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Sample records for reduction dynamical simulation

  1. Decoherence Allows Model Reduction in Nonadiabatic Dynamics Simulations.

    PubMed

    Trivedi, Dhara J; Prezhdo, Oleg V

    2015-08-20

    A nonadiabatic (NA) molecular dynamics (MD) simulation requires calculation of NA coupling matrix elements, the number of which scales as a square of the number of basis states. The basis size can be huge in studies of nanoscale materials, and calculation of the NA couplings can present a significant bottleneck. A quantum-classical approximation, NAMD overestimates coherence in the quantum, electronic subsystem, requiring decoherence correction. Generally, decoherence times decrease with increasing energy separation between pairs of states forming coherent superpositions. Since rapid decoherence stops quantum dynamics, one expects that decoherence-corrected NAMD can eliminate the need for calculation of NA couplings between energetically distant states, notably reducing the computational cost. Considering several types of dynamics in a semiconductor quantum dot, we demonstrate that indeed, decoherence allows one to reduce the number of needed NA coupling matrix elements. If the energy levels are spaced closer than 0.1 eV, one obtains good results while including only three nearest-neighbor couplings, and in some cases even with just the first nearest-neighbor coupling scheme. If the energy levels are spaced by about 0.4 eV, the nearest-neighbor model fails, while three or more nearest-neighbor schemes also provide good results. In comparison, the results of NAMD simulation without decoherence vary continuously with changes in the number of NA couplings. Thus, decoherence effects induced by coupling to a quantum-mechanical environment not only provide the physical mechanism for NAMD trajectory branding and improve the accuracy of NAMD simulations, but also afford significant computational savings. PMID:26221974

  2. Dynamical system modeling via signal reduction and neural network simulation

    SciTech Connect

    Paez, T.L.; Hunter, N.F.

    1997-11-01

    Many dynamical systems tested in the field and the laboratory display significant nonlinear behavior. Accurate characterization of such systems requires modeling in a nonlinear framework. One construct forming a basis for nonlinear modeling is that of the artificial neural network (ANN). However, when system behavior is complex, the amount of data required to perform training can become unreasonable. The authors reduce the complexity of information present in system response measurements using decomposition via canonical variate analysis. They describe a method for decomposing system responses, then modeling the components with ANNs. A numerical example is presented, along with conclusions and recommendations.

  3. A system dynamics-based environmental performance simulation of construction waste reduction management in China.

    PubMed

    Ding, Zhikun; Yi, Guizhen; Tam, Vivian W Y; Huang, Tengyue

    2016-05-01

    A huge amount of construction waste has been generated from increasingly higher number of construction activities than in the past, which has significant negative impacts on the environment if they are not properly managed. Therefore, effective construction waste management is of primary importance for future sustainable development. Based on the theory of planned behaviors, this paper develops a system dynamic model of construction waste reduction management at the construction phase to simulate the environmental benefits of construction waste reduction management. The application of the proposed model is shown using a case study in Shenzhen, China. Vensim is applied to simulate and analyze the model. The simulation results indicate that source reduction is an effective waste reduction measure which can reduce 27.05% of the total waste generation. Sorting behaviors are a premise for improving the construction waste recycling and reuse rates which account for 15.49% of the total waste generated. The environmental benefits of source reduction outweigh those of sorting behaviors. Therefore, to achieve better environmental performance of the construction waste reduction management, attention should be paid to source reduction such as low waste technologies and on-site management performance. In the meantime, sorting behaviors encouragement such as improving stakeholders' waste awareness, refining regulations, strengthening government supervision and controlling illegal dumping should be emphasized. PMID:26969286

  4. Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations.

    PubMed

    Jin, Haiyun; Goyal, Puja; Das, Akshaya Kumar; Gaus, Michael; Meuwly, Markus; Cui, Qiang

    2016-03-01

    We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution and protein. The properties of interest include the coordination structure of copper in different oxidation states in water or in a protein (plastocyanin) active site, the reduction potential of the copper ion in different environments, and the environmental response to copper oxidation. The DFTB3/MM and VALBOND simulation results are compared to DFT/MM simulations and experimental results whenever possible. For a copper ion in aqueous solution, DFTB3/MM results are generally close to B3LYP/MM with a medium basis, including both solvation structure and reduction potential for Cu(II); for Cu(I), however, DFTB3/MM finds a two-water coordination, similar to previous Born-Oppenheimer molecular dynamics simulations using BLYP and HSE, whereas B3LYP/MM leads to a tetrahedron coordination. For a tetraammonia copper complex in aqueous solution, VALBOND and DFTB3/MM are consistent in terms of both structural and dynamical properties of solvent near copper for both oxidation states. For copper reduction in plastocyanin, DFTB3/MM simulations capture the key properties of the active site, and the computed reduction potential and reorganization energy are in fair agreement with experiment, especially when the periodic boundary condition is used. Overall, the study supports the value of VALBOND and DFTB3(/MM) for the analysis of fundamental copper redox chemistry in water and protein, and the results also help highlight areas where further improvements in these methods are desirable. PMID:26624804

  5. Structured building model reduction toward parallel simulation

    SciTech Connect

    Dobbs, Justin R.; Hencey, Brondon M.

    2013-08-26

    Building energy model reduction exchanges accuracy for improved simulation speed by reducing the number of dynamical equations. Parallel computing aims to improve simulation times without loss of accuracy but is poorly utilized by contemporary simulators and is inherently limited by inter-processor communication. This paper bridges these disparate techniques to implement efficient parallel building thermal simulation. We begin with a survey of three structured reduction approaches that compares their performance to a leading unstructured method. We then use structured model reduction to find thermal clusters in the building energy model and allocate processing resources. Experimental results demonstrate faster simulation and low error without any interprocessor communication.

  6. Experiment and computational fluid dynamics (CFD) simulation of urea-based selective noncatalytic reduction (SNCR) in a pilot-scale flow reactor

    SciTech Connect

    Thanh D.B. Nguyen; Young-Il Lim; Seong-Joon Kim; Won-Hyeon Eom; Kyung-Seun Yoo

    2008-11-15

    A turbulent reacting flow computational fluid dynamics (CFD) model involving a droplet size distribution function in the discrete droplet phase is first built for selective noncatalytic reduction (SNCR) processes using urea solution as a NOx removal reagent. The model is validated with the experimental data obtained from a pilot-scale urea-based SNCR reactor installed with a 150 kW gas burner. New kinetic parameters of seven chemical reactions for the urea-based NOx reduction are identified and incorporated into the three-dimensional turbulent flow CFD model. The two-phase droplet model with the non-uniform droplet size is also combined with the CFD model to predict the trajectory of the droplets and to examine the mixing between the flue gas and reagents. The maximum NO reduction efficiency of about 80%, experimentally measured at the reactor outlet, is obtained at 940{degree}C and a normalized stoichiometric ratio (NSR) = 2.0 under the conditions of 11% excess air and low CO concentration (10-15 ppm). At the reaction temperature of 940{degree}C, the difference of a maximum of 10% between experiments and simulations of the NO reduction percentage is observed for NSR = 1.0, 1.5, and 2.0. The ammonia slip is overestimated in CFD simulation at low temperatures, especially lower than 900{degree}C. However, the CFD simulation results above 900{degree}C show a reasonable agreement with the experimental data of NOx reduction and ammonia slip as a function of the NSR. 31 refs., 3 figs., 6 tabs.

  7. Process simulation of aluminum reduction cells

    SciTech Connect

    Tabsh, I.; Dupuis, M.; Gomes, A.

    1996-10-01

    A program was developed to model the dynamic behavior of an aluminum reduction cell. The program simulates the physical process by solving the heat and mass balance equations that characterize the behavior of eleven chemical species in the system. It also models operational events (such as metal tapping, anode change, etc.) and the process control logic including various alumina feeding policies and anode effect quenching. The program is a PC based Windows{reg_sign} application that takes full advantage of the Windows user interface. This paper describes the implementation of the process model and the control logic. Various results using the simulation are compared to measured data.

  8. Understanding the structural changes that take place in a polypyrrole film during its oxi-reduction process: a molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Lopez Cascales, J. J.; Otero, T. F.

    2005-06-01

    Oxi-reduction processes of conducting polymer are the base of a great number of technological developments in the fields of polymeric actuators (artificial muscles) or smart windows. Hence, the understanding the structural changes that take place in the polymer as a function of its oxidation seems to be crucial for a proper understanding of these complicated systems. In this sense, a model with atomic detail has been simulated by Molecular Dynamics Simulation, which provides an insight of how the electrical response of the system depends of the structural changes that take place inside the polymer. In this regard, the conducting polymer, water and counterions were modeled with atomic detail with the goal of obtaining an insight of the ring orientation and reorientational relaxation time of the pyrrole rings at different oxidation states of the polymer. In addition, we studied how the above properties are greatly affected by the oxidation state of the polymer and the variation these properties changes from the polypyrrole/water interface to the polypyrrole bulk. Finally, we correlated the reorientational dynamics of pyrrole rings with the oxidation kinetic observed from a macroscopic point of view.

  9. Tether Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    1987-01-01

    The proceedings of the conference are presented. The objective was to provide a forum for the discussion of the structure and status of existing computer programs which are used to simulate the dynamics of a variety of tether applications in space. A major topic was different simulation models and the process of validating them. Guidance on future work in these areas was obtained from a panel discussion; the panel was composed of resource and technical managers and dynamic analysts in the tether field. The conclusions of this panel are also presented.

  10. Study of flow behaviors on single-cell manipulation and shear stress reduction in microfluidic chips using computational fluid dynamics simulations

    PubMed Central

    Shen, Feng; Li, XiuJun; Li, Paul C. H.

    2014-01-01

    Various single-cell retention structures (SCRSs) were reported for analysis of single cells within microfluidic devices. Undesirable flow behaviors within micro-environments not only influence single-cell manipulation and retention significantly but also lead to cell damage, biochemical heterogeneity among different individual cells (e.g., different cell signaling pathways induced by shear stress). However, the fundamentals in flow behaviors for single-cell manipulation and shear stress reduction, especially comparison of these behaviors in different microstructures, were not fully investigated in previous reports. Herein, flow distribution and induced shear stress in two different single-cell retention structures (SCRS I and SCRS II) were investigated in detail to study their effects on single-cell trapping using computational fluid dynamics (CFD) methods. The results were successfully verified by experimental results. Comparison between these two SCRS shows that the wasp-waisted configuration of SCRS II has a better performance in trapping and manipulating long cylinder-shaped cardiac myocytes and provides a safer “harbor” for fragile cells to prevent cell damage due to the shear stress induced from strong flows. The simulation results have not only explained flow phenomena observed in experiments but also predict new flow phenomena, providing guidelines for new chip design and optimization, and a better understanding of the cell micro-environment and fundamentals of microfluidic flows in single-cell manipulation and analysis. PMID:24753729

  11. Dynamic load simulator

    NASA Technical Reports Server (NTRS)

    Joncas, K. P.

    1972-01-01

    Concepts and techniques for identifying and simulating both the steady state and dynamic characteristics of electrical loads for use during integrated system test and evaluation are discussed. The investigations showed that it is feasible to design and develop interrogation and simulation equipment to perform the desired functions. During the evaluation, actual spacecraft loads were interrogated by stimulating the loads with their normal input voltage and measuring the resultant voltage and current time histories. Elements of the circuits were optimized by an iterative process of selecting element values and comparing the time-domain response of the model with those obtained from the real equipment during interrogation.

  12. Cantera Aerosol Dynamics Simulator

    SciTech Connect

    Moffat, Harry

    2004-09-01

    The Cantera Aerosol Dynamics Simulator (CADS) package is a general library for aerosol modeling to address aerosol general dynamics, including formation from gas phase reactions, surface chemistry (growth and oxidation), bulk particle chemistry, transport by Brownian diffusion, thermophoresis, and diffusiophoresis with linkage to DSMC studies, and thermal radiative transport. The library is based upon Cantera, a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. The method uses a discontinuous galerkin formulation for the condensation and coagulation operator that conserves particles, elements, and enthalpy up to round-off error. Both O-D and 1-D time dependent applications have been developed with the library. Multiple species in the solid phase are handled as well. The O-D application, called Tdcads (Time Dependent CADS) is distributed with the library. Tdcads can address both constant volume and constant pressure adiabatic homogeneous problems. An extensive set of sample problems for Tdcads is also provided.

  13. Data Systems Dynamic Simulator

    NASA Technical Reports Server (NTRS)

    Rouff, Christopher; Clark, Melana; Davenport, Bill; Message, Philip

    1993-01-01

    The Data System Dynamic Simulator (DSDS) is a discrete event simulation tool. It was developed for NASA for the specific purpose of evaluating candidate architectures for data systems of the Space Station era. DSDS provides three methods for meeting this requirement. First, the user has access to a library of standard pre-programmed elements. These elements represent tailorable components of NASA data systems and can be connected in any logical manner. Secondly, DSDS supports the development of additional elements. This allows the more sophisticated DSDS user the option of extending the standard element set. Thirdly, DSDS supports the use of data streams simulation. Data streams is the name given to a technique that ignores packet boundaries, but is sensitive to rate changes. Because rate changes are rare compared to packet arrivals in a typical NASA data system, data stream simulations require a fraction of the CPU run time. Additionally, the data stream technique is considerably more accurate than another commonly-used optimization technique.

  14. Look-ahead Dynamic Simulation

    Energy Science and Technology Software Center (ESTSC)

    2015-10-20

    Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.

  15. Automatic identification of model reductions for discrete stochastic simulation

    NASA Astrophysics Data System (ADS)

    Wu, Sheng; Fu, Jin; Li, Hong; Petzold, Linda

    2012-07-01

    Multiple time scales in cellular chemical reaction systems present a challenge for the efficiency of stochastic simulation. Numerous model reductions have been proposed to accelerate the simulation of chemically reacting systems by exploiting time scale separation. However, these are often identified and deployed manually, requiring expert knowledge. This is time-consuming, prone to error, and opportunities for model reduction may be missed, particularly for large models. We propose an automatic model analysis algorithm using an adaptively weighted Petri net to dynamically identify opportunities for model reductions for both the stochastic simulation algorithm and tau-leaping simulation, with no requirement of expert knowledge input. Results are presented to demonstrate the utility and effectiveness of this approach.

  16. Molecular dynamics simulations

    SciTech Connect

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs.

  17. Cantera Aerosol Dynamics Simulator

    Energy Science and Technology Software Center (ESTSC)

    2004-09-01

    The Cantera Aerosol Dynamics Simulator (CADS) package is a general library for aerosol modeling to address aerosol general dynamics, including formation from gas phase reactions, surface chemistry (growth and oxidation), bulk particle chemistry, transport by Brownian diffusion, thermophoresis, and diffusiophoresis with linkage to DSMC studies, and thermal radiative transport. The library is based upon Cantera, a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. The method uses a discontinuous galerkinmore » formulation for the condensation and coagulation operator that conserves particles, elements, and enthalpy up to round-off error. Both O-D and 1-D time dependent applications have been developed with the library. Multiple species in the solid phase are handled as well. The O-D application, called Tdcads (Time Dependent CADS) is distributed with the library. Tdcads can address both constant volume and constant pressure adiabatic homogeneous problems. An extensive set of sample problems for Tdcads is also provided.« less

  18. Simulation of dose reduction in tomosynthesis

    SciTech Connect

    Svalkvist, Angelica; Baath, Magnus

    2010-01-15

    Purpose: Methods for simulating dose reduction are valuable tools in the work of optimizing radiographic examinations. Using such methods, clinical images can be simulated to have been collected at other, lower, dose levels without the need of additional patient exposure. A recent technology introduced to healthcare that needs optimization is tomosynthesis, where a number of low-dose projection images collected at different angles is used to reconstruct section images of an imaged object. The aim of the present work was to develop a method of simulating dose reduction for digital radiographic systems, suitable for tomosynthesis. Methods: The developed method uses information about the noise power spectrum (NPS) at the original dose level and the simulated dose level to create a noise image that is added to the original image to produce an image that has the same noise properties as an image actually collected at the simulated dose level. As the detective quantum efficiency (DQE) of digital detectors operating at the low dose levels used for tomosynthesis may show a strong dependency on the dose level, it is important that a method for simulating dose reduction for tomosynthesis takes this dependency into account. By applying an experimentally determined relationship between pixel mean and pixel variance, variations in both dose and DQE in relevant dose ranges are taken into account. Results: The developed method was tested on a chest tomosynthesis system and was shown to produce NPS of simulated dose-reduced projection images that agreed well with the NPS of images actually collected at the simulated dose level. The simulated dose reduction method was also applied to tomosynthesis examinations of an anthropomorphic chest phantom, and the obtained noise in the reconstructed section images was very similar to that of an examination actually performed at the simulated dose level. Conclusions: In conclusion, the present article describes a method for simulating dose

  19. Experimental verification of dynamic simulation

    NASA Technical Reports Server (NTRS)

    Yae, K. Harold; Hwang, Howyoung; Chern, Su-Tai

    1989-01-01

    The dynamics model here is a backhoe, which is a four degree of freedom manipulator from the dynamics standpoint. Two types of experiment are chosen that can also be simulated by a multibody dynamics simulation program. In the experiment, recorded were the configuration and force histories; that is, velocity and position, and force output and differential pressure change from the hydraulic cylinder, in the time domain. When the experimental force history is used as driving force in the simulation model, the forward dynamics simulation produces a corresponding configuration history. Then, the experimental configuration history is used in the inverse dynamics analysis to generate a corresponding force history. Therefore, two sets of configuration and force histories--one set from experiment, and the other from the simulation that is driven forward and backward with the experimental data--are compared in the time domain. More comparisons are made in regard to the effects of initial conditions, friction, and viscous damping.

  20. Remote manipulator dynamic simulation

    NASA Technical Reports Server (NTRS)

    Wild, E. C.; Donges, P. K.; Garand, W. A.

    1972-01-01

    A simulator to generate the real time visual scenes required to perform man in the loop investigations of remote manipulator application and design concepts for the space shuttle is described. The simulated remote manipulator consists of a computed display system that uses a digital computer, the electronic scene generator, an operator's station, and associated interface hardware. A description of the capabilities of the implemented simulation is presented. The mathematical models and programs developed for the simulation are included.

  1. Validation of CT dose-reduction simulation

    SciTech Connect

    Massoumzadeh, Parinaz; Don, Steven; Hildebolt, Charles F.; Bae, Kyongtae T.; Whiting, Bruce R.

    2009-01-15

    The objective of this research was to develop and validate a custom computed tomography dose-reduction simulation technique for producing images that have an appearance consistent with the same scan performed at a lower mAs (with fixed kVp, rotation time, and collimation). Synthetic noise is added to projection (sinogram) data, incorporating a stochastic noise model that includes energy-integrating detectors, tube-current modulation, bowtie beam filtering, and electronic system noise. Experimental methods were developed to determine the parameters required for each component of the noise model. As a validation, the outputs of the simulations were compared to measurements with cadavers in the image domain and with phantoms in both the sinogram and image domain, using an unbiased root-mean-square relative error metric to quantify agreement in noise processes. Four-alternative forced-choice (4AFC) observer studies were conducted to confirm the realistic appearance of simulated noise, and the effects of various system model components on visual noise were studied. The ''just noticeable difference (JND)'' in noise levels was analyzed to determine the sensitivity of observers to changes in noise level. Individual detector measurements were shown to be normally distributed (p>0.54), justifying the use of a Gaussian random noise generator for simulations. Phantom tests showed the ability to match original and simulated noise variance in the sinogram domain to within 5.6%{+-}1.6% (standard deviation), which was then propagated into the image domain with errors less than 4.1%{+-}1.6%. Cadaver measurements indicated that image noise was matched to within 2.6%{+-}2.0%. More importantly, the 4AFC observer studies indicated that the simulated images were realistic, i.e., no detectable difference between simulated and original images (p=0.86) was observed. JND studies indicated that observers' sensitivity to change in noise levels corresponded to a 25% difference in dose, which

  2. Validation of CT dose-reduction simulation.

    PubMed

    Massoumzadeh, Parinaz; Don, Steven; Hildebolt, Charles F; Bae, Kyongtae T; Whiting, Bruce R

    2009-01-01

    The objective of this research was to develop and validate a custom computed tomography dose-reduction simulation technique for producing images that have an appearance consistent with the same scan performed at a lower mAs (with fixed kVp, rotation time, and collimation). Synthetic noise is added to projection (sinogram) data, incorporating a stochastic noise model that includes energy-integrating detectors, tube-current modulation, bowtie beam filtering, and electronic system noise. Experimental methods were developed to determine the parameters required for each component of the noise model. As a validation, the outputs of the simulations were compared to measurements with cadavers in the image domain and with phantoms in both the sinogram and image domain, using an unbiased root-mean-square relative error metric to quantify agreement in noise processes. Four-alternative forced-choice (4AFC) observer studies were conducted to confirm the realistic appearance of simulated noise, and the effects of various system model components on visual noise were studied. The "just noticeable difference (JND)" in noise levels was analyzed to determine the sensitivity of observers to changes in noise level. Individual detector measurements were shown to be normally distributed (p > 0.54), justifying the use of a Gaussian random noise generator for simulations. Phantom tests showed the ability to match original and simulated noise variance in the sinogram domain to within 5.6% +/- 1.6% (standard deviation), which was then propagated into the image domain with errors less than 4.1% +/- 1.6%. Cadaver measurements indicated that image noise was matched to within 2.6% +/- 2.0%. More importantly, the 4AFC observer studies indicated that the simulated images were realistic, i.e., no detectable difference between simulated and original images (p = 0.86) was observed. JND studies indicated that observers' sensitivity to change in noise levels corresponded to a 25% difference in dose

  3. Domain reduction method for atomistic simulations

    SciTech Connect

    Medyanik, Sergey N. . E-mail: medyanik@northwestern.edu; Karpov, Eduard G. . E-mail: edkarpov@gmail.com; Liu, Wing Kam . E-mail: w-liu@northwestern.edu

    2006-11-01

    In this paper, a quasi-static formulation of the method of multi-scale boundary conditions (MSBCs) is derived and applied to atomistic simulations of carbon nano-structures, namely single graphene sheets and multi-layered graphite. This domain reduction method allows for the simulation of deformable boundaries in periodic atomic lattice structures, reduces the effective size of the computational domain, and consequently decreases the cost of computations. The size of the reduced domain is determined by the value of the domain reduction parameter. This parameter is related to the distance between the boundary of the reduced domain, where MSBCs are applied, and the boundary of the full domain, where the standard displacement boundary conditions are prescribed. Two types of multi-scale boundary conditions are derived: one for simulating in-layer multi-scale boundaries in a single graphene sheet and the other for simulating inter-layer multi-scale boundaries in multi-layered graphite. The method is tested on benchmark nano-indentation problems and the results are consistent with the full domain solutions.

  4. Dynamic Power Grid Simulation

    Energy Science and Technology Software Center (ESTSC)

    2015-09-14

    GridDyn is a part of power grid simulation toolkit. The code is designed using modern object oriented C++ methods utilizing C++11 and recent Boost libraries to ensure compatibility with multiple operating systems and environments.

