System (ADS)

Feng, Jinglang; Hou, Xiyun

2017-07-01

Using tools such as periodic orbits and invariant manifolds, the global dynamics around equilibrium points (EPs) in a rotating second-order and degree gravitational field are studied. For EPs on the long axis, planar and vertical periodic families are computed, and their stability properties are investigated. Invariant manifolds are also computed, and their relation to the first-order resonances is briefly discussed. For EPs on the short axis, planar and vertical periodic families are studied, with special emphasis on the genealogy of the planar periodic families. Our studies show that the global dynamics around EPs are highly similar to those around libration points in the circular restricted three-body problem, such as spatial halo orbits, invariant manifolds, and the genealogy of planar periodic families.

Xcas as a Programming Environment for Stability Conditions for a Class of Differential Equation Models in Economics

NASA Astrophysics Data System (ADS)

Halkos, George E.; Tsilika, Kyriaki D.

2011-09-01

In this paper we examine the property of asymptotic stability in several dynamic economic systems, modeled in ordinary differential equation formulations of time parameter t. Asymptotic stability ensures intertemporal equilibrium for the economic quantity the solution stands for, regardless of what the initial conditions happen to be. Existence of economic equilibrium in continuous time models is checked via a Symbolic language, the Xcas program editor. Using stability theorems of differential equations as background a brief overview of symbolic capabilities of free software Xcas is given. We present computational experience with a programming style for stability results of ordinary linear and nonlinear differential equations. Numerical experiments on traditional applications of economic dynamics exhibit the simplicity clarity and brevity of input and output of our computer codes.

Finite element solution of low bond number sloshing

NASA Technical Reports Server (NTRS)

Wohlen, R. L.; Park, A. C.; Warner, D. M.

1975-01-01

The dynamics of liquid propellant in a low Bond number environment which are critical to the design of spacecraft systems with respect to orbital propellant transfer and attitude control system were investigated. Digital computer programs were developed for the determination of liquid free surface equilibrium shape, lateral slosh natural vibration mode shapes, and frequencies for a liquid in a container of arbitrary axisymmetric shape with surface tension forces the same order of magnitude as acceleration forces. A finite volume element representation of the liquid was used for the vibration analysis. The liquid free surface equilibrium shapes were computed for several tanks at various contact angles and ullage volumes. A configuration was selected for vibration analysis and lateral slosh mode shapes and natural frequencies were obtained. Results are documented.

Simplifying silicon burning: Application of quasi-equilibrium to (alpha) network nucleosynthesis

NASA Technical Reports Server (NTRS)

Hix, W. R.; Thielemann, F.-K.; Khokhlov, A. M.; Wheeler, J. C.

1997-01-01

While the need for accurate calculation of nucleosynthesis and the resulting rate of thermonuclear energy release within hydrodynamic models of stars and supernovae is clear, the computational expense of these nucleosynthesis calculations often force a compromise in accuracy to reduce the computational cost. To redress this trade-off of accuracy for speed, the authors present an improved nuclear network which takes advantage of quasi- equilibrium in order to reduce the number of independent nuclei, and hence the computational cost of nucleosynthesis, without significant reduction in accuracy. In this paper they will discuss the first application of this method, the further reduction in size of the minimal alpha network. The resultant QSE- reduced alpha network is twice as fast as the conventional alpha network it replaces and requires the tracking of half as many abundance variables, while accurately estimating the rate of energy generation. Such reduction in cost is particularly necessary for future generation of multi-dimensional models for supernovae.

Galactic evolution of copper in the light of NLTE computations

NASA Astrophysics Data System (ADS)

Andrievsky, S.; Bonifacio, P.; Caffau, E.; Korotin, S.; Spite, M.; Spite, F.; Sbordone, L.; Zhukova, A. V.

2018-01-01

We have developed a model atom for Cu with which we perform statistical equilibrium computations that allow us to compute the line formation of Cu I lines in stellar atmospheres without assuming local thermodynamic equilibrium (LTE). We validate this model atom by reproducing the observed line profiles of the Sun, Procyon and 11 metal-poor stars. Our sample of stars includes both dwarfs and giants. Over a wide range of stellar parameters, we obtain excellent agreement among different Cu I lines. The 11 metal-poor stars have iron abundances in the range - 4.2 ≤ [Fe/H] ≤ -1.4, the weighted mean of the [Cu/Fe] ratios is -0.22 dex, with a scatter of -0.15 dex. This is very different from the results from LTE analysis (the difference between NLTE and LTE abundances reaches 1 dex) and in spite of the small size of our sample, it prompts for a revision of the Galactic evolution of Cu.

A comparison of homogeneous equilibrium and relaxation model for CO2 expansion inside the two-phase ejector

NASA Astrophysics Data System (ADS)

Palacz, M.; Haida, M.; Smolka, J.; Nowak, A. J.; Hafner, A.

2016-09-01

In this study, the comparison of the accuracy of the homogeneous equilibrium model (HEM) and homogeneous relaxation model (HRM) is presented. Both models were applied to simulate the CO2 expansion inside the two-phase ejectors. Moreover, the mentioned models were implemented in the robust and efficient computational tool ejectorPL. That tool guarantees the fully automated computational process and the repeatable computations for the various ejector shapes and operating conditions. The simulated motive nozzle mass flow rates were compared to the experimentally measured mass flow rates. That comparison was made for both, HEM and HRM. The results showed the unsatisfying fidelity of the HEM for the operating regimes far from the carbon dioxide critical point. On the other hand, the HRM accuracy for such conditions was slightly higher. The approach presented in this paper, showed the limitation of applicability of both two-phase models for the expansion phenomena inside the ejectors.

A simplified implementation of van der Waals density functionals for first-principles molecular dynamics applications

NASA Astrophysics Data System (ADS)

Wu, Jun; Gygi, François

2012-06-01

We present a simplified implementation of the non-local van der Waals correlation functional introduced by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)] and reformulated by Román-Pérez et al. [Phys. Rev. Lett. 103, 096102 (2009)]. The proposed numerical approach removes the logarithmic singularity of the kernel function. Complete expressions of the self-consistent correlation potential and of the stress tensor are given. Combined with various choices of exchange functionals, five versions of van der Waals density functionals are implemented. Applications to the computation of the interaction energy of the benzene-water complex and to the computation of the equilibrium cell parameters of the benzene crystal are presented. As an example of crystal structure calculation involving a mixture of hydrogen bonding and dispersion interactions, we compute the equilibrium structure of two polymorphs of aspirin (2-acetoxybenzoic acid, C9H8O4) in the P21/c monoclinic structure.

Listening to the Shepard-Risset Glissando: the Relationship between Emotional Response, Disruption of Equilibrium, and Personality

PubMed Central

Vernooij, Eveline; Orcalli, Angelo; Fabbro, Franco; Crescentini, Cristiano

2016-01-01

The endless scale illusion, obtained by cyclically repeating a chromatic scale made up of Shepard tones, has been used in a variety of musical works. Music psychology and neuroscience has been interested in this particular psychoacoustic phenomenon mainly for studying the cognitive processes of pitch perception involved. In the present study, we investigated the emotional states induced by the Shepard-Risset glissando, a variant of the Shepard scale. For this purpose we chose three musical stimuli: a Matlab-generated Shepard Risset glissando, Jean-Claude Risset's Computer Suite from Little Boy, which presents a Shepard-Risset glissando integrated in the aesthetic context of a composition, and an ordinary orchestral glissando taken from the opening of Iannis Xenakis's Metastasis. Seventy-three volunteers completed a listening experiment during which they rated their emotional response to these stimuli on a seven-point Likert scale and indicated whether they had experienced a disruption of equilibrium. Personality was also measured with the Five-Factor Model of personality traits. The results show that negative emotions were most strongly evoked during listening to each of the stimuli. We also found that the Shepard-Risset glissando illusion, both within the aesthetic context of a musical composition and on its own, was capable of evoking disruption of equilibrium, frequently leading to the associated feeling of falling. Moreover, generally for the Shepard-Risset glissando illusion, higher negative emotional ratings were given by individuals who had experienced a feeling of disturbance of equilibrium relative to those who had not had this experience. Finally, we found a complex pattern of relationships between personality and the subjective experience of the glissando. Openness to experience correlated positively with positive emotion ratings for the Computer Suite, while agreeableness correlated negatively with positive emotion ratings for the Matlab stimulus. Moreover, results indicated higher (Bonferroni-uncorrected) neuroticism for those who experienced an equilibrium disturbance relative to subjects who did not have this experience during listening to the Computer Suite. These findings suggest that musical paradoxes may be of interest not only for the insights they provide on our perceptual system, but also for the richness of the emotional experience elicited during listening. PMID:26973584

Listening to the Shepard-Risset Glissando: the Relationship between Emotional Response, Disruption of Equilibrium, and Personality.

PubMed

Vernooij, Eveline; Orcalli, Angelo; Fabbro, Franco; Crescentini, Cristiano

2016-01-01

The endless scale illusion, obtained by cyclically repeating a chromatic scale made up of Shepard tones, has been used in a variety of musical works. Music psychology and neuroscience has been interested in this particular psychoacoustic phenomenon mainly for studying the cognitive processes of pitch perception involved. In the present study, we investigated the emotional states induced by the Shepard-Risset glissando, a variant of the Shepard scale. For this purpose we chose three musical stimuli: a Matlab-generated Shepard Risset glissando, Jean-Claude Risset's Computer Suite from Little Boy, which presents a Shepard-Risset glissando integrated in the aesthetic context of a composition, and an ordinary orchestral glissando taken from the opening of Iannis Xenakis's Metastasis. Seventy-three volunteers completed a listening experiment during which they rated their emotional response to these stimuli on a seven-point Likert scale and indicated whether they had experienced a disruption of equilibrium. Personality was also measured with the Five-Factor Model of personality traits. The results show that negative emotions were most strongly evoked during listening to each of the stimuli. We also found that the Shepard-Risset glissando illusion, both within the aesthetic context of a musical composition and on its own, was capable of evoking disruption of equilibrium, frequently leading to the associated feeling of falling. Moreover, generally for the Shepard-Risset glissando illusion, higher negative emotional ratings were given by individuals who had experienced a feeling of disturbance of equilibrium relative to those who had not had this experience. Finally, we found a complex pattern of relationships between personality and the subjective experience of the glissando. Openness to experience correlated positively with positive emotion ratings for the Computer Suite, while agreeableness correlated negatively with positive emotion ratings for the Matlab stimulus. Moreover, results indicated higher (Bonferroni-uncorrected) neuroticism for those who experienced an equilibrium disturbance relative to subjects who did not have this experience during listening to the Computer Suite. These findings suggest that musical paradoxes may be of interest not only for the insights they provide on our perceptual system, but also for the richness of the emotional experience elicited during listening.