  5. Dynamic simulation of voltage collapses

    SciTech Connect

    Deuse, J.; Stubbe, M. )

    1993-08-01

    Most of the time the voltage collapse phenomena are studied by means of computer programs designed for the calculation of steady state conditions. But in the real world, the simultaneous occurrences of losses of synchronism, of AVR dynamics or of transformer tap changes call for a full dynamic simulation of voltage phenomena. The present paper shows some examples of dynamic simulations of voltage phenomena using a new general purpose stability program (EUROSTAG), covering in a continuous way the classical fields of transient, mid-term and long-term stability, and also the quasi steady state conditions of a power system.

  6. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

    We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated. PMID:24600690

  7. Destination state screening of active spaces in spin dynamics simulations

    NASA Astrophysics Data System (ADS)

    Krzystyniak, M.; Edwards, Luke J.; Kuprov, Ilya

    2011-06-01

    We propose a novel avenue for state space reduction in time domain Liouville space spin dynamics simulations, using detectability as a selection criterion - only those states that evolve into or affect other detectable states are kept in the simulation. This basis reduction procedure (referred to as destination state screening) is formally exact and can be applied on top of the existing state space restriction techniques. As demonstrated below, in many cases this results in further reduction of matrix dimension, leading to considerable acceleration of many spin dynamics simulation types. Destination state screening is implemented in the latest version of the Spinach library (http://spindynamics.org).

  8. Tree Modeling and Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Tian-shuang, Fu; Yi-bing, Li; Dong-xu, Shen

    This paper introduces the theory about tree modeling and dynamic movements simulation in computer graphics. By comparing many methods we choose Geometry-based rendering as our method. The tree is decomposed into branches and leaves, under the rotation and quaternion methods we realize the tree animation and avoid the Gimbals Lock in Euler rotation. We take Orge 3D as render engine, which has good graphics programming ability. By the end we realize the tree modeling and dynamic movements simulation, achieve realistic visual quality with little computation cost.

  9. Dynamic stiffness removal for direct numerical simulations

    SciTech Connect

    Lu, Tianfeng; Law, Chung K.; Yoo, Chun Sang; Chen, Jacqueline H.

    2009-08-15

    A systematic approach was developed to derive non-stiff reduced mechanisms for direct numerical simulations (DNS) with explicit integration solvers. The stiffness reduction was achieved through on-the-fly elimination of short time-scales induced by two features of fast chemical reactivity, namely quasi-steady-state (QSS) species and partial-equilibrium (PE) reactions. The sparse algebraic equations resulting from QSS and PE approximations were utilized such that the efficiency of the dynamic stiffness reduction is high compared with general methods of time-scale reduction based on Jacobian decomposition. Using the dimension reduction strategies developed in our previous work, a reduced mechanism with 52 species was first derived from a detailed mechanism with 561 species. The reduced mechanism was validated for ignition and extinction applications over the parameter range of equivalence ratio between 0.5 and 1.5, pressure between 10 and 50 atm, and initial temperature between 700 and 1600 K for ignition, and worst-case errors of approximately 30% were observed. The reduced mechanism with dynamic stiffness removal was then applied in homogeneous and 1-D ignition applications, as well as a 2-D direct numerical simulation of ignition with temperature inhomogeneities at constant volume with integration time-steps of 5-10 ns. The integration was numerically stable and good accuracy was achieved. (author)

  10. Simulation visualization through dynamic instrumentation

    SciTech Connect

    Bisset, K.R.

    1998-09-01

    The goal of the instrument composition system is to allow a simulation user to dynamically create instruments as a simulation executes. Instruments can include graphical displays, data collectors, and debugging aides. Instruments are made up of small building blocks which can be easily combined into larger, more complex instruments. Through the sue of an Attribute Server (a distributed publication/subscription mechanism), the actors and instruments in a simulation can interact without direct knowledge of each other. Instead, each actor publishes the attributes which it has available. An instrument subscribes to the attributes in which it is interested, and is notified whenever the value of one of these attribute changes. An instrument can also publish attributes for use by other instruments. Since the Attribute Server is distributed, the publisher of an attribute need not execute on the same machine as the subscriber. This allows CPU intensive data visualization to execute on separate machines from the simulation, minimizing the impact on the simulation.

  11. Dose reduction using a dynamic, piecewise-linear attenuator

    SciTech Connect

    Hsieh, Scott S.; Fleischmann, Dominik; Pelc, Norbert J.

    2014-02-15

    Purpose: The authors recently proposed a dynamic, prepatient x-ray attenuator capable of producing a piecewise-linear attenuation profile customized to each patient and viewing angle. This attenuator was intended to reduce scatter-to-primary ratio (SPR), dynamic range, and dose by redistributing flux. In this work the authors tested the ability of the attenuator to reduce dose and SPR in simulations. Methods: The authors selected four clinical applications, including routine full field-of-view scans of the thorax and abdomen, and targeted reconstruction tasks for an abdominal aortic aneurysm and the pancreas. Raw data were estimated by forward projection of the image volume datasets. The dynamic attenuator was controlled to reduce dose while maintaining peak variance by solving a convex optimization problem, assuminga priori knowledge of the patient anatomy. In targeted reconstruction tasks, the noise in specific regions was given increased weighting. A system with a standard attenuator (or “bowtie filter”) was used as a reference, and used either convex optimized tube current modulation (TCM) or a standard TCM heuristic. The noise of the scan was determined analytically while the dose was estimated using Monte Carlo simulations. Scatter was also estimated using Monte Carlo simulations. The sensitivity of the dynamic attenuator to patient centering was also examined by shifting the abdomen in 2 cm intervals. Results: Compared to a reference system with optimized TCM, use of the dynamic attenuator reduced dose by about 30% in routine scans and 50% in targeted scans. Compared to the TCM heuristics which are typically used withouta priori knowledge, the dose reduction is about 50% for routine scans. The dynamic attenuator gives the ability to redistribute noise and variance and produces more uniform noise profiles than systems with a conventional bowtie filter. The SPR was also modestly reduced by 10% in the thorax and 24% in the abdomen. Imaging with the dynamic

  12. Dose reduction using a dynamic, piecewise-linear attenuator

    PubMed Central

    Hsieh, Scott S.; Fleischmann, Dominik; Pelc, Norbert J.

    2014-01-01

    Purpose: The authors recently proposed a dynamic, prepatient x-ray attenuator capable of producing a piecewise-linear attenuation profile customized to each patient and viewing angle. This attenuator was intended to reduce scatter-to-primary ratio (SPR), dynamic range, and dose by redistributing flux. In this work the authors tested the ability of the attenuator to reduce dose and SPR in simulations. Methods: The authors selected four clinical applications, including routine full field-of-view scans of the thorax and abdomen, and targeted reconstruction tasks for an abdominal aortic aneurysm and the pancreas. Raw data were estimated by forward projection of the image volume datasets. The dynamic attenuator was controlled to reduce dose while maintaining peak variance by solving a convex optimization problem, assuming a priori knowledge of the patient anatomy. In targeted reconstruction tasks, the noise in specific regions was given increased weighting. A system with a standard attenuator (or “bowtie filter”) was used as a reference, and used either convex optimized tube current modulation (TCM) or a standard TCM heuristic. The noise of the scan was determined analytically while the dose was estimated using Monte Carlo simulations. Scatter was also estimated using Monte Carlo simulations. The sensitivity of the dynamic attenuator to patient centering was also examined by shifting the abdomen in 2 cm intervals. Results: Compared to a reference system with optimized TCM, use of the dynamic attenuator reduced dose by about 30% in routine scans and 50% in targeted scans. Compared to the TCM heuristics which are typically used without a priori knowledge, the dose reduction is about 50% for routine scans. The dynamic attenuator gives the ability to redistribute noise and variance and produces more uniform noise profiles than systems with a conventional bowtie filter. The SPR was also modestly reduced by 10% in the thorax and 24% in the abdomen. Imaging with the

  13. Dynamic Simulation Nuclear Power Plants

    Energy Science and Technology Software Center (ESTSC)

    1992-03-03

    DSNP (Dynamic Simulator for Nuclear Power-Plants) is a system of programs and data files by which a nuclear power plant, or part thereof, can be simulated. The acronym DSNP is used interchangeably for the DSNP language, the DSNP libraries, the DSNP precompiler, and the DSNP document generator. The DSNP language is a special-purpose, block-oriented, digital-simulation language developed to facilitate the preparation of dynamic simulations of a large variety of nuclear power plants. It is amore » user-oriented language that permits the user to prepare simulation programs directly from power plant block diagrams and flow charts by recognizing the symbolic DSNP statements for the appropriate physical components and listing these statements in a logical sequence according to the flow of physical properties in the simulated power plant. Physical components of nuclear power plants are represented by functional blocks, or modules. Many of the more complex components are represented by several modules. The nuclear reactor, for example, has a kinetic module, a power distribution module, a feedback module, a thermodynamic module, a hydraulic module, and a radioactive heat decay module. These modules are stored in DSNP libraries in the form of a DSNP subroutine or function, a block of statements, a macro, or a combination of the above. Basic functional blocks such as integrators, pipes, function generators, connectors, and many auxiliary functions representing properties of materials used in nuclear power plants are also available. The DSNP precompiler analyzes the DSNP simulation program, performs the appropriate translations, inserts the requested modules from the library, links these modules together, searches necessary data files, and produces a simulation program in FORTRAN.« less

  14. Dynamic evaluation of the CMAQv5.0 modeling system: Assessing the model’s ability to simulate ozone changes due to NOx emission reductions

    EPA Science Inventory

    Regional air quality models are frequently used for regulatory applications to predict changes in air quality due to changes in emissions or changes in meteorology. Dynamic model evaluation is thus an important step in establishing credibility in the model predicted pollutant re...

  15. Accelerated dynamics simulations of nanotubes.

    SciTech Connect

    Uberuaga, B. P.; Stuart, S. J.; Voter, A. F.

    2002-01-01

    We report on the application of accelerated dynamics techniques to the study of carbon nanotubes. We have used the parallel replica method and temperature accelerated dynamics simulations are currently in progress. In the parallel replica study, we have stretched tubes at a rate significantly lower than that used in previous studies. In these preliminary results, we find that there are qualitative differences in the rupture of the nanotubes at different temperatures. We plan on extending this investigation to include nanotubes of various chiralities. We also plan on exploring unique geometries of nanotubes.

  16. Radiation in molecular dynamic simulations

    SciTech Connect

    Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M

    2008-10-13

    Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.

  17. Methods and systems for combustion dynamics reduction

    DOEpatents

    Kraemer, Gilbert Otto; Varatharajan, Balachandar; Srinivasan, Shiva; Lynch, John Joseph; Yilmaz, Ertan; Kim, Kwanwoo; Lacy, Benjamin; Crothers, Sarah; Singh, Kapil Kumar

    2009-08-25

    Methods and systems for combustion dynamics reduction are provided. A combustion chamber may include a first premixer and a second premixer. Each premixer may include at least one fuel injector, at least one air inlet duct, and at least one vane pack for at least partially mixing the air from the air inlet duct or ducts and fuel from the fuel injector or injectors. Each vane pack may include a plurality of fuel orifices through which at least a portion of the fuel and at least a portion of the air may pass. The vane pack or packs of the first premixer may be positioned at a first axial position and the vane pack or packs of the second premixer may be positioned at a second axial position axially staggered with respect to the first axial position.

  18. Dynamic simulations of tissue welding

    SciTech Connect

    Maitland, D.J.; Eder, D.C.; London, R.A.; Glinsky, M.E.

    1996-02-01

    The exposure of human skin to near-infrared radiation is numerically simulated using coupled laser, thermal transport and mass transport numerical models. The computer model LATIS is applied in both one-dimensional and two-dimensional geometries. Zones within the skin model are comprised of a topical solder, epidermis, dermis, and fatty tissue. Each skin zone is assigned initial optical, thermal and water density properties consistent with values listed in the literature. The optical properties of each zone (i.e. scattering, absorption and anisotropy coefficients) are modeled as a kinetic function of the temperature. Finally, the water content in each zone is computed from water diffusion where water losses are accounted for by evaporative losses at the air-solder interface. The simulation results show that the inclusion of water transport and evaporative losses in the model are necessary to match experimental observations. Dynamic temperature and damage distributions are presented for the skin simulations.

  19. Molecular dynamics simulation of benzene

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2016-03-01

    Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.

  20. Molecular Dynamics Simulations of Polymers

    NASA Astrophysics Data System (ADS)

    Han, Jie

    1995-01-01

    Molecular dynamics (MD) simulations have been undertaken in this work to explore structures and properties of polyethylene (PE), polyisobutylene (PIB), atactic polypropylene (aPP) and atactic polystyrene (aPS). This work has not only demonstrated the reliability of MD simulations by comparing results with available experiments, but more importantly has revealed structure-property relationships on a molecular level for these selected polymers. Structures of these amorphous polymers were characterized by radial distribution functions (RDFs) or scattering profiles, and properties of the polymers studied were pressure-volume -temperature (PVT) equation of state, enthalpy, cohesive energy, the diffusion coefficient of methane in the polymer, and glass transition temperature. Good agreement was found for these structures and properties between simulation and experiment. More importantly, the scientific understanding of structure-property relationships was established on a molecular level. In the order of aPP (PE), PIB and aPS, with the chain surface separation or free volume decreasing, the density increases and the diffusion coefficient decreases. Therefore, the effects of changes or modifications in the chemical structure of monomer molecules (substituting pendent hydrogen with methyl or phenyl) on polymeric materials performance were attributed to the effects of molecular chain structure on packing structure, which, in turn, affects the properties of these polymers. Local chain dynamics and relaxation have been studied for bulk PE and aPS. Cooperative transitions occur at second-neighbor bonds for PE, and first-neighbor bonds for aPS due to the role of side groups. The activation energy is a single torsional barrier for overall conformational transitions, and is single torsional barrier plus locally "trapped" barrier for relaxation. Temperature dependence is Arrhenius for transition time, and is WLF for relaxation time. The mean correlation times derived from

  1. Reduction of Large Dynamical Systems by Minimization of Evolution Rate

    NASA Technical Reports Server (NTRS)

    Girimaji, Sharath S.

    1999-01-01

    Reduction of a large system of equations to a lower-dimensional system of similar dynamics is investigated. For dynamical systems with disparate timescales, a criterion for determining redundant dimensions and a general reduction method based on the minimization of evolution rate are proposed.

  2. Improving computational efficiency of Monte Carlo simulations with variance reduction

    SciTech Connect

    Turner, A.

    2013-07-01

    CCFE perform Monte-Carlo transport simulations on large and complex tokamak models such as ITER. Such simulations are challenging since streaming and deep penetration effects are equally important. In order to make such simulations tractable, both variance reduction (VR) techniques and parallel computing are used. It has been found that the application of VR techniques in such models significantly reduces the efficiency of parallel computation due to 'long histories'. VR in MCNP can be accomplished using energy-dependent weight windows. The weight window represents an 'average behaviour' of particles, and large deviations in the arriving weight of a particle give rise to extreme amounts of splitting being performed and a long history. When running on parallel clusters, a long history can have a detrimental effect on the parallel efficiency - if one process is computing the long history, the other CPUs complete their batch of histories and wait idle. Furthermore some long histories have been found to be effectively intractable. To combat this effect, CCFE has developed an adaptation of MCNP which dynamically adjusts the WW where a large weight deviation is encountered. The method effectively 'de-optimises' the WW, reducing the VR performance but this is offset by a significant increase in parallel efficiency. Testing with a simple geometry has shown the method does not bias the result. This 'long history method' has enabled CCFE to significantly improve the performance of MCNP calculations for ITER on parallel clusters, and will be beneficial for any geometry combining streaming and deep penetration effects. (authors)

  3. Simulation of Fault Zone Dynamics

    NASA Astrophysics Data System (ADS)

    Mora, P.; Abe, S.; Place, D.

    2002-12-01

    Particle models such as the discrete element model for granular assemblies and the lattice solid model provide a means to study the dynamics of fault zones. The lattice solid model was developed with the aim of progressively building up the capacity to simulate all relevent physical processes in fault zones. The present implementation of the model is able to simulate the dynamics of a granular lattice consisting of bonded or unbonded circular (2D) or spherical (3D) particles. Thermal effects (frictional hear generation, thermal expansion, heat flow) and pore fluid effects (heat induced pore pressure gradients and the consequent Darcian flow and impact on effective friction) can be modelled. Past work involving both circular particles and non-circular grains constructed as groups of bonded particles have demonstrated that grain shape has a fundamental impact on zero-th order behaviour. When circular particles are used, rolling is the most efficient means to accomodate slip of a simulated fault gouge layer leading to unrealistically low friction, typically around 0.2. This is consistent with laboratory results by Mair and Marone which have demonstrated that gouge consisting entirely of spherical beads shows a lower coefficient of friction than gouge containing irregular shaped particles. Recent work comparing quasi-2D laboratory results using pasta (Marone) with 2D numerical results (Morgan) have confirmed that numerical and laboratory results with circular ``particles'' are in agreement. When irregular grains are modelled at the lowest scale, the friction of simulated gouge layers matches with laboratory observations of rock friction (μ ~ 0.6) and is insentitive to the value used for interparticle friction (Mora et al, 2000). This indicates a self-regulation mechanism is occurring in which the group behaviour of the gouge layer remains constant at around 0.6 by balancing the amount of slip and rolling of grains within the gouge layer. A limitation of these studies

  4. Reduction of Additive Colored Noise Using Coupled Dynamics

    NASA Astrophysics Data System (ADS)

    Kohar, Vivek; Kia, Behnam; Lindner, John F.; Ditto, William L.

    We study the effect of additive colored noise on the evolution of maps and demonstrate that the deviations caused by such noise can be reduced using coupled dynamics. We consider both Ornstein-Uhlenbeck process as well as 1/fα noise in our numerical simulations. We observe that though the variance of deviations caused by noise depends on the correlations in the noise, under optimal coupling strength, it decreases by a factor equal to the number of coupled elements in the array as compared to the variance of deviations in a single isolated map. This reduction in noise levels occurs in chaotic as well as periodic regime of the maps. Lastly, we examine the effect of colored noise in chaos computing and find that coupling the chaos computing elements enhances the robustness of chaos computing.

  5. Risk Reduction and Training using Simulation Based Tools - 12180

    SciTech Connect

    Hall, Irin P.

    2012-07-01

    Process Modeling and Simulation (M and S) has been used for many years in manufacturing and similar domains, as part of an industrial engineer's tool box. Traditionally, however, this technique has been employed in small, isolated projects where models were created from scratch, often making it time and cost prohibitive. Newport News Shipbuilding (NNS) has recognized the value of this predictive technique and what it offers in terms of risk reduction, cost avoidance and on-schedule performance of highly complex work. To facilitate implementation, NNS has been maturing a process and the software to rapidly deploy and reuse M and S based decision support tools in a variety of environments. Some examples of successful applications by NNS of this technique in the nuclear domain are a reactor refueling simulation based tool, a fuel handling facility simulation based tool and a tool for dynamic radiation exposure tracking. The next generation of M and S applications include expanding simulation based tools into immersive and interactive training. The applications discussed here take a tool box approach to creating simulation based decision support tools for maximum utility and return on investment. This approach involves creating a collection of simulation tools that can be used individually or integrated together for a larger application. The refueling simulation integrates with the fuel handling facility simulation to understand every aspect and dependency of the fuel handling evolutions. This approach translates nicely to other complex domains where real system experimentation is not feasible, such as nuclear fuel lifecycle and waste management. Similar concepts can also be applied to different types of simulation techniques. For example, a process simulation of liquid waste operations may be useful to streamline and plan operations, while a chemical model of the liquid waste composition is an important tool for making decisions with respect to waste disposition

  6. Dynamics of riboswitches: Molecular simulations.

    PubMed

    Sanbonmatsu, Karissa Y

    2014-10-01

    Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail. Molecular dynamics simulations are useful for interpreting existing experimental data and producing predictions for new experiments. Here, a wide range of computational studies on riboswitches is reviewed. By elucidating the key principles of riboswitch operation, computation may aid in the effort to design more specific antibiotics with affinities greater than those of the native ligand. Such a detailed understanding may be required to improve efficacy and reduce side effects. These studies are laying the groundwork for understanding the action mechanism of new compounds that inhibit riboswitch activity. Future directions such as magnesium effects, large-scale conformational changes, expression platforms and co-transcriptional folding are also discussed. This article is part of a Special Issue entitled: Riboswitches. PMID:24953187

  7. Simulation reduction using the Taguchi method

    NASA Technical Reports Server (NTRS)

    Mistree, Farrokh; Lautenschlager, Ume; Erikstad, Stein Owe; Allen, Janet K.

    1993-01-01

    A large amount of engineering effort is consumed in conducting experiments to obtain information needed for making design decisions. Efficiency in generating such information is the key to meeting market windows, keeping development and manufacturing costs low, and having high-quality products. The principal focus of this project is to develop and implement applications of Taguchi's quality engineering techniques. In particular, we show how these techniques are applied to reduce the number of experiments for trajectory simulation of the LifeSat space vehicle. Orthogonal arrays are used to study many parameters simultaneously with a minimum of time and resources. Taguchi's signal to noise ratio is being employed to measure quality. A compromise Decision Support Problem and Robust Design are applied to demonstrate how quality is designed into a product in the early stages of designing.

  8. Dimensionality reduction of dynamical systems with parameters

    NASA Astrophysics Data System (ADS)

    Welshman, Ch.; Brooke, J.

    2013-01-01

    We describe a method for reproducing the dynamical behaviour observed in systems of very high dimension in a state space of much lower dimension. The method is designed for systems where the solution evolves onto an attractor of dimension m which is much lower than that of the state space of the full system, n. Whitney's embedding theorem guarantees that the attractor can be embedded in a space of dimension d = 2m+1. We describe how such methods can be extended to reproducing the vector field on the attractor so that the dynamics of a parameterized family of attractors can be explored in the low dimensional space Rd.

  9. A multicomb variance reduction scheme for Monte Carlo semiconductor simulators

    SciTech Connect

    Gray, M.G.; Booth, T.E.; Kwan, T.J.T.; Snell, C.M.

    1998-04-01

    The authors adapt a multicomb variance reduction technique used in neutral particle transport to Monte Carlo microelectronic device modeling. They implement the method in a two-dimensional (2-D) MOSFET device simulator and demonstrate its effectiveness in the study of hot electron effects. The simulations show that the statistical variance of hot electrons is significantly reduced with minimal computational cost. The method is efficient, versatile, and easy to implement in existing device simulators.

  10. Magnetotail dynamics: MHD simulations of driven and spontaneous dynamic changes

    SciTech Connect

    Birn, J.; Schindler, K.; Hesse, M.

    1994-05-01

    The dynamic evolution of the magnetotail during growth phase and expansion phase of a substorm is studied through threedimensional time-dependent MHD simulations. To model growth phase effects, an external electric field with an equatorward inflow is applied at the boundaries over a finite time period. This leads to the formation of a thin current sheet with greatly enhanced current density in the near tail, embedded in the wider plasma/current sheet, which becomes diminished in strength. A faster, spontaneous current sheet formation occurs when entropy conservation is released in an isobaric model, while the ideal MHD constraint persists. This may be a suitable model for the late, explosive part of the growth phase. The transition to the substorm expansive phase is modeled by an increase in anomalous resistivity, using either uniform resistivity or a current density dependent resistivity which is turned on when the current density exceeds a certain threshold. In both cases the violation of ideal MHD leads to resistive instability and the formation of a near-Earth neutral line, fast flow, and plasmoid ejection, together with the dipolarization and current reduction in the region further earthward. The spontaneous increase in total region 1 type field-aligned currents associated with the disruptions of the thin current sheets is less significant than that found in earlier simulations of the disruption of a wider current sheet, whereas the driven increase in the region 1 type current is substantial. The results demonstrate that the same dynamic process which appears spontaneous in the behavior of some quantities might be interpreted as entirely driven from the observation of others.