Development and application of computational aerothermodynamics flowfield computer codes

NASA Technical Reports Server (NTRS)

Venkatapathy, Ethiraj

1992-01-01

Presented is a collection of papers on research activities carried out during the funding period of October 1991 to March 1992. Topics covered include: blunt body flows in thermochemical equilibrium; thermochemical relaxation in high enthalpy nozzle flow; single expansion ramp nozzle simulations; lunar return aerobraking; line boundary problem for three dimensional grids; and unsteady shock induced combustion.

Computing Models of M-type Host Stars and their Panchromatic Spectral Output

NASA Astrophysics Data System (ADS)

Linsky, Jeffrey; Tilipman, Dennis; France, Kevin

2018-06-01

We have begun a program of computing state-of-the-art model atmospheres from the photospheres to the coronae of M stars that are the host stars of known exoplanets. For each model we are computing the emergent radiation at all wavelengths that are critical for assessingphotochemistry and mass-loss from exoplanet atmospheres. In particular, we are computing the stellar extreme ultraviolet radiation that drives hydrodynamic mass loss from exoplanet atmospheres and is essential for determing whether an exoplanet is habitable. The model atmospheres are computed with the SSRPM radiative transfer/statistical equilibrium code developed by Dr. Juan Fontenla. The code solves for the non-LTE statistical equilibrium populations of 18,538 levels of 52 atomic and ion species and computes the radiation from all species (435,986 spectral lines) and about 20,000,000 spectral lines of 20 diatomic species.The first model computed in this program was for the modestly active M1.5 V star GJ 832 by Fontenla et al. (ApJ 830, 152 (2016)). We will report on a preliminary model for the more active M5 V star GJ 876 and compare this model and its emergent spectrum with GJ 832. In the future, we will compute and intercompare semi-empirical models and spectra for all of the stars observed with the HST MUSCLES Treasury Survey, the Mega-MUSCLES Treasury Survey, and additional stars including Proxima Cen and Trappist-1.This multiyear theory program is supported by a grant from the Space Telescope Science Institute.

Radioactive equilibrium in ancient marine sediments

USGS Publications Warehouse

Breger, I.A.

1955-01-01

Radioactive equilibrium in eight marine sedimentary formations has been studied by means of direct determinations of uranium, radium and thorium. Alpha-particle counting has also been carried out in order to cross-calibrate thick-source counting techniques. The maximum deviation from radioactive equilibrium that has been noted is 11 per cent-indicating that there is probably equilibrium in all the formations analyzed. Thick-source alpha-particle counting by means of a proportional counter or an ionization chamber leads to high results when the samples contain less than about 10 p.p.m. of uranium. For samples having a higher content of uranium the results are in excellent agreement with each other and with those obtained by direct analytical techniques. The thorium contents that have been obtained correspond well to the average values reported in the literature. The uranium content of marine sediments may be appreciably higher than the average values that have been reported for sedimentary rocks. Data show that there is up to fourteen times the percentage of uranium as of thorium in the formations studied and that the percentage of thorium never exceeds that of uranium. While the proximity of a depositional environment to a land mass may influence the concentration of uranium in a marine sediment, this is not true with thorium. ?? 1955.

Monte Carlo computer simulations of Venus equilibrium and global resurfacing models

NASA Technical Reports Server (NTRS)

Dawson, D. D.; Strom, R. G.; Schaber, G. G.

1992-01-01

Two models have been proposed for the resurfacing history of Venus: (1) equilibrium resurfacing and (2) global resurfacing. The equilibrium model consists of two cases: in case 1, areas less than or equal to 0.03 percent of the planet are spatially randomly resurfaced at intervals of less than or greater than 150,000 yr to produce the observed spatially random distribution of impact craters and average surface age of about 500 m.y.; and in case 2, areas greater than or equal to 10 percent of the planet are resurfaced at intervals of greater than or equal to 50 m.y. The global resurfacing model proposes that the entire planet was resurfaced about 500 m.y. ago, destroying the preexisting crater population and followed by significantly reduced volcanism and tectonism. The present crater population has accumulated since then with only 4 percent of the observed craters having been embayed by more recent lavas. To test the equilibrium resurfacing model we have run several Monte Carlo computer simulations for the two proposed cases. It is shown that the equilibrium resurfacing model is not a valid model for an explanation of the observed crater population characteristics or Venus' resurfacing history. The global resurfacing model is the most likely explanation for the characteristics of Venus' cratering record. The amount of resurfacing since that event, some 500 m.y. ago, can be estimated by a different type of Monte Carolo simulation. To date, our initial simulation has only considered the easiest case to implement. In this case, the volcanic events are randomly distributed across the entire planet and, therefore, contrary to observation, the flooded craters are also randomly distributed across the planet.

The procedure and results of calculations of the equilibrium isotopic composition of a demonstration subcritical molten salt reactor

NASA Astrophysics Data System (ADS)

Nevinitsa, V. A.; Dudnikov, A. A.; Blandinskiy, V. Yu.; Balanin, A. L.; Alekseev, P. N.; Titarenko, Yu. E.; Batyaev, V. F.; Pavlov, K. V.; Titarenko, A. Yu.

2015-12-01

A subcritical molten salt reactor with an external neutron source is studied computationally as a facility for incineration and transmutation of minor actinides from spent nuclear fuel of reactors of VVER-1000 type and for producing 233U from 232Th. The reactor configuration is chosen, the requirements to be imposed on the external neutron source are formulated, and the equilibrium isotopic composition of heavy nuclides and the key parameters of the fuel cycle are calculated.

Extension of a Kinetic-Theory Approach for Computing Chemical-Reaction Rates to Reactions with Charged Particles

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Lewis, Mark J.

2010-01-01

Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties (i.e., no macroscopic reaction rate information) are extended to include reactions involving charged particles and electronic energy levels. The proposed extensions include ionization reactions, exothermic associative ionization reactions, endothermic and exothermic charge exchange reactions, and other exchange reactions involving ionized species. The extensions are shown to agree favorably with the measured Arrhenius rates for near-equilibrium conditions.

Adaptive Implicit Non-Equilibrium Radiation Diffusion

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

Philip, Bobby; Wang, Zhen; Berrill, Mark A

2013-01-01

We describe methods for accurate and efficient long term time integra- tion of non-equilibrium radiation diffusion systems: implicit time integration for effi- cient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while control- ling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

On a numerical solving of random generated hexamatrix games

NASA Astrophysics Data System (ADS)

Orlov, Andrei; Strekalovskiy, Alexander

2016-10-01

In this paper, we develop a global search method for finding a Nash equilibrium in a hexamatrix game (polymatrix game of three players). The method, on the one hand, is based on the equivalence theorem of the problem of finding a Nash equilibrium in the game and a special mathematical optimization problem, and, on the other hand, on the usage of Global Search Theory for solving the latter problem. The efficiency of this approach is demonstrated by the results of computational testing.

Addition to the Lewis Chemical Equilibrium Program to allow computation from coal composition data

NASA Technical Reports Server (NTRS)

Sevigny, R.

1980-01-01

Changes made to the Coal Gasification Project are reported. The program was developed by equilibrium combustion in rocket engines. It can be applied directly to the entrained flow coal gasification process. The particular problem addressed is the reduction of the coal data into a form suitable to the program, since the manual process is involved and error prone. A similar problem in relating the normal output of the program to parameters meaningful to the coal gasification process is also addressed.

A Fluorescence Recovery After Photobleaching (FRAP) Technique for the Measurement of Solute Transport Across Surfactant-Laden Interfaces

NASA Technical Reports Server (NTRS)

Browne, Edward P.; Hatton, T. Alan

1996-01-01

The technique of Fluorescence Recovery After Photobleaching (FRAP) has been applied to the measurement of interfacial transport in two-phase systems. FRAP exploits the loss of fluorescence exhibited by certain fluorophores when over-stimulated (photobleached), so that a two-phase system, originally at equilibrium, can be perturbed without disturbing the interface by strong light from an argon-ion laser and its recovery monitored by a microscope-mounted CCD camera as it relaxes to a new equilibrium. During this relaxation, the concentration profiles of the probe solute are measured on both sides of the interface as a function of time, yielding information about the transport characteristics of the system. To minimize the size of the meniscus between the two phases, a photolithography technique is used to selectively treat the glass walls of the cell in which the phases are contained. This allows concentration measurements to be made very close to the interface and increases the sensitivity of the FRAP technique.

Solubility limits in quaternary SnTe-based alloys [Metastability and solubility limits in quaternary SnTe-based alloys guided by combinatorial sputtering

DOE PAGES

Siol, Sebastian; Holder, Aaron; Ortiz, Brenden R.; ...

2017-05-09

Here, the controlled decomposition of metastable alloys is an attractive route to form nanostructured thermoelectric materials with reduced thermal conductivity. The ternary SnTe–MnTe and SnTe–SnSe heterostructural alloys have been demonstrated as promising materials for thermoelectric applications. In this work, the quaternary Sn 1–yMnyTe 1–xSe x phase space serves as a relevant model system to explore how a combination of computational and combinatorial-growth methods can be used to study equilibrium and non-equilibrium solubility limits. Results from first principle calculations indicate low equilibrium solubility for x,y < 0.05 that are in good agreement with results obtained from bulk equilibrium synthesis experiments andmore » predict significantly higher spinodal limits. An experimental screening using sputtered combinatorial thin film sample libraries showed a remarkable increase in non-equilibrium solubility for x,y > 0.2. These theoretical and experimental results were used to guide the bulk synthesis of metastable alloys. The ability to reproduce the non-equilibrium solubility levels in bulk materials indicates that such theoretical calculations and combinatorial growth can inform bulk synthetic routes. Further, the large difference between equilibrium and non-equilibrium solubility limits in Sn 1–yMn yTe 1–xSe x indicates these metastable alloys are attractive in terms of nano-precipitate formation for potential thermoelectric applications.« less

Determination of free Zn2+ concentration in synthetic and natural samples with AGNES (Absence of Gradients and Nernstian Equilibrium Stripping) and DMT (Donnan Membrane Technique).

PubMed

Chito, Diana; Weng, Liping; Galceran, Josep; Companys, Encarnació; Puy, Jaume; van Riemsdijk, Willem H; van Leeuwen, Herman P

2012-04-01

The determination of free Zn(2+) ion concentration is a key in the study of environmental systems like river water and soils, due to its impact on bioavailability and toxicity. AGNES (Absence of Gradients and Nernstian Equilibrium Stripping) and DMT (Donnan Membrane Technique) are emerging techniques suited for the determination of free heavy metal concentrations, especially in the case of Zn(2+), given that there is no commercial Ion Selective Electrode. In this work, both techniques have been applied to synthetic samples (containing Zn and NTA) and natural samples (Rhine river water and soils), showing good agreement. pH fluctuations in DMT and N(2)/CO(2) purging system used in AGNES did not affect considerably the measurements done in Rhine river water and soil samples. Results of DMT in situ of Rhine river water are comparable to those of AGNES in the lab. The comparison of this work provides a cross-validation for both techniques. Copyright © 2012 Elsevier B.V. All rights reserved.

Computing diffusivities from particle models out of equilibrium

NASA Astrophysics Data System (ADS)

Embacher, Peter; Dirr, Nicolas; Zimmer, Johannes; Reina, Celia

2018-04-01

A new method is proposed to numerically extract the diffusivity of a (typically nonlinear) diffusion equation from underlying stochastic particle systems. The proposed strategy requires the system to be in local equilibrium and have Gaussian fluctuations but it is otherwise allowed to undergo arbitrary out-of-equilibrium evolutions. This could be potentially relevant for particle data obtained from experimental applications. The key idea underlying the method is that finite, yet large, particle systems formally obey stochastic partial differential equations of gradient flow type satisfying a fluctuation-dissipation relation. The strategy is here applied to three classic particle models, namely independent random walkers, a zero-range process and a symmetric simple exclusion process in one space dimension, to allow the comparison with analytic solutions.

Inclusion of pressure and flow in a new 3D MHD equilibrium code

NASA Astrophysics Data System (ADS)

Raburn, Daniel; Fukuyama, Atsushi

2012-10-01

Flow and nonsymmetric effects can play a large role in plasma equilibria and energy confinement. A concept for such a 3D equilibrium code was developed and presented in 2011. The code is called the Kyoto ITerative Equilibrium Solver (KITES) [1], and the concept is based largely on the PIES code [2]. More recently, the work-in-progress KITES code was used to calculate force-free equilibria. Here, progress and results on the inclusion of pressure and flow in the code are presented. [4pt] [1] Daniel Raburn and Atsushi Fukuyama, Plasma and Fusion Research: Regular Articles, 7:240381 (2012).[0pt] [2] H. S. Greenside, A. H. Reiman, and A. Salas, J. Comput. Phys, 81(1):102-136 (1989).

Reconstruction of equilibrium trajectories during whole-body movements.

PubMed

Domen, K; Latash, M L; Zatsiorsky, V M

1999-03-01

The framework of the equilibrium-point hypothesis was used to reconstruct equilibrium trajectories (ETs) of the ankle, hip and body center of mass during quick voluntary hip flexions ('Japanese courtesy bow') by standing subjects. Different spring loads applied to the subject's back were used to introduce smooth perturbations that are necessary to reconstruct ETs based on a series of trials at the same task. Time patterns of muscle torques were calculated using inverse dynamics techniques. A second-order linear model was employed to calculate the instantaneous position of the spring-like joint or center of mass characteristic at different times during the movement. ETs of the joints and of the center of mass had significantly different shapes from the actual trajectories. Integral measures of electromyographic bursts of activity in postural muscles demonstrated a relation to muscle length corresponding to the equilibrium-point hypothesis.

Teaching Chemical Equilibrium with the Jigsaw Technique

NASA Astrophysics Data System (ADS)

Doymus, Kemal

2008-03-01

This study investigates the effect of cooperative learning (jigsaw) versus individual learning methods on students’ understanding of chemical equilibrium in a first-year general chemistry course. This study was carried out in two different classes in the department of primary science education during the 2005-2006 academic year. One of the classes was randomly assigned as the non-jigsaw group (control) and other as the jigsaw group (cooperative). Students participating in the jigsaw group were divided into four “home groups” since the topic chemical equilibrium is divided into four subtopics (Modules A, B, C and D). Each of these home groups contained four students. The groups were as follows: (1) Home Group A (HGA), representin g the equilibrium state and quantitative aspects of equilibrium (Module A), (2) Home Group B (HGB), representing the equilibrium constant and relationships involving equilibrium constants (Module B), (3) Home Group C (HGC), representing Altering Equilibrium Conditions: Le Chatelier’s principle (Module C), and (4) Home Group D (HGD), representing calculations with equilibrium constants (Module D). The home groups then broke apart, like pieces of a jigsaw puzzle, and the students moved into jigsaw groups consisting of members from the other home groups who were assigned the same portion of the material. The jigsaw groups were then in charge of teaching their specific subtopic to the rest of the students in their learning group. The main data collection tool was a Chemical Equilibrium Achievement Test (CEAT), which was applied to both the jigsaw and non-jigsaw groups The results indicated that the jigsaw group was more successful than the non-jigsaw group (individual learning method).

Computer Aided Conceptual Design of Submarines

DTIC Science & Technology

1984-06-01

Department 5f i ngi eering . May 19134 Certified by: Thesi Supervisor Accepted Y.’.I Cr’rman, (IeaV gineer ing Departmental Comimitte C - nuusý"(Xwa has...the equilibrium polygon. The Package interfaces with a pressure hull design module developed separately in an O.E. thesis by Marvin Meade. Interactive...computers or computer aided design systems. c- A𔃺ccession -or4 Thesis Supervisor: Dr. David V. Burke NI R~ Title: Professor of Ocean Engineering DTIC

Spectro Analytical, Computational and In Vitro Biological Studies of Novel Substituted Quinolone Hydrazone and it's Metal Complexes.

PubMed

Nagula, Narsimha; Kunche, Sudeepa; Jaheer, Mohmed; Mudavath, Ravi; Sivan, Sreekanth; Ch, Sarala Devi

2018-01-01

Some novel transition metal [Cu (II), Ni (II) and Co (II)] complexes of nalidixic acid hydrazone have been prepared and characterized by employing spectro-analytical techniques viz: elemental analysis, 1 H-NMR, Mass, UV-Vis, IR, TGA-DTA, SEM-EDX, ESR and Spectrophotometry studies. The HyperChem 7.5 software was used for geometry optimization of title compound in its molecular and ionic forms. Quantum mechanical parameters, contour maps of highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) and corresponding binding energy values were computed using semi empirical single point PM3 method. The stoichiometric equilibrium studies of metal complexes carried out spectrophotometrically using Job's continuous variation and mole ratio methods inferred formation of 1:2 (ML 2 ) metal complexes in respective systems. The title compound and its metal complexes screened for antibacterial and antifungal properties, exemplified improved activity in metal complexes. The studies of nuclease activity for the cleavage of CT- DNA and MTT assay for in vitro cytotoxic properties involving metal complexes exhibited high activity. In addition, the DNA binding properties of Cu (II), Ni (II) and Co (II) complexes investigated by electronic absorption and fluorescence measurements revealed their good binding ability and commended agreement of K b values obtained from both the techniques. Molecular docking studies were also performed to find the binding affinity of synthesized compounds with DNA (PDB ID: 1N37) and "Thymidine phosphorylase from E.coli" (PDB ID: 4EAF) protein targets.

WEIGHING GALAXY CLUSTERS WITH GAS. I. ON THE METHODS OF COMPUTING HYDROSTATIC MASS BIAS

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

Lau, Erwin T.; Nagai, Daisuke; Nelson, Kaylea, E-mail: erwin.lau@yale.edu

2013-11-10

Mass estimates of galaxy clusters from X-ray and Sunyeav-Zel'dovich observations assume the intracluster gas is in hydrostatic equilibrium with their gravitational potential. However, since galaxy clusters are dynamically active objects whose dynamical states can deviate significantly from the equilibrium configuration, the departure from the hydrostatic equilibrium assumption is one of the largest sources of systematic uncertainties in cluster cosmology. In the literature there have been two methods for computing the hydrostatic mass bias based on the Euler and the modified Jeans equations, respectively, and there has been some confusion about the validity of these two methods. The word 'Jeans' wasmore » a misnomer, which incorrectly implies that the gas is collisionless. To avoid further confusion, we instead refer these methods as 'summation' and 'averaging' methods respectively. In this work, we show that these two methods for computing the hydrostatic mass bias are equivalent by demonstrating that the equation used in the second method can be derived from taking spatial averages of the Euler equation. Specifically, we identify the correspondences of individual terms in these two methods mathematically and show that these correspondences are valid to within a few percent level using hydrodynamical simulations of galaxy cluster formation. In addition, we compute the mass bias associated with the acceleration of gas and show that its contribution is small in the virialized regions in the interior of galaxy clusters, but becomes non-negligible in the outskirts of massive galaxy clusters. We discuss future prospects of understanding and characterizing biases in the mass estimate of galaxy clusters using both hydrodynamical simulations and observations and their implications for cluster cosmology.« less

Weighing Galaxy Clusters with Gas. I. On the Methods of Computing Hydrostatic Mass Bias

NASA Astrophysics Data System (ADS)

Lau, Erwin T.; Nagai, Daisuke; Nelson, Kaylea

2013-11-01

Mass estimates of galaxy clusters from X-ray and Sunyeav-Zel'dovich observations assume the intracluster gas is in hydrostatic equilibrium with their gravitational potential. However, since galaxy clusters are dynamically active objects whose dynamical states can deviate significantly from the equilibrium configuration, the departure from the hydrostatic equilibrium assumption is one of the largest sources of systematic uncertainties in cluster cosmology. In the literature there have been two methods for computing the hydrostatic mass bias based on the Euler and the modified Jeans equations, respectively, and there has been some confusion about the validity of these two methods. The word "Jeans" was a misnomer, which incorrectly implies that the gas is collisionless. To avoid further confusion, we instead refer these methods as "summation" and "averaging" methods respectively. In this work, we show that these two methods for computing the hydrostatic mass bias are equivalent by demonstrating that the equation used in the second method can be derived from taking spatial averages of the Euler equation. Specifically, we identify the correspondences of individual terms in these two methods mathematically and show that these correspondences are valid to within a few percent level using hydrodynamical simulations of galaxy cluster formation. In addition, we compute the mass bias associated with the acceleration of gas and show that its contribution is small in the virialized regions in the interior of galaxy clusters, but becomes non-negligible in the outskirts of massive galaxy clusters. We discuss future prospects of understanding and characterizing biases in the mass estimate of galaxy clusters using both hydrodynamical simulations and observations and their implications for cluster cosmology.