  11. Molecular dynamics simulations of large macromolecular complexes

    PubMed Central

    Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

    2015-01-01

    Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770

  12. Noise reduction by dynamic signal preemphasis

    NASA Astrophysics Data System (ADS)

    Takeda, Kazuyuki; Takegoshi, K.

    2011-02-01

    In this work we propose an approach to reduce the digitization noise for a given dynamic range, i.e., the number of bits, of an analog to digital converter used in an NMR receiver. In this approach, the receiver gain is dynamically increased so that the free induction decay is recorded in such an emphasized way that the decaying signal is digitized using as many number of bits as possible, and at the stage of data processing, the original signal profile is restored by applying the apodization that compensates the effect of the preemphasis. This approach, which we call APodization after Receiver gain InCrement during Ongoing sequence with Time (APRICOT), is performed in a solid-state system containing a pair of 13C spins, one of which is fully isotopically labeled and the other is naturally abundant. It is demonstrated that the exceedingly smaller peak buried in the digitization noise in the conventional approach can be revealed by employing APRICOT.

  13. Brownian Dynamics Simulations of Dispersed Graphene Sheets

    NASA Astrophysics Data System (ADS)

    Xu, Yueyi; Green, Micah

    2013-03-01

    Past simulations of the dynamics of dispersed graphene sheets are limited to static fluids on small timescales, with little attention devoted to flow dynamics. To address this need, we investigated how flow fields affect graphene morphology dynamics using a coarse-grained model; this relatively untouched area is critical given the importance of graphene solution-processing of multifunctional devices and materials. In particular, we developed a Brownian Dynamics (BD) algorithm to study the morphology of sheetlike macromolecules in dilute, flowing solutions. We used a bead-rod lattice to represent the mesoscopic conformation of individual two dimensional sheets. We then analyzed the morphology dynamic modes (stretching, tumbling, crumpling) of these molecules as a function of sheet size, Weissenberg number, and bending stiffness. Our results indicate the model can successfully simulate a range of dynamic modes in a given flow field and yield fundamental insight into the flow processing of graphene sheets.

  14. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

    Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)

  15. The Astrometric Model Implementation. Simulations and Data Reduction Compatibility Test

    NASA Astrophysics Data System (ADS)

    Anglada-Escudé, G.; Torra, J.; Masana, E.; Luri, X.

    2005-01-01

    The aim of this paper is to give a brief description of the astrometric model accuracy at the current stage of the implementation in GASS (simulator) and GDAAS2 (Data Reduction study). The astrometric model described is a set of algorithms which relate the astrometric parameters with the observed directions on the satellite quasi-intertial reference frame. This includes the kinematics of point sources, the relativistic light deflection due to Solar System gravitational field and the aberration. The description of this model was given by Klioner (2002), The form of these algorithms is slightly different in the telemetry simulations (S.A. Klioner, ANSI-C code) and in the data reduction scheme (Lindegren 2002, Fortran90). Both versions make use of the ephemeris for the Solar System by Observatoire de la Côte d'Azur (Mignard 2003, Fortran 90). All these algorithms have been wrapped or recoded since the simulations and data reduction both run in a Java environment. All these manipulations required a strict verification since these algorithms constitute the core of the GIS (Global Iterative Solution). We present the compatibility tests performed during last year that helped us to make fully compatible the simulated data with the data reduction scheme.

  16. Simulating Flexible-Spacecraft Dynamics and Control

    NASA Technical Reports Server (NTRS)

    Fedor, Joseph

    1987-01-01

    Versatile program applies to many types of spacecraft and dynamical problems. Flexible Spacecraft Dynamics and Control program (FSD) developed to aid in simulation of large class of flexible and rigid spacecraft. Extremely versatile and used in attitude dynamics and control analysis as well as in-orbit support of deployment and control of spacecraft. Applicable to inertially oriented spinning, Earth-oriented, or gravity-gradient-stabilized spacecraft. Written in FORTRAN 77.

  17. Molecular Dynamics Simulations of Simple Liquids

    ERIC Educational Resources Information Center

    Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

    2004-01-01

    An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

  18. Reduction of artifacts in computer simulation of breast Cooper's ligaments

    NASA Astrophysics Data System (ADS)

    Pokrajac, David D.; Kuperavage, Adam; Maidment, Andrew D. A.; Bakic, Predrag R.

    2016-03-01

    Anthropomorphic software breast phantoms have been introduced as a tool for quantitative validation of breast imaging systems. Efficacy of the validation results depends on the realism of phantom images. The recursive partitioning algorithm based upon the octree simulation has been demonstrated as versatile and capable of efficiently generating large number of phantoms to support virtual clinical trials of breast imaging. Previously, we have observed specific artifacts, (here labeled "dents") on the boundaries of simulated Cooper's ligaments. In this work, we have demonstrated that these "dents" result from the approximate determination of the closest simulated ligament to an examined subvolume (i.e., octree node) of the phantom. We propose a modification of the algorithm that determines the closest ligament by considering a pre-specified number of neighboring ligaments selected based upon the functions that govern the shape of ligaments simulated in the subvolume. We have qualitatively and quantitatively demonstrated that the modified algorithm can lead to elimination or reduction of dent artifacts in software phantoms. In a proof-of concept example, we simulated a 450 ml phantom with 333 compartments at 100 micrometer resolution. After the proposed modification, we corrected 148,105 dents, with an average size of 5.27 voxels (5.27nl). We have also qualitatively analyzed the corresponding improvement in the appearance of simulated mammographic images. The proposed algorithm leads to reduction of linear and star-like artifacts in simulated phantom projections, which can be attributed to dents. Analysis of a larger number of phantoms is ongoing.

  19. Observing dynamical SUSY breaking with lattice simulation

    SciTech Connect

    Kanamori, Issaku

    2008-11-23

    On the basis of the recently developed lattice formulation of supersymmetric theories which keeps a part of the supersymmetry, we propose a method of observing dynamical SUSY breaking with lattice simulation. We use Hamiltonian as an order parameter and measure the ground state energy as a zero temperature limit of the finite temperature simulation. Our method provides a way of obtaining a physical result from the lattice simulation for supersymmetric theories.

  20. Simulation of liquid dynamics onboard Sloshsat FLEVO

    NASA Astrophysics Data System (ADS)

    Vreeburg, J. P. B.

    1999-01-01

    The Sloshsat FLEVO project has an Investigators Working Group which prepared orbital experiments on the behavior of liquid in spacecraft. These are to be performed with a dedicated small satellite, of about 90 kg empty weight and about 34 kg of water in a 87 litre tank. The spacecraft dynamics are simulated by SMS, the Sloshsat Motion Simulator. SMS predictions and those generated by a CFD simulation are compared for an example.

  1. Molecular dynamics simulations: advances and applications

    PubMed Central

    Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

    2015-01-01

    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.

  2. Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein

    2015-12-01

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  3. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  4. DUVFEL PHOTOINJECTOR DYNAMICS: MEASUREMENT AND SIMULATION.

    SciTech Connect

    GRAVES, W.S.; DIMAURO, L.F.; HEESE, R.; JOHNSON, E.D.; ROSE, J.; RUDATI, J.; SHAFTAN, T.; SHEEHY, B.; YU, L.H.; DOWELL, D.H.

    2001-06-18

    The DUVFEL photoinjector consists of a 1.6 cell BNL gun IV with copper cathode, variable pulse length Ti:Sapp and solenoid magnet. The beam dynamics and the electromagnetic fields in the photoinjector have been characterized by producing a short electron beam with very low charge that is used as a field probe. Transverse beam size and divergence are measured as a function of initial RF phase and initial spot size and compared with simulations using the code HOMDYN. The electromagnetic fields used in the simulations are produced by SUPERFISH, and have been verified with RF measurements. The simulations and measurements of beam dynamics are presented.

  5. Simulation of wetlands forest vegetation dynamics

    USGS Publications Warehouse

    Phipps, R.L.

    1979-01-01

    A computer program, SWAMP, was designed to simulate the effects of flood frequency and depth to water table on southern wetlands forest vegetation dynamics. By incorporating these hydrologic characteristics into the model, forest vegetation and vegetation dynamics can be simulated. The model, based on data from the White River National Wildlife Refuge near De Witt, Arkansas, "grows" individual trees on a 20 x 20-m plot taking into account effects on the tree growth of flooding, depth to water table, shade tolerance, overtopping and crowding, and probability of death and reproduction. A potential application of the model is illustrated with simulations of tree fruit production following flood-control implementation and lumbering. ?? 1979.

  6. Dynamic system simulation of small satellite projects

    NASA Astrophysics Data System (ADS)

    Raif, Matthias; Walter, Ulrich; Bouwmeester, Jasper

    2010-11-01

    A prerequisite to accomplish a system simulation is to have a system model holding all necessary project information in a centralized repository that can be accessed and edited by all parties involved. At the Institute of Astronautics of the Technische Universitaet Muenchen a modular approach for modeling and dynamic simulation of satellite systems has been developed called dynamic system simulation (DySyS). DySyS is based on the platform independent description language SysML to model a small satellite project with respect to the system composition and dynamic behavior. A library of specific building blocks and possible relations between these blocks have been developed. From this library a system model of the satellite of interest can be created. A mapping into a C++ simulation allows the creation of an executable system model with which simulations are performed to observe the dynamic behavior of the satellite. In this paper DySyS is used to model and simulate the dynamic behavior of small satellites, because small satellite projects can act as a precursor to demonstrate the feasibility of a system model since they are less complex compared to a large scale satellite project.

  7. Discrete dislocation dynamics simulations in a cylinder

    NASA Astrophysics Data System (ADS)

    Li, Maosheng; Gao, Chan; Xu, Jianing

    2015-02-01

    Mechanical properties of material are closely related to the motion of dislocations, and predicting the interactions and resulting collective motion of dislocations is a major task in understanding and modelling plastically deforming materials. A discrete dislocation dynamics model is used to describe the orientation substructure within the microstructure. Discrete dislocation dynamics simulations in three dimensions have been used to examine the role of dislocation multiplication and mobility on the plasticity in small samples under uniaxial compression. In this paper we describe the application of the dislocation dynamics simulations in a cylindrical geometry. The boundary conditions for the simulation were estimated from the distribution of the geometrically necessary dislocation density which was obtained from the orientation map. Numerical studies benchmark could validate the accuracy of the algorithms and the importance of handling the singularity correctly. The results of the simulation explain the formation of the experimentally observed substructure.

  8. Spin dynamics simulations at AGS

    SciTech Connect

    Huang, H.; MacKay, W.W.; Meot, F.; Roser, T.

    2010-05-23

    To preserve proton polarization through acceleration, it is important to have a correct model of the process. It has been known that with the insertion of the two helical partial Siberian snakes in the Alternating Gradient Synchrotron (AGS), the MAD model of AGS can not deal with a field map with offset orbit. The stepwise ray-tracing code Zgoubi provides a tool to represent the real electromagnetic fields in the modeling of the optics and spin dynamics for the AGS. Numerical experiments of resonance crossing, including spin dynamics in presence of the snakes and Q-jump, have been performed in AGS lattice models, using Zgoubi. This contribution reports on various results so obtained.

  9. Peptide crystal simulations reveal hidden dynamics

    PubMed Central

    Janowski, Pawel A.; Cerutti, David S.; Holton, James; Case, David A.

    2013-01-01

    Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in the X-ray diffraction data. We present here 9.6 microseconds of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom rmsd; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom rmsd. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(−) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data, as well as to validate computational chemistry methods. PMID:23631449

  10. Hydrogen Reduction of Lunar Regolith Simulants for Oxygen Production

    NASA Technical Reports Server (NTRS)

    Hegde, U.; Balasubramaniam, R.; Gokoglu, S. A.; Rogers, K.; Reddington, M.; Oryshchyn, L.

    2011-01-01

    Hydrogen reduction of the lunar regolith simulants JSC-1A and LHT-2M is investigated in this paper. Experiments conducted at NASA Johnson Space Center are described and are analyzed utilizing a previously validated model developed by the authors at NASA Glenn Research Center. The effects of regolith sintering and clumping, likely in actual production operations, on the oxygen production rate are studied. Interpretations of the obtained results on the basis of the validated model are provided and linked to increase in the effective particle size and reduction in the intra-particle species diffusion rates. Initial results on the pressure dependence of the oxygen production rate are also presented and discussed

  11. Goldfish Geodesics and Hamiltonian Reduction of Matrix Dynamics

    NASA Astrophysics Data System (ADS)

    Arnlind, Joakim; Bordemann, Martin; Hoppe, Jens; Lee, Choonkyu

    2008-04-01

    We describe the Hamiltonian reduction of a time-dependent real-symmetric N× N matrix system to free vector dynamics, and also provide a geodesic interpretation of Ruijsenaars Schneider systems. The simplest of the latter, the goldfish equation, is found to represent a flat-space geodesic in curvilinear coordinates.

  12. Multibody dynamic simulation of knee contact mechanics

    PubMed Central

    Bei, Yanhong; Fregly, Benjamin J.

    2006-01-01

    Multibody dynamic musculoskeletal models capable of predicting muscle forces and joint contact pressures simultaneously would be valuable for studying clinical issues related to knee joint degeneration and restoration. Current three-dimensional multi-body knee models are either quasi-static with deformable contact or dynamic with rigid contact. This study proposes a computationally efficient methodology for combining multibody dynamic simulation methods with a deformable contact knee model. The methodology requires preparation of the articular surface geometry, development of efficient methods to calculate distances between contact surfaces, implementation of an efficient contact solver that accounts for the unique characteristics of human joints, and specification of an application programming interface for integration with any multibody dynamic simulation environment. The current implementation accommodates natural or artificial tibiofemoral joint models, small or large strain contact models, and linear or nonlinear material models. Applications are presented for static analysis (via dynamic simulation) of a natural knee model created from MRI and CT data and dynamic simulation of an artificial knee model produced from manufacturer’s CAD data. Small and large strain natural knee static analyses required 1 min of CPU time and predicted similar contact conditions except for peak pressure, which was higher for the large strain model. Linear and nonlinear artificial knee dynamic simulations required 10 min of CPU time and predicted similar contact force and torque but different contact pressures, which were lower for the nonlinear model due to increased contact area. This methodology provides an important step toward the realization of dynamic musculoskeletal models that can predict in vivo knee joint motion and loading simultaneously. PMID:15564115

  13. A comparison of variance reduction techniques for radar simulation

    NASA Astrophysics Data System (ADS)

    Divito, A.; Galati, G.; Iovino, D.

    Importance sampling and extreme value technique (EVT) and its generalization (G-EVT) were compared as to reduction of the variance of radar simulation estimates. Importance sampling has a greater potential for including a priori information in the simulation experiment, and subsequently to reduce the estimation errors. This feature is paid for by a lack of generality of the simulation procedure. The EVT technique is only valid when a probability tail should be estimated (false alarm problems) and requires, as the only a priori information, that the considered variate belongs to the exponential class. The G-EVT introducing a shape parameter to be estimated (when unknown), allows smaller estimation error to be attained than EVT. The G-EVT and, to a greater extent, the EVT, lead to a straightforward and general simulation procedure for probability tails estimations.

  14. Approximate Bisimulation-Based Reduction of Power System Dynamic Models

    SciTech Connect

    Stankovic, AM; Dukic, SD; Saric, AT

    2015-05-01

    In this paper we propose approximate bisimulation relations and functions for reduction of power system dynamic models in differential- algebraic (descriptor) form. The full-size dynamic model is obtained by linearization of the nonlinear transient stability model. We generalize theoretical results on approximate bisimulation relations and bisimulation functions, originally derived for a class of constrained linear systems, to linear systems in descriptor form. An algorithm for transient stability assessment is proposed and used to determine whether the power system is able to maintain the synchronism after a large disturbance. Two benchmark power systems are used to illustrate the proposed algorithm and to evaluate the applicability of approximate bisimulation relations and bisimulation functions for reduction of the power system dynamic models.

  15. Buckybomb: Reactive Molecular Dynamics Simulation.

    PubMed

    Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V

    2015-03-01

    Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672

  16. Methods for variance reduction in Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Bixler, Joel N.; Hokr, Brett H.; Winblad, Aidan; Elpers, Gabriel; Zollars, Byron; Thomas, Robert J.

    2016-03-01

    Monte Carlo simulations are widely considered to be the gold standard for studying the propagation of light in turbid media. However, due to the probabilistic nature of these simulations, large numbers of photons are often required in order to generate relevant results. Here, we present methods for reduction in the variance of dose distribution in a computational volume. Dose distribution is computed via tracing of a large number of rays, and tracking the absorption and scattering of the rays within discrete voxels that comprise the volume. Variance reduction is shown here using quasi-random sampling, interaction forcing for weakly scattering media, and dose smoothing via bi-lateral filtering. These methods, along with the corresponding performance enhancements are detailed here.

  17. Differential maneuvering simulator data reduction and analysis software

    NASA Technical Reports Server (NTRS)

    Beasley, G. P.; Sigman, R. S.

    1972-01-01

    A multielement data reduction and analysis software package has been developed for use with the Langley differential maneuvering simulator (DMS). This package, which has several independent elements, was developed to support all phases of DMS aircraft simulation studies with a variety of both graphical and tabular information. The overall software package is considered unique because of the number, diversity, and sophistication of the element programs available for use in a single study. The purpose of this paper is to discuss the overall DMS data reduction and analysis package by reviewing the development of the various elements of the software, showing typical results that can be obtained, and discussing how each element can be used.

  18. Dynamic procedure for filtered gyrokinetic simulations

    SciTech Connect

    Morel, P.; Banon Navarro, A.; Albrecht-Marc, M.; Carati, D.; Merz, F.; Goerler, T.; Jenko, F.

    2012-01-15

    Large eddy simulations (LES) of gyrokinetic plasma turbulence are investigated as interesting candidates to decrease the computational cost. A dynamic procedure is implemented in the gene code, allowing for dynamic optimization of the free parameters of the LES models (setting the amplitudes of dissipative terms). Employing such LES methods, one recovers the free energy and heat flux spectra obtained from highly resolved direct numerical simulations. Systematic comparisons are performed for different values of the temperature gradient and magnetic shear, parameters which are of prime importance in ion temperature gradient driven turbulence. Moreover, the degree of anisotropy of the problem, which can vary with parameters, can be adapted dynamically by the method that shows gyrokinetic large eddy simulation to be a serious candidate to reduce numerical cost of gyrokinetic solvers.

  19. Adaptive model reduction for nonsmooth discrete element simulation

    NASA Astrophysics Data System (ADS)

    Servin, Martin; Wang, Da

    2016-03-01

    A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies of the corresponding shape and mass distribution. The method also support particles merging with articulated multibody systems. A model approximation error is defined and used to derive conditions for when and where to apply reduction and refinement back into particles and smaller rigid bodies. Three methods for refinement are proposed and tested: prediction from contact events, trial solutions computed in the background and using split sensors. The computational performance can be increased by 5-50 times for model reduction level between 70-95 %.

  20. Computer simulation of microstructural dynamics

    SciTech Connect

    Grest, G.S.; Anderson, M.P.; Srolovitz, D.J.

    1985-01-01

    Since many of the physical properties of materials are determined by their microstructure, it is important to be able to predict and control microstructural development. A number of approaches have been taken to study this problem, but they assume that the grains can be described as spherical or hexagonal and that growth occurs in an average environment. We have developed a new technique to bridge the gap between the atomistic interactions and the macroscopic scale by discretizing the continuum system such that the microstructure retains its topological connectedness, yet is amenable to computer simulations. Using this technique, we have studied grain growth in polycrystalline aggregates. The temporal evolution and grain morphology of our model are in excellent agreement with experimental results for metals and ceramics.

  1. Flexible multibody simulation of automotive systems with non-modal model reduction techniques

    NASA Astrophysics Data System (ADS)

    Shiiba, Taichi; Fehr, Jörg; Eberhard, Peter

    2012-12-01

    The stiffness of the body structure of an automobile has a strong relationship with its noise, vibration, and harshness (NVH) characteristics. In this paper, the effect of the stiffness of the body structure upon ride quality is discussed with flexible multibody dynamics. In flexible multibody simulation, the local elastic deformation of the vehicle has been described traditionally with modal shape functions. Recently, linear model reduction techniques from system dynamics and mathematics came into the focus to find more sophisticated elastic shape functions. In this work, the NVH-relevant states of a racing kart are simulated, whereas the elastic shape functions are calculated with modern model reduction techniques like moment matching by projection on Krylov-subspaces, singular value decomposition-based reduction techniques, and combinations of those. The whole elastic multibody vehicle model consisting of tyres, steering, axle, etc. is considered, and an excitation with a vibration characteristics in a wide frequency range is evaluated in this paper. The accuracy and the calculation performance of those modern model reduction techniques is investigated including a comparison of the modal reduction approach.

  2. Dynamic Fracture Simulations of Explosively Loaded Cylinders

    SciTech Connect

    Arthur, Carly W.; Goto, D. M.

    2015-11-30

    This report documents the modeling results of high explosive experiments investigating dynamic fracture of steel (AerMet® 100 alloy) cylinders. The experiments were conducted at Lawrence Livermore National Laboratory (LLNL) during 2007 to 2008 [10]. A principal objective of this study was to gain an understanding of dynamic material failure through the analysis of hydrodynamic computer code simulations. Two-dimensional and three-dimensional computational cylinder models were analyzed using the ALE3D multi-physics computer code.

  3. Dynamic simulation recalls condensate piping event

    SciTech Connect

    Farrell, R.J.; Reneberg, K.O. ); Moy, H.C. )

    1994-05-01

    This article describes how experience gained from simulating and reconstructing a condensate piping event will be used by Consolidated Edison to analyze control system problems. A cooperative effort by Con Edison and the Chemical Engineering Department at Polytechnic University used modular modeling system to investigate the probable cause of a Con Edison condensate piping event. Con Edison commissioned the work to serve as a case study for the more general problem of control systems analysis using dynamic simulation and MMS.

  4. Molecular dynamic simulations of ocular tablet dissolution.

    PubMed

    Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire

    2013-11-25

    Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies. PMID:24073784

  5. Airborne Simulation of Launch Vehicle Dynamics

    NASA Technical Reports Server (NTRS)

    Miller, Christopher J.; Orr, Jeb S.; Hanson, Curtis E.; Gilligan, Eric T.

    2015-01-01

    In this paper we present a technique for approximating the short-period dynamics of an exploration-class launch vehicle during flight test with a high-performance surrogate aircraft in relatively benign endoatmospheric flight conditions. The surrogate vehicle relies upon a nonlinear dynamic inversion scheme with proportional-integral feedback to drive a subset of the aircraft states into coincidence with the states of a time-varying reference model that simulates the unstable rigid body dynamics, servodynamics, and parasitic elastic and sloshing dynamics of the launch vehicle. The surrogate aircraft flies a constant pitch rate trajectory to approximate the boost phase gravity turn ascent, and the aircraft's closed-loop bandwidth is sufficient to simulate the launch vehicle's fundamental lateral bending and sloshing modes by exciting the rigid body dynamics of the aircraft. A novel control allocation scheme is employed to utilize the aircraft's relatively fast control effectors in inducing various failure modes for the purposes of evaluating control system performance. Sufficient dynamic similarity is achieved such that the control system under evaluation is configured for the full-scale vehicle with no changes to its parameters, and pilot-control system interaction studies can be performed to characterize the effects of guidance takeover during boost. High-fidelity simulation and flight-test results are presented that demonstrate the efficacy of the design in simulating the Space Launch System (SLS) launch vehicle dynamics using the National Aeronautics and Space Administration (NASA) Armstrong Flight Research Center Fullscale Advanced Systems Testbed (FAST), a modified F/A-18 airplane (McDonnell Douglas, now The Boeing Company, Chicago, Illinois), over a range of scenarios designed to stress the SLS's Adaptive Augmenting Control (AAC) algorithm.