Predicting Transport of 3,5,6-Trichloro-2-Pyridinol Into Saliva Using a Combination Experimental and Computational Approach

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

Smith, Jordan Ned; Carver, Zana A.; Weber, Thomas J.

A combination experimental and computational approach was developed to predict chemical transport into saliva. A serous-acinar chemical transport assay was established to measure chemical transport with non-physiological (standard cell culture medium) and physiological (using surrogate plasma and saliva medium) conditions using 3,5,6-trichloro-2-pyridinol (TCPy) a metabolite of the pesticide chlorpyrifos. High levels of TCPy protein binding was observed in cell culture medium and rat plasma resulting in different TCPy transport behaviors in the two experimental conditions. In the non-physiological transport experiment, TCPy reached equilibrium at equivalent concentrations in apical and basolateral chambers. At higher TCPy doses, increased unbound TCPy was observed,more » and TCPy concentrations in apical and basolateral chambers reached equilibrium faster than lower doses, suggesting only unbound TCPy is able to cross the cellular monolayer. In the physiological experiment, TCPy transport was slower than non-physiological conditions, and equilibrium was achieved at different concentrations in apical and basolateral chambers at a comparable ratio (0.034) to what was previously measured in rats dosed with TCPy (saliva:blood ratio: 0.049). A cellular transport computational model was developed based on TCPy protein binding kinetics and accurately simulated all transport experiments using different permeability coefficients for the two experimental conditions (1.4 vs 0.4 cm/hr for non-physiological and physiological experiments, respectively). The computational model was integrated into a physiologically based pharmacokinetic (PBPK) model and accurately predicted TCPy concentrations in saliva of rats dosed with TCPy. Overall, this study demonstrates an approach to predict chemical transport in saliva potentially increasing the utility of salivary biomonitoring in the future.« less

Computation of iodine species concentrations in water

NASA Technical Reports Server (NTRS)

Schultz, John R.; Mudgett, Paul D.; Flanagan, David T.; Sauer, Richard L.

1994-01-01

During an evaluation of the use of iodine as a water disinfectant and the development of methods for measuring various iodine species in water onboard Space Freedom, it became necessary to compute the concentration of the various species based on equilibrium principles alone. Of particular concern was the case when various amounts of iodine, iodide, strong acid, and strong base are added to water. Such solutions can be used to evaluate the performance of various monitoring methods being considered. The authors of this paper present an overview of aqueous iodine chemistry, a set of nonlinear equations which can be used to model the above case, and a computer program for solving this system of equations using the Newton-Raphson method. The program was validated by comparing results over a range of concentrations and pH values with those previously presented by Gottardi for a given pH. Use of this program indicated that there are multiple roots to many cases and selecting an appropriate initial guess is important. Comparison of program results with laboratory results for the case when only iodine is added to water indicates the program gives high pH values for the iodine concentrations normally used for water disinfection. Extending the model to include the effects of iodate formation results in the computer pH values being closer to those observed, but the model with iodate does not agree well for the case in which base is added in addition to iodine to raise the pH. Potential explanations include failure to obtain equilibrium conditions in the lab, inaccuracies in published values for the equilibrium constants, and inadequate model of iodine chemistry and/or the lack of adequate analytical methods for measuring the various iodine species in water.

Viscosity Difference Measurements for Normal and Para Liquid Hydrogen Mixtures

NASA Technical Reports Server (NTRS)

Webeler, R.; Bedard, F.

1961-01-01

The absence of experimental data in the literature concerning a viscosity difference for normal and equilibrium liquid hydrogen may be attributed to the limited reproducibility of "oscillating disk" measurements in a liquid-hydrogen environment. Indeed, there is disagreement over the viscosity values for equilibrium liquid hydrogen even without proton spin considerations. Measurements presented here represent the first application of the piezoelectric alpha quartz torsional oscillator technique to liquid-hydrogen viscosity measurements.

Lattice Boltzmann accelerated direct simulation Monte Carlo for dilute gas flow simulations.

PubMed

Di Staso, G; Clercx, H J H; Succi, S; Toschi, F

2016-11-13

Hybrid particle-continuum computational frameworks permit the simulation of gas flows by locally adjusting the resolution to the degree of non-equilibrium displayed by the flow in different regions of space and time. In this work, we present a new scheme that couples the direct simulation Monte Carlo (DSMC) with the lattice Boltzmann (LB) method in the limit of isothermal flows. The former handles strong non-equilibrium effects, as they typically occur in the vicinity of solid boundaries, whereas the latter is in charge of the bulk flow, where non-equilibrium can be dealt with perturbatively, i.e. according to Navier-Stokes hydrodynamics. The proposed concurrent multiscale method is applied to the dilute gas Couette flow, showing major computational gains when compared with the full DSMC scenarios. In addition, it is shown that the coupling with LB in the bulk flow can speed up the DSMC treatment of the Knudsen layer with respect to the full DSMC case. In other words, LB acts as a DSMC accelerator.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Inverse design of an isotropic suspended Kirchhoff rod: theoretical and numerical results on the uniqueness of the natural shape.

PubMed

Bertails-Descoubes, Florence; Derouet-Jourdan, Alexandre; Romero, Victor; Lazarus, Arnaud

2018-04-01

Solving the equations for Kirchhoff elastic rods has been widely explored for decades in mathematics, physics and computer science, with significant applications in the modelling of thin flexible structures such as DNA, hair or climbing plants. As demonstrated in previous experimental and theoretical studies, the natural curvature plays an important role in the equilibrium shape of a Kirchhoff rod, even in the simple case where the rod is isotropic and suspended under gravity. In this paper, we investigate the reverse problem: can we characterize the natural curvature of a suspended isotropic rod, given an equilibrium curve? We prove that although there exists an infinite number of natural curvatures that are compatible with the prescribed equilibrium, they are all equivalent in the sense that they correspond to a unique natural shape for the rod. This natural shape can be computed efficiently by solving in sequence three linear initial value problems, starting from any framing of the input curve. We provide several numerical experiments to illustrate this uniqueness result, and finally discuss its potential impact on non-invasive parameter estimation and inverse design of thin elastic rods.

A Quasi-Dynamic Approach to modelling Hydrodynamic Focusing

NASA Astrophysics Data System (ADS)

Kommajosula, Aditya; Xu, Songzhe; Wu, Chueh-Yu; di Carlo, Dino; Ganapathysubramanian, Baskar; ComPM Lab Team; Di Carlo Lab Collaboration

2016-11-01

We examine a particle's tendency at different spatial locations to shift/rotate towards the equilibrium location, by constrained simulation. Although studies in the past have used this procedure in conjunction with FSI methods to great effect, the current work in 2D explores an alternative approach by utilizing a modified trust-region-based root-finding algorithm to solve for particle position and velocities at equilibrium, using "snapshots" of finite-element solutions to the steady-state Navier-Stokes equations iteratively over a computational domain attached to the particle reference frame. Through an assortment of test cases comprising circular and non-circular particle geometries, an incorporation of stability theory as applicable to dynamical systems is demonstrated, to locate the final focusing location and velocities. The results are compared with previous experimental/numerical reports, and found to be in close agreement. A thousand-fold increase is observed in computational time for the current workflow from its transient counterpart, for an illustrative case. The current framework is formulated in 2D for 3 Degrees-of-Freedom, and will be extended to 3D. This framework potentially allows for quick, high-throughput parametric space studies of equilibrium scaling laws.

A Pseudo-Vertical Equilibrium Model for Slow Gravity Drainage Dynamics

NASA Astrophysics Data System (ADS)

Becker, Beatrix; Guo, Bo; Bandilla, Karl; Celia, Michael A.; Flemisch, Bernd; Helmig, Rainer

2017-12-01

Vertical equilibrium (VE) models are computationally efficient and have been widely used for modeling fluid migration in the subsurface. However, they rely on the assumption of instant gravity segregation of the two fluid phases which may not be valid especially for systems that have very slow drainage at low wetting phase saturations. In these cases, the time scale for the wetting phase to reach vertical equilibrium can be several orders of magnitude larger than the time scale of interest, rendering conventional VE models unsuitable. Here we present a pseudo-VE model that relaxes the assumption of instant segregation of the two fluid phases by applying a pseudo-residual saturation inside the plume of the injected fluid that declines over time due to slow vertical drainage. This pseudo-VE model is cast in a multiscale framework for vertically integrated models with the vertical drainage solved as a fine-scale problem. Two types of fine-scale models are developed for the vertical drainage, which lead to two pseudo-VE models. Comparisons with a conventional VE model and a full multidimensional model show that the pseudo-VE models have much wider applicability than the conventional VE model while maintaining the computational benefit of the conventional VE model.

A Computational Study on the Ground and Excited States of Nickel Silicide.

PubMed

Schoendorff, George; Morris, Alexis R; Hu, Emily D; Wilson, Angela K

2015-09-17

Nickel silicide has been studied with a range of computational methods to determine the nature of the Ni-Si bond. Additionally, the physical effects that need to be addressed within calculations to predict the equilibrium bond length and bond dissociation energy within experimental error have been determined. The ground state is predicted to be a (1)Σ(+) state with a bond order of 2.41 corresponding to a triple bond with weak π bonds. It is shown that calculation of the ground state equilibrium geometry requires a polarized basis set and treatment of dynamic correlation including up to triple excitations with CR-CCSD(T)L resulting in an equilibrium bond length of only 0.012 Å shorter than the experimental bond length. Previous calculations of the bond dissociation energy resulted in energies that were only 34.8% to 76.5% of the experimental bond dissociation energy. It is shown here that use of polarized basis sets, treatment of triple excitations, correlation of the valence and subvalence electrons, and a Λ coupled cluster approach is required to obtain a bond dissociation energy that deviates as little as 1% from experiment.

Inverse design of an isotropic suspended Kirchhoff rod: theoretical and numerical results on the uniqueness of the natural shape

NASA Astrophysics Data System (ADS)

Bertails-Descoubes, Florence; Derouet-Jourdan, Alexandre; Romero, Victor; Lazarus, Arnaud

2018-04-01

Solving the equations for Kirchhoff elastic rods has been widely explored for decades in mathematics, physics and computer science, with significant applications in the modelling of thin flexible structures such as DNA, hair or climbing plants. As demonstrated in previous experimental and theoretical studies, the natural curvature plays an important role in the equilibrium shape of a Kirchhoff rod, even in the simple case where the rod is isotropic and suspended under gravity. In this paper, we investigate the reverse problem: can we characterize the natural curvature of a suspended isotropic rod, given an equilibrium curve? We prove that although there exists an infinite number of natural curvatures that are compatible with the prescribed equilibrium, they are all equivalent in the sense that they correspond to a unique natural shape for the rod. This natural shape can be computed efficiently by solving in sequence three linear initial value problems, starting from any framing of the input curve. We provide several numerical experiments to illustrate this uniqueness result, and finally discuss its potential impact on non-invasive parameter estimation and inverse design of thin elastic rods.

Development of the PARVMEC Code for Rapid Analysis of 3D MHD Equilibrium

NASA Astrophysics Data System (ADS)

Seal, Sudip; Hirshman, Steven; Cianciosa, Mark; Wingen, Andreas; Unterberg, Ezekiel; Wilcox, Robert; ORNL Collaboration

2015-11-01

The VMEC three-dimensional (3D) MHD equilibrium has been used extensively for designing stellarator experiments and analyzing experimental data in such strongly 3D systems. Recent applications of VMEC include 2D systems such as tokamaks (in particular, the D3D experiment), where application of very small (delB/B ~ 10-3) 3D resonant magnetic field perturbations render the underlying assumption of axisymmetry invalid. In order to facilitate the rapid analysis of such equilibria (for example, for reconstruction purposes), we have undertaken the task of parallelizing the VMEC code (PARVMEC) to produce a scalable and temporally rapidly convergent equilibrium code for use on parallel distributed memory platforms. The parallelization task naturally splits into three distinct parts 1) radial surfaces in the fixed-boundary part of the calculation; 2) two 2D angular meshes needed to compute the Green's function integrals over the plasma boundary for the free-boundary part of the code; and 3) block tridiagonal matrix needed to compute the full (3D) pre-conditioner near the final equilibrium state. Preliminary results show that scalability is achieved for tasks 1 and 3, with task 2 still nearing completion. The impact of this work on the rapid reconstruction of D3D plasmas using PARVMEC in the V3FIT code will be discussed. Work supported by U.S. DOE under Contract DE-AC05-00OR22725 with UT-Battelle, LLC.

Technical note: Evaluation of the simultaneous measurements of mesospheric OH, HO2, and O3 under a photochemical equilibrium assumption - a statistical approach

NASA Astrophysics Data System (ADS)

Kulikov, Mikhail Y.; Nechaev, Anton A.; Belikovich, Mikhail V.; Ermakova, Tatiana S.; Feigin, Alexander M.

2018-05-01

This Technical Note presents a statistical approach to evaluating simultaneous measurements of several atmospheric components under the assumption of photochemical equilibrium. We consider simultaneous measurements of OH, HO2, and O3 at the altitudes of the mesosphere as a specific example and their daytime photochemical equilibrium as an evaluating relationship. A simplified algebraic equation relating local concentrations of these components in the 50-100 km altitude range has been derived. The parameters of the equation are temperature, neutral density, local zenith angle, and the rates of eight reactions. We have performed a one-year simulation of the mesosphere and lower thermosphere using a 3-D chemical-transport model. The simulation shows that the discrepancy between the calculated evolution of the components and the equilibrium value given by the equation does not exceed 3-4 % in the full range of altitudes independent of season or latitude. We have developed a statistical Bayesian evaluation technique for simultaneous measurements of OH, HO2, and O3 based on the equilibrium equation taking into account the measurement error. The first results of the application of the technique to MLS/Aura data (Microwave Limb Sounder) are presented in this Technical Note. It has been found that the satellite data of the HO2 distribution regularly demonstrate lower altitudes of this component's mesospheric maximum. This has also been confirmed by model HO2 distributions and comparison with offline retrieval of HO2 from the daily zonal means MLS radiance.

An Initial Non-Equilibrium Porous-Media Model for CFD Simulation of Stirling Regenerators

NASA Technical Reports Server (NTRS)

Tew, Roy; Simon, Terry; Gedeon, David; Ibrahim, Mounir; Rong, Wei

2006-01-01

The objective of this paper is to define empirical parameters (or closwre models) for an initial thermai non-equilibrium porous-media model for use in Computational Fluid Dynamics (CFD) codes for simulation of Stirling regenerators. The two CFD codes currently being used at Glenn Research Center (GRC) for Stirling engine modeling are Fluent and CFD-ACE. The porous-media models available in each of these codes are equilibrium models, which assmne that the solid matrix and the fluid are in thermal equilibrium at each spatial location within the porous medium. This is believed to be a poor assumption for the oscillating-flow environment within Stirling regenerators; Stirling 1-D regenerator models, used in Stirling design, we non-equilibrium regenerator models and suggest regenerator matrix and gas average temperatures can differ by several degrees at a given axial location end time during the cycle. A NASA regenerator research grant has been providing experimental and computational results to support definition of various empirical coefficients needed in defining a noa-equilibrium, macroscopic, porous-media model (i.e., to define "closure" relations). The grant effort is being led by Cleveland State University, with subcontractor assistance from the University of Minnesota, Gedeon Associates, and Sunpower, Inc. Friction-factor and heat-transfer correlations based on data taken with the NASAlSunpower oscillating-flow test rig also provide experimentally based correlations that are useful in defining parameters for the porous-media model; these correlations are documented in Gedeon Associates' Sage Stirling-Code Manuals. These sources of experimentally based information were used to define the following terms and parameters needed in the non-equilibrium porous-media model: hydrodynamic dispersion, permeability, inertial coefficient, fluid effective thermal conductivity (including themal dispersion and estimate of tortuosity effects}, and fluid-solid heat transfer coefficient. Solid effective thermal conductivity (including the effect of tortuosity) was also estimated. Determination of the porous-media model parameters was based on planned use in a CFD model of Infinia's Stirling Technology Demonstration Convertor (TDC), which uses a random-fiber regenerator matrix. The non-equilibrium porous-media model presented is considered to be an initial, or "draft," model for possible incorporation in commercial CFD codes, with the expectation that the empirical parameters will likely need to be updated once resulting Stirling CFD model regenerator and engine results have been analyzed. The emphasis of the paper is on use of available data to define empirical parameters (and closure models) needed in a thermal non-equilibrium porous-media model for Stirling regenerator simulation. Such a model has not yet been implemented by the authors or their associates. However, it is anticipated that a thermal non-equilibrium model such as that presented here, when iacorporated in the CFD codes, will improve our ability to accurately model Stirling regenerators with CFD relative to current thermal-equilibrium porous-media models.

An Initial Non-Equilibrium Porous-Media Model for CFD Simulation of Stirling Regenerators

NASA Technical Reports Server (NTRS)

Tew, Roy C.; Simon, Terry; Gedeon, David; Ibrahim, Mounir; Rong, Wei

2006-01-01

The objective of this paper is to define empirical parameters for an initial thermal non-equilibrium porous-media model for use in Computational Fluid Dynamics (CFD) codes for simulation of Stirling regenerators. The two codes currently used at Glenn Research Center for Stirling modeling are Fluent and CFD-ACE. The codes porous-media models are equilibrium models, which assume solid matrix and fluid are in thermal equilibrium. This is believed to be a poor assumption for Stirling regenerators; Stirling 1-D regenerator models, used in Stirling design, use non-equilibrium regenerator models and suggest regenerator matrix and gas average temperatures can differ by several degrees at a given axial location and time during the cycle. Experimentally based information was used to define: hydrodynamic dispersion, permeability, inertial coefficient, fluid effective thermal conductivity, and fluid-solid heat transfer coefficient. Solid effective thermal conductivity was also estimated. Determination of model parameters was based on planned use in a CFD model of Infinia's Stirling Technology Demonstration Converter (TDC), which uses a random-fiber regenerator matrix. Emphasis is on use of available data to define empirical parameters needed in a thermal non-equilibrium porous media model for Stirling regenerator simulation. Such a model has not yet been implemented by the authors or their associates.

Adsorption of Uranyl Ions at the Nano-hydroxyapatite and Its Modification

NASA Astrophysics Data System (ADS)

Skwarek, Ewa; Gładysz-Płaska, Agnieszka; Bolbukh, Yuliia

2017-04-01

Nano-hydroxyapatite and its modification, hydroxyapatite with the excess of phosphorus (P-HAP) and hydroxyapatite with the carbon ions built into the structure (C-HAP), were prepared by the wet method. They were studied by means of XRD, accelerated surface area and porosimetry (ASAP), and SEM. The size of crystallites computed using the Scherrer method was nano-hydroxyapatite (HAP) = 20 nm; P-HAP—impossible to determine; C-HAP = 22 nm; nano-HAP/U(VI) = 13.7 nm; P-HAP/U(VI)—impossible to determine, C-HAP/U(VI) = 11 nm. There were determined basic parameters characterizing the double electrical layer at the nano-HAP/electrolyte and P-HAP/electrolyte, C-HAP/electrolyte inter faces: density of the surface charge and zeta potential. The adsorption properties of nano-HAP sorbent in relation to U(VI) ions were studied by the batch technique. The adsorption processes were rapid in the first 60 min and reached the equilibrium within approximately 120 min (for P-HAP) and 300 min (for C-HAP and nano-HAP). The adsorption process fitted well with the pseudo-second-order kinetics. The Freundlich, Langmuir-Freundlich, and Dubinin-Radushkevich models of isotherms were examined for their ability to the equilibrium sorption data. The maximum adsorption capabilities ( q m ) were 7.75 g/g for P-HAP, 1.77 g/g for C-HAP, and 0.8 g/g for HAP at 293 K.