  6. Airborne Simulation of Launch Vehicle Dynamics

    NASA Technical Reports Server (NTRS)

    Gilligan, Eric T.; Miller, Christopher J.; Hanson, Curtis E.; Orr, Jeb S.

    2014-01-01

    In this paper we present a technique for approximating the short-period dynamics of an exploration-class launch vehicle during flight test with a high-performance surrogate aircraft in relatively benign endoatmospheric flight conditions. The surrogate vehicle relies upon a nonlinear dynamic inversion scheme with proportional-integral feedback to drive a subset of the aircraft states into coincidence with the states of a time-varying reference model that simulates the unstable rigid body dynamics, servodynamics, and parasitic elastic and sloshing dynamics of the launch vehicle. The surrogate aircraft flies a constant pitch rate trajectory to approximate the boost phase gravity-turn ascent, and the aircraft's closed-loop bandwidth is sufficient to simulate the launch vehicle's fundamental lateral bending and sloshing modes by exciting the rigid body dynamics of the aircraft. A novel control allocation scheme is employed to utilize the aircraft's relatively fast control effectors in inducing various failure modes for the purposes of evaluating control system performance. Sufficient dynamic similarity is achieved such that the control system under evaluation is optimized for the full-scale vehicle with no changes to its parameters, and pilot-control system interaction studies can be performed to characterize the effects of guidance takeover during boost. High-fidelity simulation and flight test results are presented that demonstrate the efficacy of the design in simulating the Space Launch System (SLS) launch vehicle dynamics using NASA Dryden Flight Research Center's Full-scale Advanced Systems Testbed (FAST), a modified F/A-18 airplane, over a range of scenarios designed to stress the SLS's adaptive augmenting control (AAC) algorithm.

  7. Molecular dynamics simulation of ice XII

    NASA Astrophysics Data System (ADS)

    Borzsák, István; Cummings, Peter T.

    1999-02-01

    Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.

  8. Fully dynamical simulation of central nuclear collisions.

    PubMed

    van der Schee, Wilke; Romatschke, Paul; Pratt, Scott

    2013-11-27

    We present a fully dynamical simulation of central nuclear collisions around midrapidity at LHC energies. Unlike previous treatments, we simulate all phases of the collision, including the equilibration of the system. For the simulation, we use numerical relativity solutions to anti-de Sitter space/conformal field theory for the preequilibrium stage, viscous hydrodynamics for the plasma equilibrium stage, and kinetic theory for the low-density hadronic stage. Our preequilibrium stage provides initial conditions for hydrodynamics, resulting in sizable radial flow. The resulting light particle spectra reproduce the measurements from the ALICE experiment at all transverse momenta. PMID:24329444

  9. Digital simulation of stiff linear dynamic systems.

    NASA Technical Reports Server (NTRS)

    Holland, L. D.; Walsh, J. R., Jr.; Kerr, J. H.

    1972-01-01

    A method is derived for digital computer simulation of linear time-invariant systems when the insignificant eigenvalues involved in such systems are eliminated by an ALSAP root removal technique. The method is applied to a thirteenth-order dynamic system representing a passive RLC network.

  10. Dynamic simulation of a reverse Brayton refrigerator

    SciTech Connect

    Peng, N.; Xiong, L. Y.; Dong, B.; Liu, L. Q.; Lei, L. L.; Tang, J. C.

    2014-01-29

    A test refrigerator based on the modified Reverse Brayton cycle has been developed in the Chinese Academy of Sciences recently. To study the behaviors of this test refrigerator, a dynamic simulation has been carried out. The numerical model comprises the typical components of the test refrigerator: compressor, valves, heat exchangers, expander and heater. This simulator is based on the oriented-object approach and each component is represented by a set of differential and algebraic equations. The control system of the test refrigerator is also simulated, which can be used to optimize the control strategies. This paper describes all the models and shows the simulation results. Comparisons between simulation results and experimental data are also presented. Experimental validation on the test refrigerator gives satisfactory results.

  11. ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*

    PubMed Central

    Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan

    2014-01-01

    Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670

  12. Test of a flexible spacecraft dynamics simulator

    NASA Technical Reports Server (NTRS)

    Dichmann, Donald; Sedlak, Joseph

    1998-01-01

    There are a number of approaches one can take to modeling the dynamics of a flexible body. While one can attempt to capture the full dynamical behavior subject to disturbances from actuators and environmental torques, such a detailed description often is unnecessary. Simplification is possible either by limiting the amplitude of motion to permit linearization of the dynamics equations or by restricting the types of allowed motion. In this work, we study the nonlinear dynamics of bending deformations of wire booms on spinning spacecraft. The theory allows for large amplitude excursions from equilibrium while enforcing constraints on the dynamics to prohibit those modes that are physically less relevant or are expected to damp out fast. These constraints explicitly remove the acoustic modes (i.e., longitudinal sound waves and shear waves) while allowing for arbitrary bending and twisting, motions which typically are of lower frequency. As a test case, a spin axis reorientation maneuver by the Polar Plasma Laboratory (POLAR) spacecraft has been simulated. POLAR was chosen as a representative spacecraft because it has flexible wire antennas that extend to a length of 65 meters. Bending deformations in these antennas could be quite large and have a significant effect on the attitude dynamics of the spacecraft body. Summary results from the simulation are presented along, with a comparison with POLAR flight data.

  13. Reduced order component models for flexible multibody dynamics simulations

    NASA Technical Reports Server (NTRS)

    Tsuha, Walter S.; Spanos, John T.

    1990-01-01

    Many flexible multibody dynamics simulation codes require some form of component description that properly characterizes the dynamic behavior of the system. A model reduction procedure for producing low order component models for flexible multibody simulation is described. Referred to as projection and assembly, the method is a Rayleigh-Ritz approach that uses partitions of the system modal matrix as component Ritz transformation matrices. It is shown that the projection and assembly method yields a reduced system model that preserves a specified set of the full order system modes. Unlike classical component mode synthesis methods, the exactness of the method described is obtained at the expense of having to compute the full order system modes. The paper provides a comprehensive description of the method, a proof of exactness, and numerical results demonstrating the method's effectiveness.

  14. Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks

    NASA Astrophysics Data System (ADS)

    Fahrenthold, Eric; Bass, Joseph

    2015-06-01

    Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general these potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new noholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.

  15. Geometric reduction of dynamical nonlocality in nanoscale quantum circuits

    PubMed Central

    Strambini, E.; Makarenko, K. S.; Abulizi, G.; de Jong, M. P.; van der Wiel, W. G.

    2016-01-01

    Nonlocality is a key feature discriminating quantum and classical physics. Quantum-interference phenomena, such as Young’s double slit experiment, are one of the clearest manifestations of nonlocality, recently addressed as dynamical to specify its origin in the quantum equations of motion. It is well known that loss of dynamical nonlocality can occur due to (partial) collapse of the wavefunction due to a measurement, such as which-path detection. However, alternative mechanisms affecting dynamical nonlocality have hardly been considered, although of crucial importance in many schemes for quantum information processing. Here, we present a fundamentally different pathway of losing dynamical nonlocality, demonstrating that the detailed geometry of the detection scheme is crucial to preserve nonlocality. By means of a solid-state quantum-interference experiment we quantify this effect in a diffusive system. We show that interference is not only affected by decoherence, but also by a loss of dynamical nonlocality based on a local reduction of the number of quantum conduction channels of the interferometer. With our measurements and theoretical model we demonstrate that this mechanism is an intrinsic property of quantum dynamics. Understanding the geometrical constraints protecting nonlocality is crucial when designing quantum networks for quantum information processing. PMID:26732751

  16. Geometric reduction of dynamical nonlocality in nanoscale quantum circuits

    NASA Astrophysics Data System (ADS)

    Strambini, E.; Makarenko, K. S.; Abulizi, G.; de Jong, M. P.; van der Wiel, W. G.

    2016-01-01

    Nonlocality is a key feature discriminating quantum and classical physics. Quantum-interference phenomena, such as Young’s double slit experiment, are one of the clearest manifestations of nonlocality, recently addressed as dynamical to specify its origin in the quantum equations of motion. It is well known that loss of dynamical nonlocality can occur due to (partial) collapse of the wavefunction due to a measurement, such as which-path detection. However, alternative mechanisms affecting dynamical nonlocality have hardly been considered, although of crucial importance in many schemes for quantum information processing. Here, we present a fundamentally different pathway of losing dynamical nonlocality, demonstrating that the detailed geometry of the detection scheme is crucial to preserve nonlocality. By means of a solid-state quantum-interference experiment we quantify this effect in a diffusive system. We show that interference is not only affected by decoherence, but also by a loss of dynamical nonlocality based on a local reduction of the number of quantum conduction channels of the interferometer. With our measurements and theoretical model we demonstrate that this mechanism is an intrinsic property of quantum dynamics. Understanding the geometrical constraints protecting nonlocality is crucial when designing quantum networks for quantum information processing.

  17. Mesoscopic Simulation Methods for Polymer Dynamics

    NASA Astrophysics Data System (ADS)

    Larson, Ronald

    2015-03-01

    We assess the accuracy and efficiency of mesoscopic simulation methods, namely Brownian Dynamics (BD), Stochastic Rotation Dynamics (SRD) and Dissipative Particle Dynamics (DPD), for polymers in solution at equilibrium and in flows in microfluidic geometries. Both SRD and DPD use solvent ``particles'' to carry momentum, and so account automatically for hydrodynamic interactions both within isolated polymer coils, and with other polymer molecules and with nearby solid boundaries. We assess quantitatively the effects of artificial particle inertia and fluid compressibility and show that they can be made small with appropriate choice of simulation parameters. We then use these methods to study flow-induced migration of polymer chains produced by: 1) hydrodynamic interactions, 2) streamline curvature or stress-gradients, and 3) convection of wall depletion zones. We show that huge concentration gradients can be produced by these mechanisms in microfluidic geometries that can be exploited for separation of polymers by size in periodic contraction-expansion geometries. We also assess the range of conditions for which BD, SRD or DPD is preferable for mesoscopic simulations. Finally, we show how such methods can be used to simulate quantitatively the swimming of micro-organisms such as E. coli. In collaboration with Lei Jiang and Tongyang Zhao, University of Michigan, Ann Arbor, MI.

  18. Simulation studies using multibody dynamics code DART

    NASA Technical Reports Server (NTRS)

    Keat, James E.

    1989-01-01

    DART is a multibody dynamics code developed by Photon Research Associates for the Air Force Astronautics Laboratory (AFAL). The code is intended primarily to simulate the dynamics of large space structures, particularly during the deployment phase of their missions. DART integrates nonlinear equations of motion numerically. The number of bodies in the system being simulated is arbitrary. The bodies' interconnection joints can have an arbitrary number of degrees of freedom between 0 and 6. Motions across the joints can be large. Provision for simulating on-board control systems is provided. Conservation of energy and momentum, when applicable, are used to evaluate DART's performance. After a brief description of DART, studies made to test the program prior to its delivery to AFAL are described. The first is a large angle reorientating of a flexible spacecraft consisting of a rigid central hub and four flexible booms. Reorientation was accomplished by a single-cycle sine wave shape torque input. In the second study, an appendage, mounted on a spacecraft, was slewed through a large angle. Four closed-loop control systems provided control of this appendage and of the spacecraft's attitude. The third study simulated the deployment of the rim of a bicycle wheel configuration large space structure. This system contained 18 bodies. An interesting and unexpected feature of the dynamics was a pulsing phenomena experienced by the stays whole playout was used to control the deployment. A short description of the current status of DART is given.

  19. Reduction of overestimation in interval arithmetic simulation of biological wastewater treatment processes

    NASA Astrophysics Data System (ADS)

    Rauh, Andreas; Kletting, Marco; Aschemann, Harald; Hofer, Eberhard P.

    2007-02-01

    A novel interval arithmetic simulation approach is introduced in order to evaluate the performance of biological wastewater treatment processes. Such processes are typically modeled as dynamical systems where the reaction kinetics appears as additive nonlinearity in state. In the calculation of guaranteed bounds of state variables uncertain parameters and uncertain initial conditions are considered. The recursive evaluation of such systems of nonlinear state equations yields overestimation of the state variables that is accumulating over the simulation time. To cope with this wrapping effect, innovative splitting and merging criteria based on a recursive uncertain linear transformation of the state variables are discussed. Additionally, re-approximation strategies for regions in the state space calculated by interval arithmetic techniques using disjoint subintervals improve the simulation quality significantly if these regions are described by several overlapping subintervals. This simulation approach is used to find a practical compromise between computational effort and simulation quality. It is pointed out how these splitting and merging algorithms can be combined with other methods that aim at the reduction of overestimation by applying consistency techniques. Simulation results are presented for a simplified reduced-order model of the reduction of organic matter in the activated sludge process of biological wastewater treatment.

  20. Dynamic Simulation of a Helium Liquefier

    SciTech Connect

    Maekawa, R.; Ooba, K.; Mito, T.; Nobutoki, M.

    2004-06-23

    Dynamic behavior of a helium liquefier has been studied in detail with a Cryogenic Process REal-time SimulaTor (C-PREST) at the National Institute for Fusion Science (NIFS). The C-PREST is being developed to integrate large-scale helium cryogenic plant design, operation and maintenance for optimum process establishment. As a first step of simulations of cooldown to 4.5 K with the helium liquefier model is conducted, which provides a plant-process validation platform. The helium liquefier consists of seven heat exchangers, a liquid-nitrogen (LN2) precooler, two expansion turbines and a liquid-helium (LHe) reservoir. Process simulations are fulfilled with sequence programs, which were implemented with C-PREST based on an existing liquefier operation. The interactions of a JT valve, a JT-bypass valve and a reservoir-return valve have been dynamically simulated. The paper discusses various aspects of refrigeration process simulation, including its difficulties such as a balance between complexity of the adopted models and CPU time.

  1. Dynamic simulation of the mastication muscles

    NASA Astrophysics Data System (ADS)

    Weingaertner, Tim; Albrecht, Jochen

    1998-05-01

    The purpose of a simulated operation system in craniofacial surgery is to evaluate and visualize the results of operations on the overall facial shape of the patient and on the functionality of his jaw. This paper presents the analyzation of muscle movements in the mastication system by applying real jaw movements to the simulation. With this method an accurate modeling of the mastication muscles can be performed which is a prerequisite for a realistic simulation and precise intra- operative registration. According to this results a large- scale musculoskeletal model of the mastication system is generated including kinematic and dynamic parameters. By integrating distance sensors in the simulation of a segmented CT (computer tomograph) image of the maxilla and mandible the motions of the masticatory muscles during different kinds of jaw movements have been analyzed. The data for this motions have been recorded by a commercial system (CONDYLOCOMP LR3) on a test person and transformed to the graphical simulation system. This method for the first time allows to observe the dynamics of the mastication muscles and their different parameters like muscle length ratio and velocity. The integration of a kinematic model for the jaw movement makes it possible to analyze non traced movements.

  2. Thermostability of Enzymes from Molecular Dynamics Simulations.

    PubMed

    Zeiske, Tim; Stafford, Kate A; Palmer, Arthur G

    2016-06-14

    Thermodynamic stability is a central requirement for protein function, and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitro thermostability of members of the bacterial ribonuclease HI (RNase H) family of endonucleases. The temperature dependence of the generalized order parameter, S, for four RNase H homologues, from psychrotrophic, mesophilic, and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. PMID:27123810

  3. Reduction of dynamical biochemical reactions networks in computational biology

    PubMed Central

    Radulescu, O.; Gorban, A. N.; Zinovyev, A.; Noel, V.

    2012-01-01

    Biochemical networks are used in computational biology, to model mechanistic details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multiscaleness, an important property of these networks, can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler models, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state (QSS) and quasi-equilibrium approximations (QE), and provide practical recipes for model reduction of linear and non-linear networks. We also discuss the application of model reduction to the problem of parameter identification, via backward pruning machine learning techniques. PMID:22833754

  4. Nanoindentation of Zr by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.

    2015-12-01

    Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.

  5. Numerical Simulations of Ion Cloud Dynamics

    NASA Astrophysics Data System (ADS)

    Sillitoe, Nicolas; Hilico, Laurent

    We explain how to perform accurate numerical simulations of ion cloud dynamics by discussing the relevant orders of magnitude of the characteristic times and frequencies involved in the problem and the computer requirement with respect to the ion cloud size. We then discuss integration algorithms and Coulomb force parallelization. We finally explain how to take into account collisions, cooling laser interaction and chemical reactions in a Monte Carlo approach and discuss how to use random number generators to that end.

  6. Simulation of lead-acid battery using model order reduction

    NASA Astrophysics Data System (ADS)

    Esfahanian, Vahid; Ansari, Amir Babak; Torabi, Farschad

    2015-04-01

    In this study, a reduced order model (ROM) based on proper orthogonal decomposition (POD) method has been applied to the coupled one-dimensional electrochemical transport equations in order to efficiently simulate lead-acid batteries, numerically. The governing equations, including conservation of charge in solid and liquid phases and conservation of species are solved simultaneously. The POD-based method for a lead-acid cell is used to simulate a discharge process to show the capability of the present method. The obtained results show that not only the POD-based ROM of lead-acid battery significantly decreases the computational time but also there is an excellent agreement with the results of previous computational fluid dynamics (CFD) models.

  7. Simulation of counterflow pedestrian dynamics using spheropolygons

    NASA Astrophysics Data System (ADS)

    Alonso-Marroquín, Fernando; Busch, Jonathan; Chiew, Coraline; Lozano, Celia; Ramírez-Gómez, Álvaro

    2014-12-01

    Pedestrian dynamic models are typically designed for comfortable walking or slightly congested conditions and typically use a single disk or combination of three disks for the shape of a pedestrian. Under crowd conditions, a more accurate pedestrian shape has advantages over the traditional single or three-disks model. We developed a method for simulating pedestrian dynamics in a large dense crowd of spheropolygons adapted to the cross section of the chest and arms of a pedestrian. Our numerical model calculates pedestrian motion from Newton's second law, taking into account viscoelastic contact forces, contact friction, and ground-reaction forces. Ground-reaction torque was taken to arise solely from the pedestrians' orientation toward their preferred destination. Simulations of counterflow pedestrians dynamics in corridors were used to gain insight into a tragic incident at the Madrid Arena pavilion in Spain, where five girls were crushed to death. The incident took place at a Halloween Celebration in 2012, in a long, densely crowded hallway used as entrance and exit at the same time. Our simulations reconstruct the mechanism of clogging in the hallway. The hypothetical case of a total evacuation order was also investigated. The results highlights the importance of the pedestrians' density and the effect of counterflow in the onset of avalanches and clogging and provides an estimation of the number of injuries based on a calculation of the contact-force network between the pedestrians.

  8. Simulation of counterflow pedestrian dynamics using spheropolygons.

    PubMed

    Alonso-Marroquín, Fernando; Busch, Jonathan; Chiew, Coraline; Lozano, Celia; Ramírez-Gómez, Álvaro

    2014-12-01

    Pedestrian dynamic models are typically designed for comfortable walking or slightly congested conditions and typically use a single disk or combination of three disks for the shape of a pedestrian. Under crowd conditions, a more accurate pedestrian shape has advantages over the traditional single or three-disks model. We developed a method for simulating pedestrian dynamics in a large dense crowd of spheropolygons adapted to the cross section of the chest and arms of a pedestrian. Our numerical model calculates pedestrian motion from Newton's second law, taking into account viscoelastic contact forces, contact friction, and ground-reaction forces. Ground-reaction torque was taken to arise solely from the pedestrians' orientation toward their preferred destination. Simulations of counterflow pedestrians dynamics in corridors were used to gain insight into a tragic incident at the Madrid Arena pavilion in Spain, where five girls were crushed to death. The incident took place at a Halloween Celebration in 2012, in a long, densely crowded hallway used as entrance and exit at the same time. Our simulations reconstruct the mechanism of clogging in the hallway. The hypothetical case of a total evacuation order was also investigated. The results highlights the importance of the pedestrians' density and the effect of counterflow in the onset of avalanches and clogging and provides an estimation of the number of injuries based on a calculation of the contact-force network between the pedestrians. PMID:25615220

  9. Electronic continuum model for molecular dynamics simulations.

    PubMed

    Leontyev, I V; Stuchebrukhov, A A

    2009-02-28

    A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627

  10. Integrated computer simulation on FIR FEL dynamics

    SciTech Connect

    Furukawa, H.; Kuruma, S.; Imasaki, K.

    1995-12-31

    An integrated computer simulation code has been developed to analyze the RF-Linac FEL dynamics. First, the simulation code on the electron beam acceleration and transport processes in RF-Linac: (LUNA) has been developed to analyze the characteristics of the electron beam in RF-Linac and to optimize the parameters of RF-Linac. Second, a space-time dependent 3D FEL simulation code (Shipout) has been developed. The RF-Linac FEL total simulations have been performed by using the electron beam data from LUNA in Shipout. The number of particles using in a RF-Linac FEL total simulation is approximately 1000. The CPU time for the simulation of 1 round trip is about 1.5 minutes. At ILT/ILE, Osaka, a 8.5MeV RF-Linac with a photo-cathode RF-gun is used for FEL oscillation experiments. By using 2 cm wiggler, the FEL oscillation in the wavelength approximately 46 {mu}m are investigated. By the simulations using LUNA with the parameters of an ILT/ILE experiment, the pulse shape and the energy spectra of the electron beam at the end of the linac are estimated. The pulse shape of the electron beam at the end of the linac has sharp rise-up and it slowly decays as a function of time. By the RF-linac FEL total simulations with the parameters of an ILT/ILE experiment, the dependencies of the start up of the FEL oscillations on the pulse shape of the electron beam at the end of the linac are estimated. The coherent spontaneous emission effects and the quick start up of FEL oscillations have been observed by the RF-Linac FEL total simulations.

  11. Simulating stochastic dynamics using large time steps.

    PubMed

    Corradini, O; Faccioli, P; Orland, H

    2009-12-01

    We present an approach to investigate the long-time stochastic dynamics of multidimensional classical systems, in contact with a heat bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short- and long-time scales and both molecular dynamics or Monte Carlo (MC) simulations are generally inefficient. Using a field theoretic approach, we perform analytically the average over the short-time stochastic fluctuations. This way, we obtain an effective theory, which generates the same long-time dynamics of the original theory, but has a lower time-resolution power. Such an approach is used to develop an improved version of the MC algorithm, which is particularly suitable to investigate the dynamics of rare conformational transitions. In the specific case of molecular systems at room temperature, we show that elementary integration time steps used to simulate the effective theory can be chosen a factor approximately 100 larger than those used in the original theory. Our results are illustrated and tested on a simple system, characterized by a rugged energy landscape. PMID:20365123

  12. Molecular dynamics simulation of liquid sulfur dioxide.

    PubMed

    Ribeiro, Mauro C C

    2006-05-01

    A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k). PMID:16640437

  13. Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Byutner, Oleksiy; Smith, Grant

    2001-03-01

    In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.