Dynamics of Equilibrium Points in a Uniformly Rotating Second-Order and Degree Gravitational Field

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

Feng, Jinglang; Hou, Xiyun, E-mail: jinglang@nju.edu.cn, E-mail: silence@nju.edu.cn

2017-07-01

Using tools such as periodic orbits and invariant manifolds, the global dynamics around equilibrium points (EPs) in a rotating second-order and degree gravitational field are studied. For EPs on the long axis, planar and vertical periodic families are computed, and their stability properties are investigated. Invariant manifolds are also computed, and their relation to the first-order resonances is briefly discussed. For EPs on the short axis, planar and vertical periodic families are studied, with special emphasis on the genealogy of the planar periodic families. Our studies show that the global dynamics around EPs are highly similar to those around libration points in the circularmore » restricted three-body problem, such as spatial halo orbits, invariant manifolds, and the genealogy of planar periodic families.« less

An Analytical Investigation of Three General Methods of Calculating Chemical-Equilibrium Compositions

NASA Technical Reports Server (NTRS)

Zeleznik, Frank J.; Gordon, Sanford

1960-01-01

The Brinkley, Huff, and White methods for chemical-equilibrium calculations were modified and extended in order to permit an analytical comparison. The extended forms of these methods permit condensed species as reaction products, include temperature as a variable in the iteration, and permit arbitrary estimates for the variables. It is analytically shown that the three extended methods can be placed in a form that is independent of components. In this form the Brinkley iteration is identical computationally to the White method, while the modified Huff method differs only'slightly from these two. The convergence rates of the modified Brinkley and White methods are identical; and, further, all three methods are guaranteed to converge and will ultimately converge quadratically. It is concluded that no one of the three methods offers any significant computational advantages over the other two.

Efficient and robust relaxation procedures for multi-component mixtures including phase transition

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

Han, Ee, E-mail: eehan@math.uni-bremen.de; Hantke, Maren, E-mail: maren.hantke@ovgu.de; Müller, Siegfried, E-mail: mueller@igpm.rwth-aachen.de

We consider a thermodynamic consistent multi-component model in multi-dimensions that is a generalization of the classical two-phase flow model of Baer and Nunziato. The exchange of mass, momentum and energy between the phases is described by additional source terms. Typically these terms are handled by relaxation procedures. Available relaxation procedures suffer from efficiency and robustness resulting in very costly computations that in general only allow for one-dimensional computations. Therefore we focus on the development of new efficient and robust numerical methods for relaxation processes. We derive exact procedures to determine mechanical and thermal equilibrium states. Further we introduce a novelmore » iterative method to treat the mass transfer for a three component mixture. All new procedures can be extended to an arbitrary number of inert ideal gases. We prove existence, uniqueness and physical admissibility of the resulting states and convergence of our new procedures. Efficiency and robustness of the procedures are verified by means of numerical computations in one and two space dimensions. - Highlights: • We develop novel relaxation procedures for a generalized, thermodynamically consistent Baer–Nunziato type model. • Exact procedures for mechanical and thermal relaxation procedures avoid artificial parameters. • Existence, uniqueness and physical admissibility of the equilibrium states are proven for special mixtures. • A novel iterative method for mass transfer is introduced for a three component mixture providing a unique and admissible equilibrium state.« less

Strength measurement of optical fibers by bending

NASA Astrophysics Data System (ADS)

Srubshchik, Leonid S.

1999-01-01

A two-point bending technique has been used not only to measure the breaking stress of optical fiber but also to predict its static and dynamic fatigue. The present theory of this test is based on elastica theory of rod. However, within the limits of elastica theory the tensile and shear stresses cannot be determined. In this paper we study dynamic and static problems for optical fiber in the two- point bending test on the base of geometrically exact theory in which rod can suffer flexure, extension, and shear. We obtain the governing partial differential equations taking into account the fact that the lateral motion of the fiber is restrained by the presence of flat parallel plates. We develop the computational methods for solving the initial and equilibrium free-boundary nonlinear planar problems. We derive the formulas for predicting of the tensile strength from strength in the bending and calculate one example.

Image texture segmentation using a neural network

NASA Astrophysics Data System (ADS)

Sayeh, Mohammed R.; Athinarayanan, Ragu; Dhali, Pushpuak

1992-09-01

In this paper we use a neural network called the Lyapunov associative memory (LYAM) system to segment image texture into different categories or clusters. The LYAM system is constructed by a set of ordinary differential equations which are simulated on a digital computer. The clustering can be achieved by using a single tuning parameter in the simplest model. Pattern classes are represented by the stable equilibrium states of the system. Design of the system is based on synthesizing two local energy functions, namely, the learning and recall energy functions. Before the implementation of the segmentation process, a Gauss-Markov random field (GMRF) model is applied to the raw image. This application suitably reduces the image data and prepares the texture information for the neural network process. We give a simple image example illustrating the capability of the technique. The GMRF-generated features are also used for a clustering, based on the Euclidean distance.

A fully non-linear multi-species Fokker–Planck–Landau collision operator for simulation of fusion plasma

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

Hager, Robert, E-mail: rhager@pppl.gov; Yoon, E.S., E-mail: yoone@rpi.edu; Ku, S., E-mail: sku@pppl.gov

2016-06-15

Fusion edge plasmas can be far from thermal equilibrium and require the use of a non-linear collision operator for accurate numerical simulations. In this article, the non-linear single-species Fokker–Planck–Landau collision operator developed by Yoon and Chang (2014) [9] is generalized to include multiple particle species. The finite volume discretization used in this work naturally yields exact conservation of mass, momentum, and energy. The implementation of this new non-linear Fokker–Planck–Landau operator in the gyrokinetic particle-in-cell codes XGC1 and XGCa is described and results of a verification study are discussed. Finally, the numerical techniques that make our non-linear collision operator viable onmore » high-performance computing systems are described, including specialized load balancing algorithms and nested OpenMP parallelization. The collision operator's good weak and strong scaling behavior are shown.« less

Combining configurational energies and forces for molecular force field optimization

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

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Combining configurational energies and forces for molecular force field optimization

DOE PAGES

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

2017-07-21

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Quasinormal modes of a strongly coupled nonconformal plasma and approach to criticality

NASA Astrophysics Data System (ADS)

Betzios, Panagiotis; Gürsoy, Umut; Järvinen, Matti; Policastro, Giuseppe

2018-04-01

We study fluctuations around equilibrium in a class of strongly interacting nonconformal plasmas using holographic techniques. In particular, we calculate the quasinormal mode spectrum of black hole backgrounds that approach Chamblin-Reall plasmas in the IR. In a specific limit, related to the exact linear-dilaton background in string theory, we observe that the plasma approaches criticality and we obtain the quasinormal spectrum analytically. We regulate the critical limit by gluing the IR geometry that corresponds to the nonconformal plasma to a part of AdS space-time in the UV. Near criticality, the spectrum can still be computed analytically and we find two sets of quasinormal modes, related to the IR and UV parts of the geometry. In the critical limit, the quasinormal modes accumulate to form a branch cut in the correlators of the energy-momentum tensor on the real axis of the complex frequency plane.

Ab Initio Effective Rovibrational Hamiltonians for Non-Rigid Molecules via Curvilinear VMP2

NASA Astrophysics Data System (ADS)

Changala, Bryan; Baraban, Joshua H.

2017-06-01

Accurate predictions of spectroscopic constants for non-rigid molecules are particularly challenging for ab initio theory. For all but the smallest systems, ``brute force'' diagonalization of the full rovibrational Hamiltonian is computationally prohibitive, leaving us at the mercy of perturbative approaches. However, standard perturbative techniques, such as second order vibrational perturbation theory (VPT2), are based on the approximation that a molecule makes small amplitude vibrations about a well defined equilibrium structure. Such assumptions are physically inappropriate for non-rigid systems. In this talk, we will describe extensions to curvilinear vibrational Møller-Plesset perturbation theory (VMP2) that account for rotational and rovibrational effects in the molecular Hamiltonian. Through several examples, we will show that this approach provides predictions to nearly microwave accuracy of molecular constants including rotational and centrifugal distortion parameters, Coriolis coupling constants, and anharmonic vibrational and tunneling frequencies.

Interfacial Force Field Characterization in a Constrained Vapor Bubble Thermosyphon

NASA Technical Reports Server (NTRS)

DasGupta, Sunando; Plawsky, Joel L.; Wayner, Peter C., Jr.

1995-01-01

Isothermal profiles of the extended meniscus in a quartz cuvette were measured in the earth's gravitational field using an image-analyzing interferometer that is based on computer-enhanced video microscopy of the naturally occurring interference fringes. These profiles are a function of the stress field. Experimentally, the augmented Young-Laplace equation is an excellent model for the force field at the solid-liquid-vapor interfaces for heptane and pentane menisci on quartz and tetradecane on SFL6. The effects of refractive indices of the solid and liquid on the measurement techniques were demonstrated. Experimentally obtained values of the disjoining pressure and dispersion constants were compared to those predicted from the Dzyaloshinskii - Lifshitz - Pilaevskii theory for an ideal surface and reasonable agreements were obtained. A parameter introduced gives a quantitative measurement of the closeness of the system to equilibrium. The nonequilibrium behavior of this parameter is also presented

Studies on molecular structure, vibrational spectra and molecular docking analysis of 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate

NASA Astrophysics Data System (ADS)

Suresh, D. M.; Amalanathan, M.; Hubert Joe, I.; Bena Jothy, V.; Diao, Yun-Peng

2014-09-01

The molecular structure, vibrational analysis and molecular docking analysis of the 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate (MDDNAB) molecule have been carried out using FT-IR and FT-Raman spectroscopic techniques and DFT method. The equilibrium geometry, harmonic vibrational wave numbers, various bonding features have been computed using density functional method. The calculated molecular geometry has been compared with experimental data. The detailed interpretation of the vibrational spectra has been carried out by using VEDA program. The hyper-conjugative interactions and charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The simulated FT-IR and FT-Raman spectra satisfactorily coincide with the experimental spectra. The PES and charge analysis have been made. The molecular docking was done to identify the binding energy and the Hydrogen bonding with the cancer protein molecule.

Self-Organization of Metal Nanoparticles in Light: Electrodynamics-Molecular Dynamics Simulations and Optical Binding Experiments.

PubMed

McCormack, Patrick; Han, Fei; Yan, Zijie

2018-02-01

Light-driven self-organization of metal nanoparticles (NPs) can lead to unique optical matter systems, yet simulation of such self-organization (i.e., optical binding) is a complex computational problem that increases nonlinearly with system size. Here we show that a combined electrodynamics-molecular dynamics simulation technique can simulate the trajectories and predict stable configurations of silver NPs in optical fields. The simulated dynamic equilibrium of a two-NP system matches the probability density of oscillations for two optically bound NPs obtained experimentally. The predicted stable configurations for up to eight NPs are further compared to experimental observations of silver NP clusters formed by optical binding in a Bessel beam. All configurations are confirmed to form in real systems, including pentagonal clusters with five-fold symmetry. Our combined simulations and experiments have revealed a diverse optical matter system formed by anisotropic optical binding interactions, providing a new strategy to discover artificial materials.

Binding of warfarin influences the acid-base equilibrium of H242 in sudlow site I of human serum albumin.

PubMed

Perry, Jennifer L; Goldsmith, Michael R; Williams, T Richard; Radack, Kyle P; Christensen, Trine; Gorham, Justin; Pasquinelli, Melissa A; Toone, Eric J; Beratan, David N; Simon, John D

2006-01-01

Sudlow Site I of human serum albumin (HSA) is located in subdomain IIA of the protein and serves as a binding cavity for a variety of ligands. In this study, the binding of warfarin (W) is examined using computational techniques and isothermal titration calorimetry (ITC). The structure of the docked warfarin anion (W-) to Site I is similar to that revealed by X-ray crystallography, with a calculated binding constant of 5.8 x 10(5) M(-1). ITC experiments (pH 7.13 and I = 0.1) carried out in three different buffers (MOPs, phosphate and Tris) reveal binding of W- is accompanied by uptake of 0.30+/-0.02 protons from the solvent. This measurement suggests that the binding of W- is stabilized by an ion-pair interaction between protonated H242 and the phenoxide group of W-.

The mode branching route to localization of the finite-length floating elastica

NASA Astrophysics Data System (ADS)

Rivetti, Marco; Neukirch, Sébastien

2014-09-01

The beam on elastic foundation is a general model used in physical, biological, and technological problems to study delamination, wrinkling, or pattern formation. Recent focus has been given to the buckling of beams deposited on liquid baths, and in the regime where the beam is soft compared to hydrostatic forces the wrinkling pattern observed at buckling has been shown to lead to localization of the deformation when the confinement is increased. Here we perform a global study of the general case where the intensity of the liquid foundation and the confinement are both varied. We compute equilibrium and stability of the solutions and unravel secondary bifurcations that play a major role in the route to localization. Moreover we classify the post-buckling solutions and shed light on the mechanism leading to localization. Finally, using an asymptotic technique imported from fluid mechanics, we derive an approximated analytical solution to the problem.

Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins.

PubMed

Langó, Tamás; Róna, Gergely; Hunyadi-Gulyás, Éva; Turiák, Lilla; Varga, Julia; Dobson, László; Várady, György; Drahos, László; Vértessy, Beáta G; Medzihradszky, Katalin F; Szakács, Gergely; Tusnády, Gábor E

2017-02-13

Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins.

The development of flux-split algorithms for flows with non-equilibrium thermodynamics and chemical reactions

NASA Technical Reports Server (NTRS)

Grossman, B.; Cinella, P.

1988-01-01

A finite-volume method for the numerical computation of flows with nonequilibrium thermodynamics and chemistry is presented. A thermodynamic model is described which simplifies the coupling between the chemistry and thermodynamics and also results in the retention of the homogeneity property of the Euler equations (including all the species continuity and vibrational energy conservation equations). Flux-splitting procedures are developed for the fully coupled equations involving fluid dynamics, chemical production and thermodynamic relaxation processes. New forms of flux-vector split and flux-difference split algorithms are embodied in a fully coupled, implicit, large-block structure, including all the species conservation and energy production equations. Several numerical examples are presented, including high-temperature shock tube and nozzle flows. The methodology is compared to other existing techniques, including spectral and central-differenced procedures, and favorable comparisons are shown regarding accuracy, shock-capturing and convergence rates.

Natural bond orbital analysis, electronic structure, non-linear properties and vibrational spectral analysis of L-histidinium bromide monohydrate: a density functional theory.

PubMed

Sajan, D; Joseph, Lynnette; Vijayan, N; Karabacak, M

2011-10-15

The spectroscopic properties of the crystallized nonlinear optical molecule L-histidinium bromide monohydrate (abbreviated as L-HBr-mh) have been recorded and analyzed by FT-IR, FT-Raman and UV techniques. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability of the crystal were calculated with the help of density functional theory computations. The optimized geometric bond lengths and bond angles obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The natural bond orbital (NBO) analysis confirms the occurrence of strong intra and intermolecular N-H⋯O hydrogen bonding. Copyright © 2011 Elsevier B.V. All rights reserved.

NUMERICAL TECHNIQUES TO SOLVE CONDENSATIONAL AND DISSOLUTIONAL GROWTH EQUATIONS WHEN GROWTH IS COUPLED TO REVERSIBLE REACTIONS (R823186)

EPA Science Inventory

Noniterative, unconditionally stable numerical techniques for solving condensational and
dissolutional growth equations are given. Growth solutions are compared to Gear-code solutions for
three cases when growth is coupled to reversible equilibrium chemistry. In all cases, ...

HST3D; a computer code for simulation of heat and solute transport in three-dimensional ground-water flow systems

USGS Publications Warehouse

Kipp, K.L.

1987-01-01

The Heat- and Soil-Transport Program (HST3D) simulates groundwater flow and associated heat and solute transport in three dimensions. The three governing equations are coupled through the interstitial pore velocity, the dependence of the fluid density on pressure, temperature, the solute-mass fraction , and the dependence of the fluid viscosity on temperature and solute-mass fraction. The solute transport equation is for only a single, solute species with possible linear equilibrium sorption and linear decay. Finite difference techniques are used to discretize the governing equations using a point-distributed grid. The flow-, heat- and solute-transport equations are solved , in turn, after a particle Gauss-reduction scheme is used to modify them. The modified equations are more tightly coupled and have better stability for the numerical solutions. The basic source-sink term represents wells. A complex well flow model may be used to simulate specified flow rate and pressure conditions at the land surface or within the aquifer, with or without pressure and flow rate constraints. Boundary condition types offered include specified value, specified flux, leakage, heat conduction, and approximate free surface, and two types of aquifer influence functions. All boundary conditions can be functions of time. Two techniques are available for solution of the finite difference matrix equations. One technique is a direct-elimination solver, using equations reordered by alternating diagonal planes. The other technique is an iterative solver, using two-line successive over-relaxation. A restart option is available for storing intermediate results and restarting the simulation at an intermediate time with modified boundary conditions. This feature also can be used as protection against computer system failure. Data input and output may be in metric (SI) units or inch-pound units. Output may include tables of dependent variables and parameters, zoned-contour maps, and plots of the dependent variables versus time. (Lantz-PTT)

A numerical tool for the calculation of non-equilibrium ionisation states in the solar corona and other astrophysical plasma environments

NASA Astrophysics Data System (ADS)

Bradshaw, S. J.

2009-07-01

Context: The effects of non-equilibrium processes on the ionisation state of strongly emitting elements in the solar corona can be extremely difficult to assess and yet they are critically important. For example, there is much interest in dynamic heating events localised in the solar corona because they are believed to be responsible for its high temperature and yet recent work has shown that the hottest (≥107 K) emission predicted to be associated with these events can be observationally elusive due to the difficulty of creating the highly ionised states from which the expected emission arises. This leads to the possibility of observing instruments missing such heating events entirely. Aims: The equations describing the evolution of the ionisaton state are a very stiff system of coupled, partial differential equations whose solution can be numerically challenging and time-consuming. Without access to specialised codes and significant computational resources it is extremely difficult to avoid the assumption of an equilibrium ionisation state even when it clearly cannot be justified. The aim of the current work is to develop a computational tool to allow straightforward calculation of the time-dependent ionisation state for a wide variety of physical circumstances. Methods: A numerical model comprising the system of time-dependent ionisation equations for a particular element and tabulated values of plasma temperature as a function of time is developed. The tabulated values can be the solutions of an analytical model, the output from a numerical code or a set of observational measurements. An efficient numerical method to solve the ionisation equations is implemented. Results: A suite of tests is designed and run to demonstrate that the code provides reliable and accurate solutions for a number of scenarios including equilibration of the ion population and rapid heating followed by thermal conductive cooling. It is found that the solver can evolve the ionisation state to recover exactly the equilibrium state found by an independent, steady-state solver for all temperatures, resolve the extremely small ionisation/recombination timescales associated with rapid temperature changes at high densities, and provide stable and accurate solutions for both dominant and minor ion population fractions. Rapid heating and cooling of low to moderate density plasma is characterised by significant non-equilibrium ionisation conditions. The effective ionisation temperatures are significantly lower than the electron temperature and the values found are in close agreement with the previous work of others. At the very highest densities included in the present study an assumption of equilibrium ionisation is found to be robust. Conclusions: The computational tool presented here provides a straightforward and reliable way to calculate ionisation states for a wide variety of physical circumstances. The numerical code gives results that are accurate and consistent with previous studies, has relatively undemanding computational requirements and is freely available from the author.

Development of numerical techniques for simulation of magnetogasdynamics and hypersonic chemistry

NASA Astrophysics Data System (ADS)

Damevin, Henri-Marie

Magnetogasdynamics, the science concerned with the mutual interaction between electromagnetic field and flow of electrically conducting gas, offers promising advances in flow control and propulsion of future hypersonic vehicles. Numerical simulations are essential for understanding phenomena, and for research and development. The current dissertation is devoted to the development and validation of numerical algorithms for the solution of multidimensional magnetogasdynamic equations and the simulation of hypersonic high-temperature effects. Governing equations are derived, based on classical magnetogasdynamic assumptions. Two sets of equations are considered, namely the full equations and equations in the low magnetic Reynolds number approximation. Equations are expressed in a suitable formulation for discretization by finite differences in a computational space. For the full equations, Gauss law for magnetism is enforced using Powell's methodology. The time integration method is a four-stage modified Runge-Kutta scheme, amended with a Total Variation Diminishing model in a postprocessing stage. The eigensystem, required for the Total Variation Diminishing scheme, is derived in generalized three-dimensional coordinate system. For the simulation of hypersonic high-temperature effects, two chemical models are utilized, namely a nonequilibrium model and an equilibrium model. A loosely coupled approach is implemented to communicate between the magnetogasdynamic equations and the chemical models. The nonequilibrium model is a one-temperature, five-species, seventeen-reaction model solved by an implicit flux-vector splitting scheme. The chemical equilibrium model computes thermodynamics properties using curve fit procedures. Selected results are provided, which explore the different features of the numerical algorithms. The shock-capturing properties are validated for shock-tube simulations using numerical solutions reported in the literature. The computations of superfast flows over corners and in convergent channels demonstrate the performances of the algorithm in multiple dimensions. The implementation of diffusion terms is validated by solving the magnetic Rayleigh problem and Hartmann problem, for which analytical solutions are available. Prediction of blunt-body type flow are investigated and compared with numerical solutions reported in the literature. The effectiveness of the chemical models for hypersonic flow over blunt body is examined in various flow conditions. It is shown that the proposed schemes perform well in a variety of test cases, though some limitations have been identified.