  14. Simulating coronal condensation dynamics in 3D

    NASA Astrophysics Data System (ADS)

    Moschou, S. P.; Keppens, R.; Xia, C.; Fang, X.

    2015-12-01

    We present numerical simulations in 3D settings where coronal rain phenomena take place in a magnetic configuration of a quadrupolar arcade system. Our simulation is a magnetohydrodynamic simulation including anisotropic thermal conduction, optically thin radiative losses, and parametrised heating as main thermodynamical features to construct a realistic arcade configuration from chromospheric to coronal heights. The plasma evaporation from chromospheric and transition region heights eventually causes localised runaway condensation events and we witness the formation of plasma blobs due to thermal instability, that evolve dynamically in the heated arcade part and move gradually downwards due to interchange type dynamics. Unlike earlier 2.5D simulations, in this case there is no large scale prominence formation observed, but a continuous coronal rain develops which shows clear indications of Rayleigh-Taylor or interchange instability, that causes the denser plasma located above the transition region to fall down, as the system moves towards a more stable state. Linear stability analysis is used in the non-linear regime for gaining insight and giving a prediction of the system's evolution. After the plasma blobs descend through interchange, they follow the magnetic field topology more closely in the lower coronal regions, where they are guided by the magnetic dips.

  15. Molecular Dynamics Simulation of Shock Induced Detonation

    NASA Astrophysics Data System (ADS)

    Tomar, Vikas; Zhou, Min

    2004-07-01

    This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.

  16. Dynamic simulator for PEFC propulsion plant

    SciTech Connect

    Hiraide, Masataka; Kaneda, Eiichi; Sato, Takao

    1996-12-31

    This report covers part of a joint study on a PEFC propulsion system for surface ships, summarized in a presentation to this Seminar, entitled {open_quote}Study on a Polymer Electrolyte Fuel Cell (PEFC) Propulsion System for Surface Ships{close_quotes}, and which envisages application to a 1,500 DWT cargo vessel. The work presented here focuses on a simulation study on PEFC propulsion plant performance, and particularly on the system response to changes in load. Using a dynamic simulator composed of system components including fuel cell, various simulations were executed, to examine the performance of the system as a whole and of the individual system components under quick and large load changes such as occasioned by maneuvering operations and by racing when the propeller emerges above water in heavy sea.

  17. Molecular-dynamics simulations of lead clusters

    NASA Astrophysics Data System (ADS)

    Hendy, S. C.; Hall, B. D.

    2001-08-01

    Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.

  18. Exploiting Enzymatic Dynamic Reductive Kinetic Resolution (DYRKR) in Stereocontrolled Synthesis

    PubMed Central

    Applegate, Gregory A.; Berkowitz, David B.

    2015-01-01

    Over the past two decades, the domains of both frontline synthetic organic chemistry and process chemistry and have seen an increase in crosstalk between asymmetric organic/organometallic approaches and enzymatic approaches to stereocontrolled synthesis. This review highlights the particularly auspicious role for dehydrogenase enzymes in this endeavor, with a focus on dynamic reductive kinetic resolutions (DYRKR) to “deracemize” building blocks, often setting two stereocenters in so doing. The scope and limitations of such dehydrogenase-mediated processes are overviewed, as are future possibilities for the evolution of enzymatic DYRKR. PMID:26622223

  19. An adaptive model order reduction by proper snapshot selection for nonlinear dynamical problems

    NASA Astrophysics Data System (ADS)

    Nigro, P. S. B.; Anndif, M.; Teixeira, Y.; Pimenta, P. M.; Wriggers, P.

    2016-04-01

    Model Order Reduction (MOR) methods are employed in many fields of Engineering in order to reduce the processing time of complex computational simulations. A usual approach to achieve this is the application of Galerkin projection to generate representative subspaces (reduced spaces). However, when strong nonlinearities in a dynamical system are present and this technique is employed several times along the simulation, it can be very inefficient. This work proposes a new adaptive strategy, which ensures low computational cost and small error to deal with this problem. This work also presents a new method to select snapshots named Proper Snapshot Selection (PSS). The objective of the PSS is to obtain a good balance between accuracy and computational cost by improving the adaptive strategy through a better snapshot selection in real time (online analysis). With this method, it is possible a substantial reduction of the subspace, keeping the quality of the model without the use of the Proper Orthogonal Decomposition (POD).

  20. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    SciTech Connect

    Steven R Prescott; Curtis Smith

    2011-07-01

    provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.

  1. Brownian Dynamics Simulation of Macromolecule Diffusion in a Protocell

    NASA Astrophysics Data System (ADS)

    Ando, Tadashi; Skolnick, Jeffrey

    2011-01-01

    The interiors of all living cells are highly crowded with macro molecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green fluorescent protein (GFP) in E. coli is ~10-fold slower than in dilute conditions. In this study, we performed Brownian dynamics (BD) simulations of rigid macromolecules in a crowded environment mimicking the cytosol of E. coli to study the motions of macromolecules. The simulation systems contained 35 70S ribosomes, 750 glycolytic enzymes, 75 GFPs, and 392 tRNAs in a 100 nm × 100 nm × 100 nm simulation box, where the macromolecules were represented by rigid-objects of one bead per amino acid or four beads per nucleotide models. Diffusion tensors of these molecules in dilute solutions were estimated by using a hydrodynamic theory to take into account the diffusion anisotropy of arbitrary shaped objects in the BD simulations. BD simulations of the system where each macromolecule is represented by its Stokes radius were also performed for comparison. Excluded volume effects greatly reduce the mobility of molecules in crowded environments for both molecular-shaped and equivalent sphere systems. Additionally, there were no significant differences in the reduction of diffusivity over the entire range of molecular size between two systems. However, the reduction in diffusion of GFP in these systems was still 4-5 times larger than for the in vivo experiment. We will discuss other plausible factors that might cause the large reduction in diffusion in vivo.

  2. Stress Reduction in Adjacent Level Discs via Dynamic Instrumentation: A Finite Element Analysis

    PubMed Central

    Castellvi, Antonio E.; Huang, Hao; Vestgaarden, Tov; Saigal, Sunil; Pienkowski, David

    2007-01-01

    Background Conventional (rigid) fusion instrumentation is believed to accelerate the degeneration of adjacent discs by increasing stresses caused by motion discontinuity. Fusion instrumentation that employs reduced rod stiffness and increased axial motion, or dynamic instrumentation, may partially alleviate this problem, but the effects of this instrumentation on the stresses in the adjacent disc are unknown. We used a finiteelement model to calculate and compare the stresses in the adjacent-level disc that are induced by rigid and dynamic posterior lumbar fusion instrumentation. Methods A 3-dimensional finite-element model of the lumbar spine was obtained that simulated flexion and extension. The L5–S1 segment of this model was fused, and the L4–L5 segment was fixed with rigid or dynamic instrumentation. The mechanical properties of the dynamic instrumentation were determined by laboratory testing and then used in the finite-element model. Peak stresses in the lumbar discs were calculated and compared. Results The reduced-stiffness component of the dynamic instrumentation was associated with a 1% to 2% reduction in peak compressive stresses in the adjacent-level disc (at 45° flexion), and the increased axial motion component of this instrumentation reduced peak disc stress by 8% to 9%. Areas of disc tissue exposed to 80% of peak stresses of 6.17 MPa were 47% less for discs adjacent to dynamic instrumentation than for those adjacent to rigid instrumentation. Conclusions Reduced stiffness and increased axial motion of dynamic posterior lumbar fusion instrumentation designs result in an approximately 10% cumulative stress reduction for each flexion cycle. The effect of this stress reduction over many cycles may be substantial. Clinical Relevance The cumulative effect of this reduced amplitude and distribution of peak stresses in the adjacent disc may partially alleviate the problem of adjacent-level disc degeneration. PMID:25802582

  3. Monoamine transporters: insights from molecular dynamics simulations

    PubMed Central

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  4. Local Refinements in Classical Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Fackeldey, Konstantin; Weber, Marcus

    2014-03-01

    Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.

  5. Biofilm attachment reduction on bioinspired, dynamic, micro-wrinkling surfaces

    NASA Astrophysics Data System (ADS)

    Epstein, Alexander K.; Hong, Donggyoon; Kim, Philseok; Aizenberg, Joanna

    2013-09-01

    Most bacteria live in multicellular communities known as biofilms that are adherent to surfaces in our environment, from sea beds to plumbing systems. Biofilms are often associated with clinical infections, nosocomial deaths and industrial damage such as bio-corrosion and clogging of pipes. As mature biofilms are extremely challenging to eradicate once formed, prevention is advantageous over treatment. However, conventional surface chemistry strategies are either generally transient, due to chemical masking, or toxic, as in the case of leaching marine antifouling paints. Inspired by the nonfouling skins of echinoderms and other marine organisms, which possess highly dynamic surface structures that mechanically frustrate bio-attachment, we have developed and tested a synthetic platform based on both uniaxial mechanical strain and buckling-induced elastomer microtopography. Bacterial biofilm attachment to the dynamic substrates was studied under an array of parameters, including strain amplitude and timescale (1-100 mm s-1), surface wrinkle length scale, bacterial species and cell geometry, and growth time. The optimal conditions for achieving up to ˜ 80% Pseudomonas aeruginosa biofilm reduction after 24 h growth and ˜ 60% reduction after 48 h were combinatorially elucidated to occur at 20% strain amplitude, a timescale of less than ˜ 5 min between strain cycles and a topography length scale corresponding to the cell dimension of ˜ 1 μm. Divergent effects on the attachment of P. aeruginosa, Staphylococcus aureus and Escherichia coli biofilms showed that the dynamic substrate also provides a new means of species-specific biofilm inhibition, or inversely, selection for a desired type of bacteria, without reliance on any toxic or transient surface chemical treatments.

  6. Dynamical simulation of dipolar Janus colloids: Dynamical properties

    NASA Astrophysics Data System (ADS)

    Hagy, Matthew C.; Hernandez, Rigoberto

    2013-05-01

    The dynamical properties of dipolar Janus particles are studied through simulation using our previously-developed detailed pointwise (PW) model and an isotropically coarse-grained (CG) model [M. C. Hagy and R. Hernandez, J. Chem. Phys. 137, 044505 (2012), 10.1063/1.4737432]. The CG model is found to have accelerated dynamics relative to the PW model over a range of conditions for which both models have near identical static equilibrium properties. Physically, this suggests dipolar Janus particles have slower transport properties (such as diffusion) in comparison to isotropically attractive particles. Time rescaling and damping with Langevin friction are explored to map the dynamics of the CG model to that of the PW model. Both methods map the diffusion constant successfully and improve the velocity autocorrelation function and the mean squared displacement of the CG model. Neither method improves the distribution of reversible bond durations f(tb) observed in the CG model, which is found to lack the longer duration reversible bonds observed in the PW model. We attribute these differences in f(tb) to changes in the energetics of multiple rearrangement mechanisms. This suggests a need for new methods that map the coarse-grained dynamics of such systems to the true time scale.

  7. Dynamic transitions in molecular dynamics simulations of supercooled silicon

    NASA Astrophysics Data System (ADS)

    Mei, Xiaojun; Eapen, Jacob

    2013-04-01

    Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.

  8. Dynamic simulations of membranes with cytoskeletal interactions

    NASA Astrophysics Data System (ADS)

    Lin, Lawrence C.-L.; Brown, Frank L. H.

    2005-07-01

    We describe a simulation algorithm for the dynamics of elastic membrane sheets over long length and time scales. Our model includes implicit hydrodynamic coupling between membrane and surrounding solvent and allows for arbitrary external forces acting on the membrane surface. In particular, the methodology is well suited to studying membranes in interaction with cytoskeletal filaments. We present results for the thermal undulations of a lipid bilayer attached to a regular network of spectrin filaments as a model for the red blood cell membrane. The dynamic fluctuations of the bilayer over the spectrin network are quantified and used to predict the macroscopic diffusion constant of band 3 on the surface of the red blood cell. We find that thermal undulations likely play a role in the mobility of band 3 in the plane of the erythrocyte membrane.

  9. Molecular Dynamics Simulations of Graphene Oxide Frameworks

    SciTech Connect

    Zhu, Pan; Sumpter, Bobby G; Meunier, V.; Nicolai, Adrien

    2013-01-01

    We use quantum mechanical calculations to develop a full set of force field parameters in order to perform molecular dynamics simulations to understand and optimize the molecular storage properties inside Graphene Oxide Frameworks (GOFs). A set of boron-related parameters for commonly used empirical force fields is determined to describe the non-bonded and bonded interactions between linear boronic acid linkers and graphene sheets of GOF materials. The transferability of the parameters is discussed and their validity is quantified by comparing quantum mechanical and molecular mechanical structural and vibrational properties. The application of the model to the dynamics of water inside the GOFs reveals significant variations in structural flexibility of GOF depending on the linker density, which is shown to be usable as a tuning parameter for desired diffusion properties.

  10. Finite element simulation of pipe dynamic response

    SciTech Connect

    Slagis, G.C.; Litton, R.W.

    1996-12-01

    Nonlinear finite element dynamic analyses of the response of a pipe span to controlled-displacement, sinusoidal vibration have been performed. The objective of this preliminary study is to compare strain and acceleration response data to those generated by Beaney in the Berkeley Nuclear Laboratories experiments. Results for an unpressurized, 5 Hz, carbon steel pipe are in good agreement with the experiments. Hence, it appears that analytical simulation will be useful to assess seismic margins. Recommendations for additional studies are provided. The analyses confirm the test results--dynamic response is greatly attenuated by material plasticity. Analytical strains and accelerations are about 30% higher than test data. There are several possible explanations for the differences. To assess the effect of frequency on response, the length of the pipe span was increased. Analysis of the longer, 2 Hz, pipe span shows significantly greater cyclic strains than the 5 Hz span at the same input excitation levels.

  11. Molecular dynamics simulations of weak detonations.

    PubMed

    Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie

    2011-12-01

    Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055

  12. Osmosis : a molecular dynamics computer simulation study

    NASA Astrophysics Data System (ADS)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  13. Isotropic MD simulations of dynamic brittle fracture

    SciTech Connect

    Espanol, P.; Rubio, M.A.; Zuniga, I.

    1996-12-01

    The authors present results obtained by molecular dynamics simulations on the propagation of fast cracks in triangular 2D lattices. Their aim is to simulate Mode 1 fracture of brittle isotropic materials. They propose a force law that respects the isotropy of the material. The code yields the correct imposed sound c{sub {parallel}}, shear c{sub {perpendicular}} and surface V{sub R} wave speeds. Different notch lengths are systematically studied. They observed that initially the cracks are linear and always branch at a particular critical velocity c* {approx} 0.8V{sub R} and that this occurs when the crack tip reaches the position of a front emitted from the initial crack tip and propagating at a speed c = 0.68V{sub R}.

  14. Dynamic Curving Simulation of Tilting Train

    NASA Astrophysics Data System (ADS)

    Zeng, Jing; Luo, Ren

    The application of carbody tilting technology is the most efficient way to raise train speed during curve negotiations. This paper mainly deals with the dynamic performance simulation of the tilting train. Through the establishment of the nonlinear mathematical model for the titling train electromechanical coupled system, the carbody tilting control law, bogie radial steering mechanism, and titling train curving performance are investigated. The effect of time delay caused by the sensing and control system on the tilting performance of the train is analyzed, and the compensation methods for the time delay effect are studied.

  15. Dynamic Deployment Simulations of Inflatable Space Structures

    NASA Technical Reports Server (NTRS)

    Wang, John T.

    2005-01-01

    The feasibility of using Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method in LSDYNA to simulate the dynamic deployment of inflatable space structures is investigated. The CV and ALE methods were used to predict the inflation deployments of three folded tube configurations. The CV method was found to be a simple and computationally efficient method that may be adequate for modeling slow inflation deployment sine the inertia of the inflation gas can be neglected. The ALE method was found to be very computationally intensive since it involves the solving of three conservative equations of fluid as well as dealing with complex fluid structure interactions.

  16. Molecular dynamics simulations of dense plasmas

    SciTech Connect

    Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.

    1993-12-31

    We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.

  17. All-atom simulations of crowding effects on ubiquitin dynamics

    NASA Astrophysics Data System (ADS)

    Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo

    2013-08-01

    It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (˜0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.

  18. Molecular dynamics simulation of amorphous indomethacin.

    PubMed

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-01-01

    Molecular dynamics (MD) simulations have been conducted using an assembly consisting of 105 indomethacin (IMC) molecules and 12 water molecules to investigate the underlying dynamic (e.g., rotational and translational diffusivities and conformation relaxation rates) and structural properties (e.g., conformation, hydrogen-bonding distributions, and interactions of water with IMC) of amorphous IMC. These properties may be important in predicting physical stability of this metastable material. The IMC model was constructed using X-ray diffraction data with the force-field parameters mostly assigned by analogy with similar groups in Amber-ff03 and atomic charges calculated with the B3LYP/ccpVTZ30, IEFPCM, and RESP models. The assemblies were initially equilibrated in their molten state and cooled through the glass transition temperature to form amorphous solids. Constant temperature dynamic runs were then carried out above and below the T(g) (i.e., at 600 K (10 ns), 400 K (350 ns), and 298 K (240 ns)). The density (1.312 ± 0.003 g/cm(3)) of the simulated amorphous solid at 298 K was close to the experimental value (1.32 g/cm(3)) while the estimated T(g) (384 K) was ~64 degrees higher than the experimental value (320 K) due to the faster cooling rate. Due to the hindered rotation of its amide bond, IMC can exist in different diastereomeric states. Different IMC conformations were sufficiently sampled in the IMC melt or vapor, but transitions occurred rarely in the glass. The hydrogen-bonding patterns in amorphous IMC are more complex in the amorphous state than in the crystalline polymorphs. Carboxylic dimers that are dominant in α- and γ-crystals were found to occur at a much lower probability in the simulated IMC glasses while hydrogen-bonded IMC chains were more easily identified patterns in the simulated amorphous solids. To determine molecular diffusivity, a novel analytical method is proposed to deal with the non-Einsteinian behavior, in which the temporal

  19. Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations.

    PubMed

    Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong

    2016-08-21

    Herein we have used combined static electronic structure calculations and "on-the-fly" global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the (1)ππ(∗), (1)nπ(∗), and S0 states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated (1)ππ(∗) system. The first is the diabatic ESIPT process along the (1)ππ(∗) potential energy profile. The generated (1)ππ(∗) keto species then decays to the S0 state via the keto (1)ππ(∗)/gs conical intersection. The second is internal conversion to the dark (1)nπ(∗) state near the (1)ππ(∗) /(1)nπ(∗) crossing point in the course of the diabatic (1)ππ(∗) ESIPT process. Our following dynamics simulations have shown that the ESIPT and (1)ππ(∗) → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the (1)ππ(∗) → S0 internal conversion in the keto region, the (1)ππ(∗) → (1)nπ(∗) internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone. PMID:27544106

  20. Atomistic molecular dynamic simulations of multiferroics.

    PubMed

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

    2012-08-10

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300

  1. Atomistic Molecular Dynamic Simulations of Multiferroics

    NASA Astrophysics Data System (ADS)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  2. Dynamical simulations of vesicle growth and division

    NASA Astrophysics Data System (ADS)

    Ruiz-Herrero, Teresa; Mahadevan, L.

    2015-03-01

    Prebiotic cells constitute a beautiful and intriguing example of self-replicating vesicles. How these cells managed to grow and divide without sophisticated machinery is still an open question. The properties of these primitive vesicles can shed light on the ways modern cells have evolved by exploiting those characteristics to develop their replication mechanisms. The equilibrium configurations of elastic shells are well understood, however the dynamical behavior during growth still lacks of a deep theoretical understanding. To study vesicle growth from a general perspective, we have developed a minimal generic model where vesicles are represented by a 2D spring network and characterized by a minimum set of magnitudes: growth rate, permeability, bending stiffness, viscosity and temperature. We have performed hybrid molecuar dynamic simulations as a function of a reduced set of dimensionless parameters. Three main outcomes were observed: vesicles that grow without division, vesicles that divide symmetrically, and vesicles that act as generators of daughter vesicles. The type of outcome depends on the system parameters and specifically on its dynamics via two timescales. Furthermore, we found sets of parameters where the system shows size homeostasis. TRH was supported by Ramon Areces Foundation.

  3. Quantum molecular dynamics simulations of dense matter

    SciTech Connect

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  4. Digital system for structural dynamics simulation

    NASA Technical Reports Server (NTRS)

    Krauter, A. I.; Lagace, L. J.; Wojnar, M. K.; Glor, C.

    1982-01-01

    State-of-the-art digital hardware and software for the simulation of complex structural dynamic interactions, such as those which occur in rotating structures (engine systems). System were incorporated in a designed to use an array of processors in which the computation for each physical subelement or functional subsystem would be assigned to a single specific processor in the simulator. These node processors are microprogrammed bit-slice microcomputers which function autonomously and can communicate with each other and a central control minicomputer over parallel digital lines. Inter-processor nearest neighbor communications busses pass the constants which represent physical constraints and boundary conditions. The node processors are connected to the six nearest neighbor node processors to simulate the actual physical interface of real substructures. Computer generated finite element mesh and force models can be developed with the aid of the central control minicomputer. The control computer also oversees the animation of a graphics display system, disk-based mass storage along with the individual processing elements.

  5. Dynamics simulations for engineering macromolecular interactions

    PubMed Central

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-01-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

  6. Dynamics simulations for engineering macromolecular interactions

    NASA Astrophysics Data System (ADS)

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-06-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

  7. A family of dynamic models for large-eddy simulation

    NASA Technical Reports Server (NTRS)

    Carati, D.; Jansen, K.; Lund, T.

    1995-01-01

    Since its first application, the dynamic procedure has been recognized as an effective means to compute rather than prescribe the unknown coefficients that appear in a subgrid-scale model for Large-Eddy Simulation (LES). The dynamic procedure is usually used to determine the nondimensional coefficient in the Smagorinsky (1963) model. In reality the procedure is quite general and it is not limited to the Smagorinsky model by any theoretical or practical constraints. The purpose of this note is to consider a generalized family of dynamic eddy viscosity models that do not necessarily rely on the local equilibrium assumption built into the Smagorinsky model. By invoking an inertial range assumption, it will be shown that the coefficients in the new models need not be nondimensional. This additional degree of freedom allows the use of models that are scaled on traditionally unknown quantities such as the dissipation rate. In certain cases, the dynamic models with dimensional coefficients are simpler to implement, and allow for a 30% reduction in the number of required filtering operations.

  8. CADS:Cantera Aerosol Dynamics Simulator.

    SciTech Connect

    Moffat, Harry K.

    2007-07-01

    This manual describes a library for aerosol kinetics and transport, called CADS (Cantera Aerosol Dynamics Simulator), which employs a section-based approach for describing the particle size distributions. CADS is based upon Cantera, a set of C++ libraries and applications that handles gas phase species transport and reactions. The method uses a discontinuous Galerkin formulation to represent the particle distributions within each section and to solve for changes to the aerosol particle distributions due to condensation, coagulation, and nucleation processes. CADS conserves particles, elements, and total enthalpy up to numerical round-off error, in all of its formulations. Both 0-D time dependent and 1-D steady state applications (an opposing-flow flame application) have been developed with CADS, with the initial emphasis on developing fundamental mechanisms for soot formation within fires. This report also describes the 0-D application, TDcads, which models a time-dependent perfectly stirred reactor.