CFD analysis of laboratory scale phase equilibrium cell operation

NASA Astrophysics Data System (ADS)

Jama, Mohamed Ali; Nikiforow, Kaj; Qureshi, Muhammad Saad; Alopaeus, Ville

2017-10-01

For the modeling of multiphase chemical reactors or separation processes, it is essential to predict accurately chemical equilibrium data, such as vapor-liquid or liquid-liquid equilibria [M. Šoóš et al., Chem. Eng. Process.: Process Intensif. 42(4), 273-284 (2003)]. The instruments used in these experiments are typically designed based on previous experiences, and their operation verified based on known equilibria of standard components. However, mass transfer limitations with different chemical systems may be very different, potentially falsifying the measured equilibrium compositions. In this work, computational fluid dynamics is utilized to design and analyze laboratory scale experimental gas-liquid equilibrium cell for the first time to augment the traditional analysis based on plug flow assumption. Two-phase dilutor cell, used for measuring limiting activity coefficients at infinite dilution, is used as a test case for the analysis. The Lagrangian discrete model is used to track each bubble and to study the residence time distribution of the carrier gas bubbles in the dilutor cell. This analysis is necessary to assess whether the gas leaving the cell is in equilibrium with the liquid, as required in traditional analysis of such apparatus. Mass transfer for six different bio-oil compounds is calculated to determine the approach equilibrium concentration. Also, residence times assuming plug flow and ideal mixing are used as reference cases to evaluate the influence of mixing on the approach to equilibrium in the dilutor. Results show that the model can be used to predict the dilutor operating conditions for which each of the studied gas-liquid systems reaches equilibrium.

CFD analysis of laboratory scale phase equilibrium cell operation.

PubMed

Jama, Mohamed Ali; Nikiforow, Kaj; Qureshi, Muhammad Saad; Alopaeus, Ville

2017-10-01

For the modeling of multiphase chemical reactors or separation processes, it is essential to predict accurately chemical equilibrium data, such as vapor-liquid or liquid-liquid equilibria [M. Šoóš et al., Chem. Eng. Process Intensif. 42(4), 273-284 (2003)]. The instruments used in these experiments are typically designed based on previous experiences, and their operation verified based on known equilibria of standard components. However, mass transfer limitations with different chemical systems may be very different, potentially falsifying the measured equilibrium compositions. In this work, computational fluid dynamics is utilized to design and analyze laboratory scale experimental gas-liquid equilibrium cell for the first time to augment the traditional analysis based on plug flow assumption. Two-phase dilutor cell, used for measuring limiting activity coefficients at infinite dilution, is used as a test case for the analysis. The Lagrangian discrete model is used to track each bubble and to study the residence time distribution of the carrier gas bubbles in the dilutor cell. This analysis is necessary to assess whether the gas leaving the cell is in equilibrium with the liquid, as required in traditional analysis of such apparatus. Mass transfer for six different bio-oil compounds is calculated to determine the approach equilibrium concentration. Also, residence times assuming plug flow and ideal mixing are used as reference cases to evaluate the influence of mixing on the approach to equilibrium in the dilutor. Results show that the model can be used to predict the dilutor operating conditions for which each of the studied gas-liquid systems reaches equilibrium.

Application of a fast Newton-Krylov solver for equilibrium simulations of phosphorus and oxygen

NASA Astrophysics Data System (ADS)

Fu, Weiwei; Primeau, François

2017-11-01

Model drift due to inadequate spinup is a serious problem that complicates the interpretation of climate change simulations. Even after a 300 year spinup we show that solutions are not only still drifting but often drifting away from their eventual equilibrium over large parts of the ocean. Here we present a Newton-Krylov solver for computing cyclostationary equilibrium solutions of a biogeochemical model for the cycling of phosphorus and oxygen. In addition to using previously developed preconditioning strategies - time-averaging and coarse-graining the Jacobian matrix - we also introduce a new strategy: the adiabatic elimination of a fast variable (particulate organic phosphorus) by slaving it to a slow variable (dissolved inorganic phosphorus). We use transport matrices derived from the Community Earth System Model (CESM) with a nominal horizontal resolution of 1° × 1° and 60 vertical levels to implement and test the solver. We find that the new solver obtains seasonally-varying equilibrium solutions with no visible drift using no more than 80 simulation years.

Equilibrium shapes of a heterogeneous bubble in an electric field: a variational formulation and numerical verifications

NASA Astrophysics Data System (ADS)

Wang, Hanxiong; Liu, Liping; Liu, Dong

2017-03-01

The equilibrium shape of a bubble/droplet in an electric field is important for electrowetting over dielectrics (EWOD), electrohydrodynamic (EHD) enhancement for heat transfer and electro-deformation of a single biological cell among others. In this work, we develop a general variational formulation in account of electro-mechanical couplings. In the context of EHD, we identify the free energy functional and the associated energy minimization problem that determines the equilibrium shape of a bubble in an electric field. Based on this variational formulation, we implement a fixed mesh level-set gradient method for computing the equilibrium shapes. This numerical scheme is efficient and validated by comparing with analytical solutions at the absence of electric field and experimental results at the presence of electric field. We also present simulation results for zero gravity which will be useful for space applications. The variational formulation and numerical scheme are anticipated to have broad applications in areas of EWOD, EHD and electro-deformation in biomechanics.

Evolution of recombination rates in a multi-locus, haploid-selection, symmetric-viability model.

PubMed

Chasnov, J R; Ye, Felix Xiaofeng

2013-02-01

A fast algorithm for computing multi-locus recombination is extended to include a recombination-modifier locus. This algorithm and a linear stability analysis is used to investigate the evolution of recombination rates in a multi-locus, haploid-selection, symmetric-viability model for which stable equilibria have recently been determined. When the starting equilibrium is symmetric with two selected loci, we show analytically that modifier alleles that reduce recombination always invade. When the starting equilibrium is monomorphic, and there is a fixed nonzero recombination rate between the modifier locus and the selected loci, we determine analytical conditions for which a modifier allele can invade. In particular, we show that a gap exists between the recombination rates of modifiers that can invade and the recombination rate that specifies the lower stability boundary of the monomorphic equilibrium. A numerical investigation shows that a similar gap exists in a weakened form when the starting equilibrium is fully polymorphic but asymmetric. Copyright © 2012 Elsevier Inc. All rights reserved.

Multistability of memristive Cohen-Grossberg neural networks with non-monotonic piecewise linear activation functions and time-varying delays.

PubMed

Nie, Xiaobing; Zheng, Wei Xing; Cao, Jinde

2015-11-01

The problem of coexistence and dynamical behaviors of multiple equilibrium points is addressed for a class of memristive Cohen-Grossberg neural networks with non-monotonic piecewise linear activation functions and time-varying delays. By virtue of the fixed point theorem, nonsmooth analysis theory and other analytical tools, some sufficient conditions are established to guarantee that such n-dimensional memristive Cohen-Grossberg neural networks can have 5(n) equilibrium points, among which 3(n) equilibrium points are locally exponentially stable. It is shown that greater storage capacity can be achieved by neural networks with the non-monotonic activation functions introduced herein than the ones with Mexican-hat-type activation function. In addition, unlike most existing multistability results of neural networks with monotonic activation functions, those obtained 3(n) locally stable equilibrium points are located both in saturated regions and unsaturated regions. The theoretical findings are verified by an illustrative example with computer simulations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Assembly of hard spheres in a cylinder: a computational and experimental study.

PubMed

Fu, Lin; Bian, Ce; Shields, C Wyatt; Cruz, Daniela F; López, Gabriel P; Charbonneau, Patrick

2017-05-14

Hard spheres are an important benchmark of our understanding of natural and synthetic systems. In this work, colloidal experiments and Monte Carlo simulations examine the equilibrium and out-of-equilibrium assembly of hard spheres of diameter σ within cylinders of diameter σ≤D≤ 2.82σ. Although phase transitions formally do not exist in such systems, marked structural crossovers can nonetheless be observed. Over this range of D, we find in simulations that structural crossovers echo the structural changes in the sequence of densest packings. We also observe that the out-of-equilibrium self-assembly depends on the compression rate. Slow compression approximates equilibrium results, while fast compression can skip intermediate structures. Crossovers for which no continuous line-slip exists are found to be dynamically unfavorable, which is the main source of this difference. Results from colloidal sedimentation experiments at low diffusion rate are found to be consistent with the results of fast compressions, as long as appropriate boundary conditions are used.

A Bayesian test for Hardy–Weinberg equilibrium of biallelic X-chromosomal markers

PubMed Central

Puig, X; Ginebra, J; Graffelman, J

2017-01-01

The X chromosome is a relatively large chromosome, harboring a lot of genetic information. Much of the statistical analysis of X-chromosomal information is complicated by the fact that males only have one copy. Recently, frequentist statistical tests for Hardy–Weinberg equilibrium have been proposed specifically for dealing with markers on the X chromosome. Bayesian test procedures for Hardy–Weinberg equilibrium for the autosomes have been described, but Bayesian work on the X chromosome in this context is lacking. This paper gives the first Bayesian approach for testing Hardy–Weinberg equilibrium with biallelic markers at the X chromosome. Marginal and joint posterior distributions for the inbreeding coefficient in females and the male to female allele frequency ratio are computed, and used for statistical inference. The paper gives a detailed account of the proposed Bayesian test, and illustrates it with data from the 1000 Genomes project. In that implementation, a novel approach to tackle multiple testing from a Bayesian perspective through posterior predictive checks is used. PMID:28900292