  9. Mathematical simulation of Earth system dynamics

    NASA Astrophysics Data System (ADS)

    Dymnikov, V. P.; Lykosov, V. N.; Volodin, E. M.

    2015-05-01

    The mathematical simulation of the Earth system, the dynamics of which depends on physical, chemical, biological, and other processes and which requires interdisciplinary approaches to studying this problem, is considered. The term "the Earth system" extends the concept "the climatic system," since additional geospheres (lithosphere, heliosphere, etc.) are taken into account and a wider range of physical, chemical, biological, and social interactions is described. The present-day level of climate modeling is discussed, and some data obtained at the Institute of Numerical Mathematics, Russian Academy of Sciences (INM RAS), are presented for this purpose. The prospects for further development of climate models toward the creation of the Earth system models based on a seamless approach, according to which a unified model is used to make short-term (several days) and long-term (climatic) prediction, are considered.

  10. Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.

    PubMed

    Schwabe, Tobias

    2015-08-20

    For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273

  11. Molecular Dynamics Simulations of Water Evaporation

    NASA Astrophysics Data System (ADS)

    Wen, Chengyuan; Grest, Gary; Cheng, Shengfeng

    2015-03-01

    The evaporation of water from the liquid/vapor interface is studied via large-scale molecular dynamics simulations for systems of more than a million atoms at 550K and 600K. The TIP4P-2005 water model whose liquid/vapor surface tension is in excellent agreement with experiments is used. Evaporative cooling at the interface is observed from temperature profiles determined from both translational and rotational kinetic energy. During evaporation, the density of water is slightly enhanced near the liquid-vapor interface. The velocity distribution of water molecules in the vapor phase during evaporation at various distances relative to the interface fit a Maxwell-Boltzmann distribution. While our results indicate an imbalance between evaporating and condensing water molecules, local thermal equilibrium is found to hold in addition to mechanical equilibrium. Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

  12. A dynamic model for assessing the effects of management strategies on the reduction of construction and demolition waste

    SciTech Connect

    Yuan Hongping; Chini, Abdol R.; Lu Yujie; Shen Liyin

    2012-03-15

    Highlights: Black-Right-Pointing-Pointer We proposes a model for projecting C and D waste reduction of construction projects. Black-Right-Pointing-Pointer The model can simulate effects of various management strategies on waste reduction. Black-Right-Pointing-Pointer The model integrates all essential variables that affect C and D waste reduction. Black-Right-Pointing-Pointer By using the model, best strategies could be identified before being implemented. - Abstract: During the past few decades, construction and demolition (C and D) waste has received increasing attention from construction practitioners and researchers worldwide. A plethora of research regarding C and D waste management has been published in various academic journals. However, it has been determined that existing studies with respect to C and D waste reduction are mainly carried out from a static perspective, without considering the dynamic and interdependent nature of the whole waste reduction system. This might lead to misunderstanding about the actual effect of implementing any waste reduction strategies. Therefore, this research proposes a model that can serve as a decision support tool for projecting C and D waste reduction in line with the waste management situation of a given construction project, and more importantly, as a platform for simulating effects of various management strategies on C and D waste reduction. The research is conducted using system dynamics methodology, which is a systematic approach that deals with the complexity - interrelationships and dynamics - of any social, economic and managerial system. The dynamic model integrates major variables that affect C and D waste reduction. In this paper, seven causal loop diagrams that can deepen understanding about the feedback relationships underlying C and D waste reduction system are firstly presented. Then a stock-flow diagram is formulated by using software for system dynamics modeling. Finally, a case study is used to

  13. Fiber lubrication: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Liu, Hongyi

    Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence

  14. Simulations of Operation Dynamics of Different Type GaN Particle Sensors

    PubMed Central

    Gaubas, Eugenijus; Ceponis, Tomas; Kalesinskas, Vidas; Pavlov, Jevgenij; Vysniauskas, Juozas

    2015-01-01

    The operation dynamics of the capacitor-type and PIN diode type detectors based on GaN have been simulated using the dynamic and drift-diffusion models. The drift-diffusion current simulations have been implemented by employing the software package Synopsys TCAD Sentaurus. The monopolar and bipolar drift regimes have been analyzed by using dynamic models based on the Shockley-Ramo theorem. The carrier multiplication processes determined by impact ionization have been considered in order to compensate carrier lifetime reduction due to introduction of radiation defects into GaN detector material. PMID:25751080

  15. In silico FRET from simulated dye dynamics

    NASA Astrophysics Data System (ADS)

    Hoefling, Martin; Grubmüller, Helmut

    2013-03-01

    Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via the Förster formula, E=1/(1+(). The energy transfer however also depends on the mutual orientation of the two dyes used as distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on approximations, which reduce the accuracy of these distance measurements. A common approximation is an isotropic and uncorrelated dye orientation distribution. To assess the impact of such approximations, we present the algorithms and implementation of a computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated using a Monte Carlo algorithm. The application of the developed toolkit on a poly-proline system demonstrated good agreement between smFRET simulations and experimental results and therefore confirms our computational method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity. The presented computational toolkit is written in Python, available as open-source, applicable to arbitrary systems and can easily be extended and adapted to further problems. Catalogue identifier: AENV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3, the bundled SIMD friendly Mersenne twister implementation [1] is provided under the SFMT-License. No. of lines in distributed program, including test data, etc.: 317880 No. of bytes in distributed program, including test data, etc.: 54774217 Distribution format: tar.gz Programming language

  16. Numerical simulations of Modified Newtonian Dynamics

    NASA Astrophysics Data System (ADS)

    Candlish, G. N.; Smith, R.; Fellhauer, M.

    2016-05-01

    The ΛCDM standard cosmological model is strongly supported by multiple lines of evidence, particularly from observations at large scales such as the CMB and large scale structure. There are some indications, however, of problems at smaller scales. An alternative to the CDM approach is to modify the gravitational force, as exemplified by the MOdified Newtonian Dynamics (MOND) idea. While evidence suggests MOND cannot account for dynamics at all scales without dark matter, it has been successful at galactic scales. Due to the complexity of the theory, however, most tests of MOND have extended no further than using a simple scaling relation to determine rotation curves or velocity dispersions. Therefore, to test the concept more thoroughly we require numerical simulations. We discuss the development and testing of a new N-body solver, using two distinct formulations of MOND, that is incorporated into the RAMSES code. The theory of MOND as a modification of Newtonian gravity is briefly summarised. We then show how it is implemented in the code, providing an example of an idealised test case and future applications.

  17. Numerical simulation of tulip flame dynamics

    SciTech Connect

    Cloutman, L.D.

    1991-11-30

    A finite difference reactive flow hydrodynamics program based on the full Navier-Stokes equations was used to simulate the combustion process in a homogeneous-charge, constant-volume combustion bomb in which an oddly shaped flame, known as a ``tulip flame`` in the literature, occurred. The ``tulip flame`` was readily reproduced in the numerical simulations, producing good agreement with the experimental flame shapes and positions at various times. The calculations provide sufficient detail about the dynamics of the experiment to provide some insight into the physical mechanisms responsible for the peculiar flame shape. Several factors seem to contribute to the tulip formation. The most important process is the baroclinic production of vorticity by the flame front, and this rate of production appears to be dramatically increased by the nonaxial flow generated when the initial semicircular flame front burns out along the sides of the chamber. The vorticity produces a pair of vortices behind the flame that advects the flame into the tulip shape. Boundary layer effects contribute to the details of the flame shape next to the walls of the chamber, but are otherwise not important. 24 refs.

  18. Numerical simulation of tulip flame dynamics

    SciTech Connect

    Cloutman, L.D.

    1991-11-30

    A finite difference reactive flow hydrodynamics program based on the full Navier-Stokes equations was used to simulate the combustion process in a homogeneous-charge, constant-volume combustion bomb in which an oddly shaped flame, known as a tulip flame'' in the literature, occurred. The tulip flame'' was readily reproduced in the numerical simulations, producing good agreement with the experimental flame shapes and positions at various times. The calculations provide sufficient detail about the dynamics of the experiment to provide some insight into the physical mechanisms responsible for the peculiar flame shape. Several factors seem to contribute to the tulip formation. The most important process is the baroclinic production of vorticity by the flame front, and this rate of production appears to be dramatically increased by the nonaxial flow generated when the initial semicircular flame front burns out along the sides of the chamber. The vorticity produces a pair of vortices behind the flame that advects the flame into the tulip shape. Boundary layer effects contribute to the details of the flame shape next to the walls of the chamber, but are otherwise not important. 24 refs.

  19. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect

    Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.

    1998-02-01

    Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.

  20. Dissipative particle dynamics simulation of a colloidal micropump

    NASA Astrophysics Data System (ADS)

    De Palma, Pietro; Valentini, P.; Napolitano, M.

    2006-02-01

    Dissipative particle dynamics (DPD) is a recently developed model for computing complex fluid flows at mesoscopic scales. This article provides a novel DPD simulation of complex microfluidic devices involving the momentum exchange between a body moving with a prescribed law of motion and the surrounding fluid. To this purpose, a DPD computational method is developed and equipped with an elastic collision model between the moving body and the DPD fluid particles surrounding it. The method is first validated versus well known theoretical, numerical, and experimental results, providing a sensitivity analysis of the dependence of continuum-flow properties on DPD parameters, as well as verifying its reliability for well known continuum-flow test cases. The method is then applied to its main goal, namely, the simulation of the flow driven by a peristaltic micropump, constructed by assembling several colloidal spheres. The DPD fluid model provides quite accurate results with respect to the experimental data and gives a detailed description of local flow properties. It is found that a careful choice of the DPD parameters is needed to avoid spurious compressibility effects and to match the real fluid characteristics; furthermore, due to the very coarse graining used in the present simulation, the thermal kinetic energy of the DPD particles needs to be reduced, in order to correctly evaluate their displacement, which is determined mainly by the momentum driving the flow. Finally, thanks to such a very coarse graining, the proposed DPD method provides an accurate prediction of local mesoscale flow properties with a dramatic reduction of the computational cost with respect to molecular dynamics simulations.

  1. Consequence modeling using the fire dynamics simulator.

    PubMed

    Ryder, Noah L; Sutula, Jason A; Schemel, Christopher F; Hamer, Andrew J; Van Brunt, Vincent

    2004-11-11

    The use of Computational Fluid Dynamics (CFD) and in particular Large Eddy Simulation (LES) codes to model fires provides an efficient tool for the prediction of large-scale effects that include plume characteristics, combustion product dispersion, and heat effects to adjacent objects. This paper illustrates the strengths of the Fire Dynamics Simulator (FDS), an LES code developed by the National Institute of Standards and Technology (NIST), through several small and large-scale validation runs and process safety applications. The paper presents two fire experiments--a small room fire and a large (15 m diameter) pool fire. The model results are compared to experimental data and demonstrate good agreement between the models and data. The validation work is then extended to demonstrate applicability to process safety concerns by detailing a model of a tank farm fire and a model of the ignition of a gaseous fuel in a confined space. In this simulation, a room was filled with propane, given time to disperse, and was then ignited. The model yields accurate results of the dispersion of the gas throughout the space. This information can be used to determine flammability and explosive limits in a space and can be used in subsequent models to determine the pressure and temperature waves that would result from an explosion. The model dispersion results were compared to an experiment performed by Factory Mutual. Using the above examples, this paper will demonstrate that FDS is ideally suited to build realistic models of process geometries in which large scale explosion and fire failure risks can be evaluated with several distinct advantages over more traditional CFD codes. Namely transient solutions to fire and explosion growth can be produced with less sophisticated hardware (lower cost) than needed for traditional CFD codes (PC type computer verses UNIX workstation) and can be solved for longer time histories (on the order of hundreds of seconds of computed time) with

  2. Consistent model reduction of polymer chains in solution in dissipative particle dynamics: Model description

    NASA Astrophysics Data System (ADS)

    Moreno, Nicolas; Nunes, Suzana P.; Calo, Victor M.

    2015-11-01

    We introduce a framework for model reduction of polymer chain models for dissipative particle dynamics (DPD) simulations, where the properties governing the phase equilibria such as the characteristic size of the chain, compressibility, density, and temperature are preserved. The proposed methodology reduces the number of degrees of freedom required in traditional DPD representations to model equilibrium properties of systems with complex molecules (e.g., linear polymers). Based on geometrical considerations we explicitly account for the correlation between beads in fine-grained DPD models and consistently represent the effect of these correlations in a reduced model, in a practical and simple fashion via power laws and the consistent scaling of the simulation parameters. In order to satisfy the geometrical constraints in the reduced model we introduce bond-angle potentials that account for the changes in the chain free energy after the model reduction. Following this coarse-graining process we represent high molecular weight DPD chains (i.e.,  ≥ 200 beads per chain) with a significant reduction in the number of particles required (i.e.,  ≥ 20 times the original system). We show that our methodology has potential applications modeling systems of high molecular weight molecules at large scales, such as diblock copolymer and DNA.

  3. Erbium Implantation in Silica Studied by Molecular Dynamics Simulations

    SciTech Connect

    Du, Jincheng; Corrales, Louis R.

    2007-02-01

    Defect formation induced by erbium implantation in silica glass and cristobalite was studied using molecular dynamics simulations employing a partial charge model in combination with the ZBL potential. The results show that the number of displaced atoms generated at the same PKA energy is similar in silica and cristobalite but the number of coordination defects created is much lower in the cristobalite than in silica glass. In both cases, the erbium ion is able to create an optimal coordination environment at the end of the collision cascade. Subsequent thermal annealing causes the relaxation of the silicon oxygen network structure along with a reduction of silicon and oxygen defects. This research is supported by the Divisions of Materials Sciences and Engineering and Chemical Science, Office of Basic Energy Sciences, U.S. Department of Energy. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  4. Dynamic Shade and Irradiance Simulation of Aquatic Landscapes and Watersheds

    EPA Science Inventory

    Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulate...

  5. Validation of vehicle dynamics simulation models - a review

    NASA Astrophysics Data System (ADS)

    Kutluay, Emir; Winner, Hermann

    2014-02-01

    In this work, a literature survey on the validation of vehicle dynamics simulation models is presented. Estimating the dynamic responses of existing or proposed vehicles has a wide array of applications in the development of vehicle technologies, e.g. active suspensions, controller design, driver assistance systems, etc. Although simulation environments, measurement tools and mathematical theories on vehicle dynamics are well established, the methodical link between the experimental test data and validity analysis of the simulation model is still lacking. This report presents different views on the definition of validation, and its usage in vehicle dynamics simulation models.

  6. Studying Interactions by Molecular Dynamics Simulations at High Concentration

    PubMed Central

    Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro

    2012-01-01

    Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085

  7. Nonlinear dynamics of turbulent drag reduction by polymers

    NASA Astrophysics Data System (ADS)

    Graham, Michael; Wang, Sung-Ning; Hahn, Friedemann

    2012-11-01

    Minimal channel flow of Newtonian and drag-reducing polymer solutions is studied computationally. Even in the Newtonian limit, intervals of ``active'' and ``hibernating'' turbulence exist, the latter displaying many features of the maximum drag reduction (MDR) asymptote observed in polymer solutions: weak streamwise vortices, nearly nonexistent streamwise variations and a mean velocity gradient that quantitatively matches experiments (i.e. the Virk log-law). Polymer stretching is very weak during hibernation. As viscoelasticity increases, the frequency of the hibernation intervals increases, leading to flows that increasingly resemble MDR. This observation can be explained with a simple mathematical model that posits that the lifetime of an active turbulence interval is the time that it takes for the turbulence to stretch polymer molecules to a certain threshold value beyond which the active turbulence is suppressed. An extended Karhunen-Loeve analysis is introduced and used to illustrate how the velocity and stress fields change as MDR is approached. These results and others indicate that the MDR dynamics are governed by an underlying Newtonian state - a saddle point in phase space - that is unmasked as viscoelasticity suppresses normal turbulent fluctuations.

  8. Analysis & Simulation of Dynamics in Supercooled Liquids

    NASA Astrophysics Data System (ADS)

    Elmatad, Yael Sarah

    2011-12-01

    The nature of supercooled liquids and the glass transition has been debated by many scientists. Several theories have been put forth to describe the remarkable properties of this out-of-equilibrium material. Each of these theories makes specific predictions as to how the scaling of various transport properties in supercooled materials should behave. Given access to a large pool of high-quality supercooled liquid data we seek to compare these theories to one another. Moreover, we explore properties of a pair of models which are the basis for one particularly attractive theory---Chandler-Garrahan theory---and discuss the models' behavior in space-time and possible implications to the behavior of experimental supercooled liquids. Here we investigate the nature of dynamics in supercooled liquids using a two pronged approach. First we analyze the transport properties found in experiments and simulations of supercooled liquids. Then, we analyze simulation trajectories for lattice models which reproduce many of the interesting properties of supercooled liquids. In doing so, we illuminate several glass universalities, common properties of a wide variety of glass formers. By analyzing relaxation time and viscosity data for over 50 data sets and 1200 points, we find that relaxation time can be collapsed onto a single, parabolic curve. This collapse supports a theory of universal glass behavior based on facilitated models proposed by David Chandler and Juan Garrahan in 2003. We then show that the parabolic fit parameters for any particular liquid are a material property: they converge fast and are capable of predicting behavior in regions beyond the included data sets. We compare this property to other popular fitting schemes such as the Vogel-Fulcher, double exponential, and fractional exponential forms and conclude that these three forms result in parameters which are non predictive and therefore not material properties. Additionally, we examine the role of attractive

  9. Dynamic Simulation of EAF on RTDS for Compensation Sizing

    NASA Astrophysics Data System (ADS)

    Meera, K. S.

    2016-06-01

    Large sized electric arc furnaces (EAF) causes power quality problems such as flicker, harmonics etc. due to their unbalanced and non-linear behavior characteristics. The rapid swings in real and reactive power of such non-linear loads causes fast repetitive voltage variations with appreciable voltage distortion caused by harmonics and unbalance. Some form of reactive compensation is usually adopted to limit the disturbances caused by EAF in electric power system, in particular the flicker. This paper highlights the results of a case study, where the arc furnace is modelled using statistical dynamic model of the furnace using real time digital simulator which allows more real time simulations tests to be conducted in a shorter time and also provides a more detailed power system representation for the tests. The investigation of the simulation study results showed that static VAR compensators can be successfully used for reduction of flicker levels, compensation of reactive power and for the regulation of voltage levels in the EAF plant under study.

  10. Granular Flow and Dynamics of Lunar Simulants in Excavating Implements

    NASA Technical Reports Server (NTRS)

    Agui, Juan H.; Wilkinson, R. Allen

    2010-01-01

    The exploration of the lunar surface will rely on properly designed excavation equipment for surface preparations and for collection of lunar regolith in In-Situ Resource Utilization (ISRU) processes. Performance efficiency, i.e minimizing loading forces while maximizing material collection, and mass and volume reductions are major design goals. The NASA Glenn Research Center has embarked on an experimental program to determine the flow characteristics and dynamic forces produced by excavation operations using various excavator bucket designs. A new large scale soil bin facility, 2.27 m x 5.94 m x 0.76 m (nominally 8 ft. x 20 ft. x 27 in.) in size, capable of accommodating moderately large test implements was used for the simulations of lunar operations. The soil bin is filled with GRC-3simulant (a mixture of industrial sands and silt with a particle size distribution and the bulk mechanical (shear) strength representative of an average of lunar regolith from different regions) and uses motorized horizontal rails and a vertical actuator to drive the implement through the lunar simulant soil. A six-axis load cell and encoders provide well resolved measurements of the three dimensional forces and torques and motion of the bucket. In addition, simultaneous video allows for the analysis of the flow behavior and structure formation of the regolith during excavation. The data may be useful in anchoring soil mechanic models and to provide engineering data for design consideration.

  11. Rotational Brownian Dynamics simulations of clathrin cage formation

    SciTech Connect

    Ilie, Ioana M.; Briels, Wim J.; Otter, Wouter K. den

    2014-08-14

    The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.

  12. Drag reduction and the dynamics of turbulence in simple and complex fluidsa)

    NASA Astrophysics Data System (ADS)

    Graham, Michael D.

    2014-10-01

    Addition of a small amount of very large polymer molecules or micelle-forming surfactants to a liquid can dramatically reduce the energy dissipation it exhibits in the turbulent flow regime. This rheological drag reduction phenomenon is widely used, for example, in the Alaska pipeline, but it is not well-understood, and no comparable technology exists to reduce turbulent energy consumption in flows of gases, in which polymers or surfactants cannot be dissolved. The most striking feature of this phenomenon is the existence of a so-called maximum drag reduction (MDR) asymptote: for a given geometry and driving force, there is a maximum level of drag reduction that can be achieved through addition of polymers. Changing the concentration, molecular weight or even the chemical structure of the additives has little to no effect on this asymptotic value. This universality is the major puzzle of drag reduction. We describe direct numerical simulations of turbulent minimal channel flow of Newtonian fluids and viscoelastic polymer solutions. Even in the absence of polymers, we show that there are intervals of "hibernating" turbulence that display very low drag as well as many other features of the MDR asymptote observed in polymer solutions. As Weissenberg number increases to moderate values the frequency of these intervals also increases, and a simple theory captures key features of the intermittent dynamics observed in the simulations. At higher Weissenberg number, these intervals are altered - for example, their duration becomes substantially longer and the instantaneous Reynolds shear stress during them becomes very small. Additionally, simulations of "edge states," dynamical trajectories that lie on the boundary between turbulent and laminar flow, display characteristics that are similar to those of hibernating turbulence and thus to the MDR asymptote, again even in the absence of polymer additives. Based on these observations, we propose a tentative unified description

  13. Drag reduction and the dynamics of turbulence in simple and complex fluids

    NASA Astrophysics Data System (ADS)

    Graham, Michael

    2013-11-01

    Addition of a small amount of very large polymer molecules or micelle-forming surfactants to a liquid can dramatically reduce the energy dissipation it exhibits in the turbulent flow regime. This rheological drag reduction phenomenon is widely used, for example in the Alaska pipeline, but it is not well-understood, and no comparable technology exists to reduce turbulent energy consumption in flows of gases, in which polymers or surfactants cannot be dissolved. The most striking feature of this phenomenon is the existence of a so-called maximum drag reduction (MDR) asymptote: for a given geometry and driving force, there is a maximum level of drag reduction that can be achieved through addition of polymers. Changing the concentration, molecular weight or even the chemical structure of the additives has no effect on this asymptotic value. This universality is the major puzzle of drag reduction. We describe direct numerical simulations of turbulent channel flow of Newtonian fluids and viscoelastic polymer solutions. Even in the absence of polymers, we show that there are intervals of ``hibernating'' turbulence that display very low drag as well as many other features of the MDR asymptote observed in polymer solutions. As viscoelasticity increases, the frequency of these intervals also increases, leading to flows that increasingly resemble MDR. A simple theory captures key features of the intermittent dynamics observed in the simulations. Additionally, simulations of ``edge states,'' dynamical trajectories that lie on the boundary between turbulent and laminar flow, display characteristics that are similar to those of hibernating turbulence and thus to the MDR asymptote, again even in the absence of polymer additives. Based on these observations, we propose a tentative unified description of rheological drag reduction. The existence of ``MDR-like'' intervals even in the absence of additives sheds light on the observed universality of MDR and may ultimately lead to new

  14. High frequency dynamic engine simulation. [TF-30 engine

    NASA Technical Reports Server (NTRS)

    Schuerman, J. A.; Fischer, K. E.; Mclaughlin, P. W.

    1977-01-01

    A digital computer simulation of a mixed flow, twin spool turbofan engine was assembled to evaluate and improve the dynamic characteristics of the engine simulation to disturbance frequencies of at least 100 Hz. One dimensional forms of the dynamic mass, momentum and energy equations were used to model the engine. A TF30 engine was simulated so that dynamic characteristics could be evaluated against results obtained from testing of the TF30 engine at the NASA Lewis Research Center. Dynamic characteristics of the engine simulation were improved by modifying the compression system model. Modifications to the compression system model were established by investigating the influence of size and number of finite dynamic elements. Based on the results of this program, high frequency engine simulations using finite dynamic elements can be assembled so that the engine dynamic configuration is optimum with respect to dynamic characteristics and computer execution time. Resizing of the compression systems finite elements improved the dynamic characteristics of the engine simulation but showed that additional refinements are required to obtain close agreement simulation and actual engine dynamic characteristics.

  15. Nanoscale deicing by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-07-01

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice

  16. Molecular dynamics simulations of supramolecular polymer rheology

    NASA Astrophysics Data System (ADS)

    Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.

    2010-11-01

    Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.

  17. Numerical simulation of magma chamber dynamics.

    NASA Astrophysics Data System (ADS)

    Longo, Antonella; Papale, Paolo; Montagna, Chiara Paola; Vassalli, Melissa; Giudice, Salvatore; Cassioli, Andrea

    2010-05-01

    Magma chambers are characterized by periodic arrivals of deep magma batches that give origin to complex patterns of magma convection and mixing, and modify the distribution of physical quantities inside the chamber. We simulate the transient, 2D, multi-component homogeneous dynamics in geometrically complex dyke+chamber systems, by means of GALES, a finite element parallel C++ code solving mass, momentum and energy equations for multi-component homogeneous gas-liquid (± crystals) mixtures in compressible-to-incompressible flow conditions. Code validation analysis includes several cases from the classical engineering literature, corresponding to a variety of subsonic to supersonic gas-liquid flow regimes (see http://www.pi.ingv.it/~longo/gales/gales.html). The model allows specification of the composition of the different magmas in the domain, in terms of ten major oxides plus the two volatile species H2O and CO2. Gas-liquid thermodynamics are modeled by using the compositional dependent, non-ideal model in Papale et al. (Chem.. Geol., 2006). Magma properties are defined in terms of local pressure, temperature, and composition including volatiles. Several applications are performed within domains characterized by the presence of one or more magma chambers and one or more dykes, with different geometries and characteristic size from hundreds of m to several km. In most simulations an initial compositional interface is placed at the top of a feeding dyke, or at larger depth, with the deeper magma having a lower density as a consequence of larger volatile content. The numerical results show complex patterns of magma refilling in the chamber, with alternating phases of magma ingression and magma sinking from the chamber into the feeding dyke. Intense mixing takes place in feeding dykes, so that the new magma entering the chamber is always a mixture of the deep and the initially resident magma. Buoyant plume rise occurs through the formation of complex convective

  18. Molecular Dynamics Simulation of Disordered Zircon

    SciTech Connect

    Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin

    2004-02-27

    The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.

  19. Simulation of chemical isomerization reaction dynamics on a NMR quantum simulator.

    PubMed

    Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng

    2011-07-01

    Quantum simulation can beat current classical computers with minimally a few tens of qubits. Here we report an experimental demonstration that a small nuclear-magnetic-resonance quantum simulator is already able to simulate the dynamics of a prototype laser-driven isomerization reaction using engineered quantum control pulses. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future. PMID:21797586

  20. Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition

    PubMed Central

    Weksberg, Tiffany E.; Lynch, Gillian C.; Krause, Kurt L.; Pettitt, B. Montgomery

    2007-01-01

    The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2 Å. However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential. PMID:17325017

  1. Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition.

    SciTech Connect

    Weksberg, Tiffany E; Lynch, Gillian C; Krause, Kurt; Pettitt, Bernard M

    2007-05-01

    The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2Å. However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential.

  2. Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition

    SciTech Connect

    Weksberg, Tiffany E; Lynch, Gillian C; Krause, Kurt; Pettitt, Bernard M

    2007-05-01

    The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2Å . However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential.

  3. Staggered solution procedures for multibody dynamics simulation

    NASA Technical Reports Server (NTRS)

    Park, K. C.; Chiou, J. C.; Downer, J. D.

    1990-01-01

    The numerical solution procedure for multibody dynamics (MBD) systems is termed a staggered MBD solution procedure that solves the generalized coordinates in a separate module from that for the constraint force. This requires a reformulation of the constraint conditions so that the constraint forces can also be integrated in time. A major advantage of such a partitioned solution procedure is that additional analysis capabilities such as active controller and design optimization modules can be easily interfaced without embedding them into a monolithic program. After introducing the basic equations of motion for MBD system in the second section, Section 3 briefly reviews some constraint handling techniques and introduces the staggered stabilized technique for the solution of the constraint forces as independent variables. The numerical direct time integration of the equations of motion is described in Section 4. As accurate damping treatment is important for the dynamics of space structures, we have employed the central difference method and the mid-point form of the trapezoidal rule since they engender no numerical damping. This is in contrast to the current practice in dynamic simulations of ground vehicles by employing a set of backward difference formulas. First, the equations of motion are partitioned according to the translational and the rotational coordinates. This sets the stage for an efficient treatment of the rotational motions via the singularity-free Euler parameters. The resulting partitioned equations of motion are then integrated via a two-stage explicit stabilized algorithm for updating both the translational coordinates and angular velocities. Once the angular velocities are obtained, the angular orientations are updated via the mid-point implicit formula employing the Euler parameters. When the two algorithms, namely, the two-stage explicit algorithm for the generalized coordinates and the implicit staggered procedure for the constraint Lagrange

  4. A novel coupling of noise reduction algorithms for particle flow simulations

    NASA Astrophysics Data System (ADS)

    Zimoń, M. J.; Reese, J. M.; Emerson, D. R.

    2016-09-01

    Proper orthogonal decomposition (POD) and its extension based on time-windows have been shown to greatly improve the effectiveness of recovering smooth ensemble solutions from noisy particle data. However, to successfully de-noise any molecular system, a large number of measurements still need to be provided. In order to achieve a better efficiency in processing time-dependent fields, we have combined POD with a well-established signal processing technique, wavelet-based thresholding. In this novel hybrid procedure, the wavelet filtering is applied within the POD domain and referred to as WAVinPOD. The algorithm exhibits promising results when applied to both synthetically generated signals and particle data. In this work, the simulations compare the performance of our new approach with standard POD or wavelet analysis in extracting smooth profiles from noisy velocity and density fields. Numerical examples include molecular dynamics and dissipative particle dynamics simulations of unsteady force- and shear-driven liquid flows, as well as phase separation phenomenon. Simulation results confirm that WAVinPOD preserves the dimensionality reduction obtained using POD, while improving its filtering properties through the sparse representation of data in wavelet basis. This paper shows that WAVinPOD outperforms the other estimators for both synthetically generated signals and particle-based measurements, achieving a higher signal-to-noise ratio from a smaller number of samples. The new filtering methodology offers significant computational savings, particularly for multi-scale applications seeking to couple continuum informations with atomistic models. It is the first time that a rigorous analysis has compared de-noising techniques for particle-based fluid simulations.

  5. Molecular Dynamics Simulations of Coulomb Explosion

    SciTech Connect

    Bringa, E M

    2002-05-17

    A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a ''Coulomb Explosion'', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) simulations of Coulomb explosion for a cylindrical track as a function of charge density and neutralization/quenching time, {tau}. Screening by the free electrons is accounted for using a screened Coulomb potential for the interaction among charges. The yield exhibits a prompt component from the track core and a component, which dominates at higher excitation density, from the heated region produced. For the cases studied, the number of atoms ejected per incident ion, i.e. the sputtering yield Y, is quadratic with charge density along the track as suggested by simple models. Y({tau} = 0.2 Debye periods) is nearly 20% of the yield when there is no neutralization ({tau} {yields} {infinity}). The connections between ''Coulomb explosions'', thermal spikes and measurements of electronic sputtering are discussed.

  6. Annual Report 1999 Environmental Dynamics and Simulation

    SciTech Connect

    NS Foster-Mills

    2000-06-28

    This annual report describes selected 1999 research accomplishments for the Environmental Dynamics and Simulation (ED and S) directorate, one of six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). These accomplishments are representative of the different lines of research underway in the ED and S directorate. EMSL is one of US Department of Energy's (DOE) national scientific user facilities and is the centerpiece of DOE's commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems. Capabilities in the EMSL include over 100 major instrument systems for use by the resident research staff, their collaborators, and users of the EMSL. These capabilities are used to address the fundamental science that will be the basis for finding solutions to national environmental issues such as cleaning up contamianted areas at DOE sites across the country and developing green technologies that will reduce or eliminate future pollution production. The capabilities are also used to further the understanding of global climate change and environmental issues relevant to energy production and use and health effects resulting from exposure to contaminated environments.

  7. System dynamic simulation of precision segmented reflector

    NASA Technical Reports Server (NTRS)

    Shih, Choon-Foo; Lou, Michael C.

    1991-01-01

    A joint effort was undertaken on a Precision Segmented Reflector (PSR) Project. The missions in which the PSR is to be used will use large (up to 20 m in diameter) telescopes. The essential requirement for the telescopes is that the reflector surface of the primary mirror must be made extremely precise to allow no more than a few microns of errors and, additionally, this high surface precision must be maintained when the telescope is subjected to on-orbital mechanical and thermal disturbances. Based on the mass, size, and stability considerations, reflector surface formed by segmented, probably actively or passively controlled, composite panels are regarded as most suitable for future space based astronomical telescope applications. In addition to the design and fabrication of composite panels with a surface error of less than 3 microns RMS, PSR also develops related reflector structures, materials, control, and sensing technologies. As part of the planning effort for PSR Technology Demonstration, a system model which couples the reflector, consisting of panels, support truss and actuators, and the optical bench was assembled for dynamic simulations. Random vibration analyses using seismic data obtained from actual measurements at the test site designated for PSR Technology Demonstration are described.

  8. Kinetic simulations of plasmoid chain dynamics

    SciTech Connect

    Markidis, S.; Henri, P.; Lapenta, G.; Divin, A.; Goldman, M.; Newman, D.; Laure, E.

    2013-08-15

    The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids.

  9. Expansion techniques for collisionless stellar dynamical simulations

    SciTech Connect

    Meiron, Yohai; Li, Baile; Holley-Bockelmann, Kelly; Spurzem, Rainer

    2014-09-10

    We present graphics processing unit (GPU) implementations of two fast force calculation methods based on series expansions of the Poisson equation. One method is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other method is the multipole expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field methods and optimized for collisionless galactic dynamics, but while SCF is a 'pure' expansion, MEX is an expansion in just the angular part; thus, MEX is capable of capturing radial structure easily, while SCF needs a large number of radial terms. We show that despite the expansion bias, these methods are more accurate than direct techniques for the same number of particles. The performance of our GPU code, which we call ETICS, is profiled and compared to a CPU implementation. On the tested GPU hardware, a full force calculation for one million particles took ∼0.1 s (depending on expansion cutoff), making simulations with as many as 10{sup 8} particles fast for a comparatively small number of nodes.

  10. Nanoscale deicing by molecular dynamics simulation.

    PubMed

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-08-14

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion. PMID:27431975

  11. Dynamic Simulation over Long Time Periods with 100% Solar Generation.

    SciTech Connect

    Concepcion, Ricky James; Elliott, Ryan Thomas

    2015-12-01

    This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.

  12. Application of control theory to dynamic systems simulation

    NASA Technical Reports Server (NTRS)

    Auslander, D. M.; Spear, R. C.; Young, G. E.

    1982-01-01

    The application of control theory is applied to dynamic systems simulation. Theory and methodology applicable to controlled ecological life support systems are considered. Spatial effects on system stability, design of control systems with uncertain parameters, and an interactive computing language (PARASOL-II) designed for dynamic system simulation, report quality graphics, data acquisition, and simple real time control are discussed.

  13. Reduction of the Germano-identity error in the dynamic Smagorinsky model

    NASA Astrophysics Data System (ADS)

    Park, Noma; Mahesh, Krishnan

    2009-06-01

    We revisit the Germano-identity error in the dynamic modeling procedure in the sense that the current modeling procedure to obtain the dynamic coefficient may not truly minimize the error in the mean and global sense. A "corrector step" to the conventional dynamic Smagorinsky model is proposed to obtain a corrected eddy viscosity which further reduces the error. The change in resolved velocity due to the coefficient variation as well as nonlocal nature of the filter and flow unsteadiness is accounted for by a simplified suboptimal control formalism without resorting to the adjoint equations. The objective function chosen is the Germano-identity error integrated over the entire computational volume and pathline. In order to determine corrected eddy viscosity, the Fréchet derivative of the objective function is directly evaluated by a finite-differencing formula in an efficient predictor-corrector-type framework. The proposed model is applied to decaying isotropic turbulence and turbulent channel flow at various Reynolds numbers and resolutions to obtain noticeable reduction in the Germano-identity error and significantly improved flow statistics. From channel flow large-eddy simulation, it is shown that conventional dynamic model underestimates subgrid scale eddy viscosity when the resolution gets coarse, and this underestimation is responsible for increased anisotropy of predicted Reynolds stress. The proposed model raises both the overall and near-wall subgrid scale eddy viscosity to reduce exaggerated Reynolds stress anisotropy and yield significantly improved flow statistics.

  14. Molecular Dynamics Simulations of Glycerol Monooleate Confined between Mica Surfaces.

    PubMed

    Bradley-Shaw, Joshua L; Camp, Philip J; Dowding, Peter J; Lewtas, Ken

    2016-08-01

    The structure and frictional properties of glycerol monooleate (GMO) in organic solvents, with and without water impurity, confined and sheared between two mica surfaces are examined using molecular dynamics simulations. The structure of the fluid is characterized in various ways, and the differences between systems with nonaggregated GMO and with preformed GMO reverse micelles are examined. Preformed reverse micelles are metastable under static conditions in all systems. In n-heptane under shear conditions, with or without water, preformed GMO reverse micelles remain intact and adsorb onto one surface or another, becoming surface micelles. In dry toluene, preformed reverse micelles break apart under shear, while in the presence of water, the reverse micelles survive and become surface micelles. In all systems under static and shear conditions, nonaggregated GMO adsorbs onto both surfaces with roughly equal probability. Added water is strongly associated with the GMO, irrespective of shear or the form of the added GMO. In all cases, with increasing shear rate, the GMO molecules flatten on the surface, and the kinetic friction coefficient increases. Under low-shear conditions, the friction is insensitive to the form of the GMO added, whereas the presence of water is found to lead to a small reduction in friction. Under high-shear conditions, the presence of reverse micelles leads to a significant reduction in friction, whereas the presence of water increases the friction in n-heptane and decreases the friction in toluene. PMID:27429247

  15. A dynamic simulation of a lead blast furnace

    NASA Astrophysics Data System (ADS)

    Chao, John T.

    1981-06-01

    A dynamic model has been developed to simulate the operation of the stack zone of a lead blast furnace. The mathematical formulation of the governing equations of change leads to a system of 2nd order partial differential equations, which is solved by finite difference methods. A reduction model of ash-layer diffusion controlled mechanism, which allows the stepwise reduction to the lowest oxide or metal thermodynamically possible for the local gas composition within the sinter, is employed in this model. The surface reaction and the internal diffusion in the porous solid particles are taken into account in the coke gasification reaction. The profiles of the temperatures of gases and solids, solid compositions, and gas compositions and pressure in both radial and axial directions are predicted by the model. The results provide a good representation of the experimental data obtained for the blast furnace at Brunswick Mining and Smelting Corp., Ltd., New Brunswick, Canada and also of the less extensive data available for the Cominco blast furnace at Trail, British Columbia, Canada. In addition to the modelling of the stack, a mass and energy balance for the bosh zone is also included in the present calculation. The improvement of coke efficiency due to oxygen enrichment in the blast air for the Brunswick Furnace were interpreted semiquantitatively. The effect of sinter size distribution on the furnace performance has also been studied.

  16. Reaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties of chemically reacting mixtures

    NASA Astrophysics Data System (ADS)

    Brennan, John K.; Lísal, Martin; Gubbins, Keith E.; Rice, Betsy M.

    2004-12-01

    A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2+3H2⇔2NH3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.

  17. Flight Hour Reductions in Fleet Replacement Pilot Training through Simulation.

    ERIC Educational Resources Information Center

    Smode, Alfred F.

    A project was undertaken to integrate the 2F87F operational flight trainer into the program for training replacement patrol plane pilots. The objectives were to determine the potential of the simulator as a substitute environment for learning aircraft tasks and to effectively utilize the simulator in pilot training. The students involved in the…

  18. An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks

    NASA Astrophysics Data System (ADS)

    Zañudo, Jorge G. T.; Albert, Réka

    2013-06-01

    Discrete dynamic models are a powerful tool for the understanding and modeling of large biological networks. Although a lot of progress has been made in developing analysis tools for these models, there is still a need to find approaches that can directly relate the network structure to its dynamics. Of special interest is identifying the stable patterns of activity, i.e., the attractors of the system. This is a problem for large networks, because the state space of the system increases exponentially with network size. In this work, we present a novel network reduction approach that is based on finding network motifs that stabilize in a fixed state. Notably, we use a topological criterion to identify these motifs. Specifically, we find certain types of strongly connected components in a suitably expanded representation of the network. To test our method, we apply it to a dynamic network model for a type of cytotoxic T cell cancer and to an ensemble of random Boolean networks of size up to 200. Our results show that our method goes beyond reducing the network and in most cases can actually predict the dynamical repertoire of the nodes (fixed states or oscillations) in the attractors of the system.

  19. Controlled multibody dynamics simulation for large space structures

    NASA Technical Reports Server (NTRS)

    Housner, J. M.; Wu, S. C.; Chang, C. W.

    1989-01-01

    Multibody dynamics discipline, and dynamic simulation in control structure interaction (CSI) design are discussed. The use, capabilities, and architecture of the Large Angle Transient Dynamics (LATDYN) code as a simulation tool are explained. A generic joint body with various types of hinge connections; finite element and element coordinate systems; results of a flexible beam spin-up on a plane; mini-mast deployment; space crane and robotic slewing manipulations; a potential CSI test article; and multibody benchmark experiments are also described.

  20. A note on simulation and dynamical hierarchies

    SciTech Connect

    Rasmussen, S.; Barrett, C.L. |; Baas, N.A.; Olesen, M.W.

    1996-02-22

    This paper summarizes some of the problems associated with the generation of higher order emergent structures in formal dynamical systems as well as some of the formal properties of dynamical systems capable of generating higher order structures.

  1. Research on hyperspectral dynamic infrared scene simulation technology

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Hu, Yu; Ding, Na; Sun, Kefeng; Sun, Dandan; Xie, Junhu; Wu, Wenli; Gao, Jiaobo

    2015-02-01

    The paper presents a hardware in loop dynamic IR scene simulation technology for IR hyperspectral imaging system. Along with fleetly development of new type EO detecting, remote sensing and hyperspectral imaging technique, not only static parameters' calibration of hyperspectral IR imaging system but also dynamic parameters' testing and evaluation are required, thus hyperspectral dynamic IR simulation and evaluation become more and more important. Hyperspectral dynamic IR scene projector utilizes hyperspectral space and time domain features controlling spectrum and time synchronously to realize hardware in loop simulation. Hyperspectral IR target and background simulating image can be gained by the accomplishment of 3D model and IR characteristic romancing, hyperspectral dynamic IR scene is produced by image converting device. The main parameters of a developed hyperspectral dynamic IR scene projector: wave band range is 3~5μm, 8~12μm Field of View (FOV) is 8°; spatial resolution is 1024×768 spectrum resolution is 1%~2%. IR source and simulating scene features should be consistent with spectrum characters of target, and different spectrum channel's images can be gotten from calibration. A hyperspectral imaging system splits light with dispersing type grating, pushbrooms and collects the output signal of dynamic IR scene projector. With hyperspectral scene spectrum modeling, IR features romancing, atmosphere transmission feature modeling and IR scene projecting, target and scene in outfield can be simulated ideally, simulation and evaluation of IR hyperspectral imaging system's dynamic features are accomplished in laboratory.

  2. Kinetic distance and kinetic maps from molecular dynamics simulation.

    PubMed

    Noé, Frank; Clementi, Cecilia

    2015-10-13

    Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly interconverting states. Here, we build upon diffusion map theory and define a kinetic distance metric for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here, we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets. PMID:26574285

  3. Simulating system dynamics with arbitrary time step

    NASA Astrophysics Data System (ADS)

    Kantorovich, L.

    2007-02-01

    We suggest a dynamic simulation method that allows efficient and realistic modeling of kinetic processes, such as atomic diffusion, in which time has its actual meaning. Our method is similar in spirit to widely used kinetic Monte Carlo (KMC) techniques; however, in our approach, the time step can be chosen arbitrarily. This has an advantage in some cases, e.g., when the transition rates change with time sufficiently fast over the period of the KMC time step (e.g., due to time dependence of some external factors influencing kinetics such as moving scanning probe microscopy tip or external time-dependent field) or when the clock time is set by some external conditions, and it is convenient to use equal time steps instead of the random choice of the KMC algorithm in order to build up probability distribution functions. We show that an arbitrary choice of the time step can be afforded by building up the complete list of events including the “residence site” and multihop transitions. The idea of the method is illustrated in a simple “toy” model of a finite one-dimensional lattice of potential wells with unequal jump rates to either side, which can be studied analytically. We show that for any choice of the time step, our general kinetics method reproduces exactly the solution of the corresponding master equations for any choice of the time steps. The final kinetics also matches the standard KMC, and this allows better understanding of this algorithm, in which the time step is chosen in a certain way and the system always advances by a single hop.

  4. Molecular dynamics simulations of He bubble nucleation at grain boundaries

    SciTech Connect

    Yongfeng Zhang; Paul C Millett; Michael Tonks; Liangzhe Zhang; Bulent Biner

    2012-08-01

    The nucleation behavior of He bubbles in nano-grained body-centered-cubic (BCC) Mo is simulated using molecular dynamics (MD) simulations with a bicrystal model, focusing on the effect of grain boundary (GB) structure. Three types of GBs, the (100) twist S29, the ?110? symmetrical tilt (tilt angle of 10.1?), and the (112) twin boundaries, are studied as representatives of random GB, low angle GB with misfit dislocations, and special sigma boundaries. With the same amount of He, more He clusters form in nano-grained Mo with smaller average size compared to that in bulk. The effects of the GB structure originate from the excess volume in GBs. Trapping by excess volume results in reduction in mobility of He atoms, which enhances the nucleation with higher density of bubbles, and impedes the growth of He bubbles by absorption of mobile He atoms. Furthermore, the distribution of excess volume in GBs determines the distribution of He clusters. The effect of GBs becomes less pronounced with increasing vacancy concentration in the matrix.

  5. Post-processing interstitialcy diffusion from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Bhardwaj, U.; Bukkuru, S.; Warrier, M.

    2016-01-01

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms.

  6. Thermal Transport in Fullerene Derivatives Using Molecular Dynamics Simulations

    PubMed Central

    Chen, Liang; Wang, Xiaojia; Kumar, Satish

    2015-01-01

    In order to study the effects of alkyl chain on the thermal properties of fullerene derivatives, we perform molecular dynamics (MD) simulations to predict the thermal conductivity of fullerene (C60) and its derivative phenyl-C61-butyric acid methyl ester (PCBM). The results of non-equilibrium MD simulations show a length-dependent thermal conductivity for C60 but not for PCBM. The thermal conductivity of C60, obtained from the linear extrapolation of inverse conductivity vs. inverse length curve, is 0.2  W m−1 K−1 at room temperature, while the thermal conductivity of PCBM saturates at ~0.075  W m−1 K−1 around 20 nm. The different length-dependence behavior of thermal conductivity indicates that the long-wavelength and low-frequency phonons have large contribution to the thermal conduction in C60. The decrease in thermal conductivity of fullerene derivatives can be attributed to the reduction in group velocities, the decrease of the frequency range of acoustic phonons, and the strong scattering of low-frequency phonons with the alkyl chains due to the significant mismatch of vibrational density of states in low frequency regime between buckyball and alkyl chains in PCBM. PMID:26238607

  7. A Simulation Program for Dynamic Infrared (IR) Spectra

    ERIC Educational Resources Information Center

    Zoerb, Matthew C.; Harris, Charles B.

    2013-01-01

    A free program for the simulation of dynamic infrared (IR) spectra is presented. The program simulates the spectrum of two exchanging IR peaks based on simple input parameters. Larger systems can be simulated with minor modifications. The program is available as an executable program for PCs or can be run in MATLAB on any operating system. Source…

  8. Binary-fluid turbulence: Signatures of multifractal droplet dynamics and dissipation reduction

    NASA Astrophysics Data System (ADS)

    Pal, Nairita; Perlekar, Prasad; Gupta, Anupam; Pandit, Rahul

    2016-06-01

    We study the challenging problem of the advection of an active, deformable, finite-size droplet by a turbulent flow via a simulation of the coupled Cahn-Hilliard-Navier-Stokes (CHNS) equations. In these equations, the droplet has a natural two-way coupling to the background fluid. We show that the probability distribution function of the droplet center of mass acceleration components exhibit wide, non-Gaussian tails, which are consistent with the predictions based on pressure spectra. We also show that the droplet deformation displays multifractal dynamics. Our study reveals that the presence of the droplet enhances the energy spectrum E (k ) , when the wave number k is large; this enhancement leads to dissipation reduction.

  9. Binary-fluid turbulence: Signatures of multifractal droplet dynamics and dissipation reduction.

    PubMed

    Pal, Nairita; Perlekar, Prasad; Gupta, Anupam; Pandit, Rahul

    2016-06-01

    We study the challenging problem of the advection of an active, deformable, finite-size droplet by a turbulent flow via a simulation of the coupled Cahn-Hilliard-Navier-Stokes (CHNS) equations. In these equations, the droplet has a natural two-way coupling to the background fluid. We show that the probability distribution function of the droplet center of mass acceleration components exhibit wide, non-Gaussian tails, which are consistent with the predictions based on pressure spectra. We also show that the droplet deformation displays multifractal dynamics. Our study reveals that the presence of the droplet enhances the energy spectrum E(k), when the wave number k is large; this enhancement leads to dissipation reduction. PMID:27415366

  10. Three-Dimensional Molecular Dynamics Simulations of Void Coalescence during Dynamic Fracture of Ductile Metals

    SciTech Connect

    Seppala, E T; Belak, J; Rudd, R E

    2004-09-02

    Void coalescence and interaction in dynamic fracture of ductile metals have been investigated using three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. The interaction of the voids is not reflected in the volumetric asymptotic growth rate of the voids, as demonstrated here. Finally, the practice of using a single void and periodic boundary conditions to study coalescence is examined critically and shown to produce results markedly different than the coalescence of a pair of isolated voids.

  11. Modal reduction strategies for interconnected flexible bodies simulation

    NASA Technical Reports Server (NTRS)

    Eke, F. O.; Man, G. K.

    1989-01-01

    Multi-body dynamics programs require characterization of each body. The Galileo spacecraft system modes to be retained were determined using available criteria, modal influence coefficients, and bode. The descent to component level was achieved via a two-phase diagonalization process starting with submatrices of truncated augmented system modal matrix.

  12. Enhancing simulation of efficiency with analytical tools. [combining computer simulation and analytical techniques for cost reduction

    NASA Technical Reports Server (NTRS)

    Seltzer, S. M.

    1974-01-01

    Some means of combining both computer simulation and anlytical techniques are indicated in order to mutually enhance their efficiency as design tools and to motivate those involved in engineering design to consider using such combinations. While the idea is not new, heavy reliance on computers often seems to overshadow the potential utility of analytical tools. Although the example used is drawn from the area of dynamics and control, the principles espoused are applicable to other fields. In the example the parameter plane stability analysis technique is described briefly and extended beyond that reported in the literature to increase its utility (through a simple set of recursive formulas) and its applicability (through the portrayal of the effect of varying the sampling period of the computer). The numerical values that were rapidly selected by analysis were found to be correct for the hybrid computer simulation for which they were needed. This obviated the need for cut-and-try methods to choose the numerical values, thereby saving both time and computer utilization.

  13. Stochastic rotation dynamics simulation of electro-osmosis

    NASA Astrophysics Data System (ADS)

    Ceratti, Davide R.; Obliger, Amaël; Jardat, Marie; Rotenberg, Benjamin; Dahirel, Vincent

    2015-09-01

    Stochastic Rotation Dynamics (SRD) is a mesoscale simulation technique that captures hydrodynamic couplings in simple and complex fluids. It can be used in various hydrodynamic regimes and it is not restricted to specific geometries. We show here that SRD using the collisional coupling approach to capture momentum transfer between the semi-implicit solvent and the explicit counterions, is able to describe electro-kinetic effects, i.e. coupled electrostatic and hydrodynamic phenomena occurring at charged solid-liquid interfaces. The method is first validated for electro-osmosis in the simple case of a slit pore without added salt, for which an analytical solution of the Helmholtz-Smoluchowski theory is known, in a physical regime where this mean-field theory is valid. We then discuss the predictions of SRD for electro-osmosis beyond the range of validity of the Helmholtz-Smoluchowski (or Poisson-Nernst-Planck) theory, in particular due to ion-ion correlations at the surface, to charge localisation on discrete sites at the solid surface and to surface charge heterogeneity, that all contribute to a reduction of the electro-osmotic flow. In order to disentangle these last two aspects, we also investigate at the mean-field level a simple system with alternate charged and neutral stripes, using lattice-Boltzmann electro-kinetics simulations. Overall, this work opens new perspectives for the use of SRD as a generic mesoscopic simulation method for soft matter problems, in particular under confinement, since in practice many interfaces between fluids and solids are charged.

  14. A POLLUTION REDUCTION METHODOLOGY FOR CHEMICAL PROCESS SIMULATORS

    EPA Science Inventory

    A pollution minimization methodology was developed for chemical process design using computer simulation. It is based on a pollution balance that at steady state is used to define a pollution index with units of mass of pollution per mass of products. The pollution balance has be...

  15. Quantification of Ground Motion Reductions by Fault Zone Plasticity with 3D Spontaneous Rupture Simulations

    NASA Astrophysics Data System (ADS)

    Roten, D.; Olsen, K. B.; Cui, Y.; Day, S. M.

    2015-12-01

    We explore the effects of fault zone nonlinearity on peak ground velocities (PGVs) by simulating a suite of surface rupturing earthquakes in a visco-plastic medium. Our simulations, performed with the AWP-ODC 3D finite difference code, cover magnitudes from 6.5 to 8.0, with several realizations of the stochastic stress drop for a given magnitude. We test three different models of rock strength, with friction angles and cohesions based on criteria which are frequently applied to fractured rock masses in civil engineering and mining. We use a minimum shear-wave velocity of 500 m/s and a maximum frequency of 1 Hz. In rupture scenarios with average stress drop (~3.5 MPa), plastic yielding reduces near-fault PGVs by 15 to 30% in pre-fractured, low-strength rock, but less than 1% in massive, high quality rock. These reductions are almost insensitive to the scenario earthquake magnitude. In the case of high stress drop (~7 MPa), however, plasticity reduces near-fault PGVs by 38 to 45% in rocks of low strength and by 5 to 15% in rocks of high strength. Because plasticity reduces slip rates and static slip near the surface, these effects can partially be captured by defining a shallow velocity-strengthening layer. We also perform a dynamic nonlinear simulation of a high stress drop M 7.8 earthquake rupturing the southern San Andreas fault along 250 km from Indio to Lake Hughes. With respect to the viscoelastic solution (a), nonlinearity in the fault damage zone and in near-surface deposits would reduce long-period (> 1 s) peak ground velocities in the Los Angeles basin by 15-50% (b), depending on the strength of crustal rocks and shallow sediments. These simulation results suggest that nonlinear effects may be relevant even at long periods, especially for earthquakes with high stress drop.

  16. Microwave tomography of extremities: 2) Functional fused imaging of flow reduction and simulated compartment syndrome

    PubMed Central

    Semenov, Serguei; Kellam, James; Nair, Bindu; Williams, Thomas; Quinn, Michael; Sizov, Yuri; Nazarov, Alexei; Pavlovsky, Andrey

    2011-01-01

    Medical imaging has recently expanded into the dual- or multi-modality fusion of anatomical and functional imaging modalities. This significantly improves the diagnostic power while simultaneously increasing the cost of an already expensive medical devices or investigations and decreasing their mobility. We are introducing a novel imaging concept of four-dimensional (4D) Microwave Tomographic (MWT) functional imaging: three-dimensional (3D) in spatial domain plus one-dimension (1D) in the time, functional dynamic domain. Instead of a fusion of images obtained by different imaging modalities, 4D MWT fuses absolute anatomical images with dynamic, differential images of the same imaging technology. The approach was successively validated in animal experiments with short term arterial flow reduction and a simulated compartment syndrome in an initial simplified experimental setting using dedicated microwave tomographic system. The presented fused images are not perfect as MWT is a novel imaging modality at its early stage of the development and ways of reading of reconstructed MWT images need to be further studied and understood. However, the reconstructed fused images present clear evidence that microwave tomography is an emerging imaging modality with great potentials for functional imaging. PMID:21364266

  17. Microwave tomography of extremities: 2. Functional fused imaging of flow reduction and simulated compartment syndrome.

    PubMed

    Semenov, Serguei; Kellam, James; Nair, Bindu; Williams, Thomas; Quinn, Michael; Sizov, Yuri; Nazarov, Alexei; Pavlovsky, Andrey

    2011-04-01

    Medical imaging has recently expanded into the dual- or multi-modality fusion of anatomical and functional imaging modalities. This significantly improves the diagnostic power while simultaneously increasing the cost of already expensive medical devices or investigations and decreasing their mobility. We are introducing a novel imaging concept of four-dimensional (4D) microwave tomographic (MWT) functional imaging: three dimensional (3D) in the spatial domain plus one dimensional (1D) in the time, functional dynamic domain. Instead of a fusion of images obtained by different imaging modalities, 4D MWT fuses absolute anatomical images with dynamic, differential images of the same imaging technology. The approach was successively validated in animal experiments with short-term arterial flow reduction and a simulated compartment syndrome in an initial simplified experimental setting using a dedicated MWT system. The presented fused images are not perfect as MWT is a novel imaging modality at its early stage of the development and ways of reading reconstructed MWT images need to be further studied and understood. However, the reconstructed fused images present clear evidence that microwave tomography is an emerging imaging modality with great potentials for functional imaging. PMID:21364266

  18. Microwave tomography of extremities: 2. Functional fused imaging of flow reduction and simulated compartment syndrome

    NASA Astrophysics Data System (ADS)

    Semenov, Serguei; Kellam, James; Nair, Bindu; Williams, Thomas; Quinn, Michael; Sizov, Yuri; Nazarov, Alexei; Pavlovsky, Andrey

    2011-04-01

    Medical imaging has recently expanded into the dual- or multi-modality fusion of anatomical and functional imaging modalities. This significantly improves the diagnostic power while simultaneously increasing the cost of already expensive medical devices or investigations and decreasing their mobility. We are introducing a novel imaging concept of four-dimensional (4D) microwave tomographic (MWT) functional imaging: three dimensional (3D) in the spatial domain plus one dimensional (1D) in the time, functional dynamic domain. Instead of a fusion of images obtained by different imaging modalities, 4D MWT fuses absolute anatomical images with dynamic, differential images of the same imaging technology. The approach was successively validated in animal experiments with short-term arterial flow reduction and a simulated compartment syndrome in an initial simplified experimental setting using a dedicated MWT system. The presented fused images are not perfect as MWT is a novel imaging modality at its early stage of the development and ways of reading reconstructed MWT images need to be further studied and understood. However, the reconstructed fused images present clear evidence that microwave tomography is an emerging imaging modality with great potentials for functional imaging.

  19. Dynamic Reduction Effect of CO2 Gas Discharge in Introducing Electric Vehicles

    NASA Astrophysics Data System (ADS)

    Liu, Bin; Inaba, Tsuginori

    For this study, the dynamic reduction effect of CO2 gas discharge for change from internal combustion engines to electric vehicles, EVs, was investigated quantitatively. The Japanese power generation status, which shows characteristics of electricity generation, and optimized adjustment to electricity demand, load and environment was examined. Based on a CO2 gas discharge basic unit, the estimated reduction quantity of CO2 gas discharge from EVs was calculated. The reduction effect of CO2 gas discharge is expected to be 52% by changing gas-fuelled vehicles to EVs. However, the dynamic differential is only 19% reduction by using the thermal power and -2% if only the coal thermal power is used.

  20. Dynamics modeling and simulation of autonomous underwater vehicles with appendages

    NASA Astrophysics Data System (ADS)

    Su, Yumin; Zhao, Jinxin; Cao, Jian; Zhang, Guocheng

    2013-03-01

    To provide a simulation system platform for designing and debugging a small autonomous underwater vehicle's (AUV) motion controller, a six-degree of freedom (6-DOF) dynamic model for AUV controlled by thruster and fins with appendages is examined. Based on the dynamic model, a simulation system for the AUV's motion is established. The different kinds of typical motions are simulated to analyze the motion performance and the maneuverability of the AUV. In order to evaluate the influences of appendages on the motion performance of the AUV, simulations of the AUV with and without appendages are performed and compared. The results demonstrate the AUV has good maneuverability with and without appendages.

  1. Self-organization and dynamics reduction in recurrent networks: stimulus presentation and learning.

    PubMed

    Samuelides, Manuel; Doyon, Bernard; Cessac, Bruno; Quoy, Mathias; Dauce, Emmanuel

    1998-04-01

    Freeman's investigations on the olfactory bulb of the rabbit showed that its signal dynamics was chaotic, and that recognition of a learned stimulus is linked to a dimension reduction of the dynamics attractor. In this paper we address the question whether this behavior is specific of this particular architecture, or if it is a general property. We study the dynamics of a non-convergent recurrent model-the random recurrent neural networks. In that model a mean-field theory can be used to analyze the autonomous dynamics. We extend this approach with various observations on significant changes in the dynamical regime when sending static random stimuli. Then we propose a Hebb-like learning rule, viewed as a self-organization dynamical process inducing specific reactivity to one random stimulus. We numerically show the dynamics reduction during learning and recognition processes and analyze it in terms of dynamical repartition of local neural activity. PMID:12662827

  2. Comparisons of Kinematics and Dynamics Simulation Software Tools

    NASA Technical Reports Server (NTRS)

    Shiue, Yeu-Sheng Paul

    2002-01-01

    Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.

  3. Dynamical simulations of strongly correlated electron materials

    NASA Astrophysics Data System (ADS)

    Kress, Joel; Barros, Kipton; Batista, Cristian; Chern, Gia-Wei; Kotliar, Gabriel

    We present a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. We use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms.

  4. Mosquito population dynamics from cellular automata-based simulation

    NASA Astrophysics Data System (ADS)

    Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning

    2016-02-01

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

  5. An electro-fluid-dynamic simulator for the cardiovascular system.

    PubMed

    Felipini, Celso Luiz; de Andrade, Aron José Pazin; Lucchi, Júlio César; da Fonseca, Jeison Willian Gomes; Nicolosi, Denys

    2008-04-01

    This work presents the initial studies and the proposal for a cardiovascular system electro-fluid-dynamic simulator to be applied in the development of left ventricular assist devices (LVADs). The simulator, which is being developed at University Sao Judas Tadeu and at Institute Dante Pazzanese of Cardiology, is composed of three modules: (i) an electrical analog model of the cardiovascular system operating in the PSpice electrical simulator environment; (ii) an electronic controller, based on laboratory virtual instrumentation engineering workbench (LabVIEW) acquisition and control tool, which will act over the physical simulator; and (iii) the physical simulator: a fluid-dynamic equipment composed of pneumatic actuators and compliance tubes for the simulation of active cardiac chambers and big vessels. The physical simulator (iii) is based on results obtained from the electrical analog model (i) and physiological parameters. PMID:18370952

  6. Dynamics of water confined in lyotropic liquid crystals: Molecular dynamics simulations of the dynamic structure factor

    NASA Astrophysics Data System (ADS)

    Mantha, Sriteja; Yethiraj, Arun

    2016-02-01

    The properties of water under confinement are of practical and fundamental interest. In this work, we study the properties of water in the self-assembled lyotropic phases of Gemini surfactants with a focus on testing the standard analysis of quasi-elastic neutron scattering (QENS) experiments. In QENS experiments, the dynamic structure factor is measured and fit to models to extract the translational diffusion constant, DT, and rotational relaxation time, τR. We test this procedure by using simulation results for the dynamic structure factor, extracting the dynamic parameters from the fit as is typically done in experiments, and comparing the values to those directly measured in the simulations. We find that the de-coupling approximation, where the intermediate scattering function is assumed to be a product of translational and rotational contributions, is quite accurate. The jump-diffusion and isotropic rotation models, however, are not accurate when the degree of confinement is high. In particular, the exponential approximations for the intermediate scattering function fail for highly confined water and the values of DT and τR can differ from the measured value by as much as a factor of two. Other models have more fit parameters, however, and with the range of energies and wave-vectors accessible to QENS, the typical analysis appears to be the best choice. In the most confined lamellar phase, the dynamics are sufficiently slow that QENS does not access a large enough time scale.

  7. Dynamically Tuned Blade Pitch Links for Vibration Reduction

    NASA Technical Reports Server (NTRS)

    Milgram, Judah; Chopra, Inderjit; Kottapalli, Sesi

    1994-01-01

    A passive vibration reduction device in which the conventional main rotor blade pitch link is replaced by a spring/damper element is investigated using a comprehensive rotorcraft analysis code. A case study is conducted for a modern articulated helicopter main rotor. Correlation of vibratory pitch link loads with wind tunnel test data is satisfactory for lower harmonics. Inclusion of unsteady aerodynamics had little effect on the correlation. In the absence of pushrod damping, reduction in pushrod stiffness from the baseline value had an adverse effect on vibratory hub loads in forward flight. However, pushrod damping in combination with reduced pushrod stiffness resulted in modest improvements in fixed and rotating system hub loads.

  8. Dynamics of adaptive structures: Design through simulations

    NASA Technical Reports Server (NTRS)

    Park, K. C.; Alexander, S.

    1993-01-01

    The use of a helical bi-morph actuator/sensor concept by mimicking the change of helical waveform in bacterial flagella is perhaps the first application of bacterial motions (living species) to longitudinal deployment of space structures. However, no dynamical considerations were analyzed to explain the waveform change mechanisms. The objective is to review various deployment concepts from the dynamics point of view and introduce the dynamical considerations from the outset as part of design considerations. Specifically, the impact of the incorporation of the combined static mechanisms and dynamic design considerations on the deployment performance during the reconfiguration stage is studied in terms of improved controllability, maneuvering duration, and joint singularity index. It is shown that intermediate configurations during articulations play an important role for improved joint mechanisms design and overall structural deployability.

  9. Simulating Hamiltonian Dynamics with a Truncated Taylor Series

    NASA Astrophysics Data System (ADS)

    Somma, Rolando

    2015-03-01

    One of the main motivations for quantum computers is their ability to efficiently simulate the dynamics of quantum systems. Since the mid-1990s, many algorithms have been developed to simulate Hamiltonian dynamics on a quantum computer, with applications to problems such as simulating spin models and quantum chemistry. While it is now well known that quantum computers can efficiently simulate Hamiltonian dynamics, ongoing work has improved the performance and expanded the scope of such simulations. In this talk, I will describe a very simple and efficient algorithm for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. This algorithm can simulate the time evolution of a wide variety of physical systems. The cost of this algorithm depends only logarithmically on the inverse of the desired precision, and can be shown to be optimal. Such a cost also represents an exponential improvement over known methods for Hamiltonian simulation based on, e.g., Trotter-Suzuki approximations. Roughly speaking, doubling the number of digits of accuracy of the simulation only doubles the complexity. The new algorithm and its analysis are highly simplified due to a technique for implementing linear combinations of unitary operations to directly apply the truncated Taylor series. This is joint work with Dominic Berry, Andrew Childs, Richard Cleve, and Robin Kothari.

  10. Perspective: Computer simulations of long time dynamics.

    PubMed

    Elber, Ron

    2016-02-14

    Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473

  11. Perspective: Computer simulations of long time dynamics

    PubMed Central

    Elber, Ron

    2016-01-01

    Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473

  12. A fast recursive algorithm for molecular dynamics simulation

    NASA Technical Reports Server (NTRS)

    Jain, A.; Vaidehi, N.; Rodriguez, G.

    1993-01-01

    The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

  13. Colloidal suspension simulates linear dynamic pressure profile

    NASA Technical Reports Server (NTRS)

    Mc Cann, R. J.

    1966-01-01

    Missile nose fairings immersed in colloidal suspension prepared with various specific gravities simulate pressure profiles very similar to those encountered during reentry. Stress and deflection conditions similar to those expected during atmospheric reentry are thus attained in the laboratory.

  14. Model reduction in the simulation of interconnected flexible bodies

    NASA Technical Reports Server (NTRS)

    Eke, Fidelis O.; Man, Guy K.

    1988-01-01

    Given the control system specifications for a system of interconnected rigid and flexible bodies, methods now exist for determining the system modes that do not interact 'strongly' with the controller. Once these important system modes are known, there still remains the problem of determining the modes of individual bodies that should be retained, since, in the final analysis, it is the modal information at the component level that must be fed into any multibody simulation code. Systematic identification of these component modes is achieved through a two-phase matrix diagonalization process starting with judiciously chosen submatrices of the system modal matrix.

  15. Direct Statistical Simulation: Ensemble Averaging and Basis Reduction

    NASA Astrophysics Data System (ADS)

    Allawala, Altan; Marston, Brad

    2015-11-01

    Low-order statistics of models of geophysical fluids may be directly accessed by solving the equations of motion for the equal-time cumulants themselves. We investigate a variant of the second-order cumulant expansion (CE2) in which zonal averaging is replaced by ensemble averaging. Proper orthogonal decomposition (POD) of the second cumulant is used to reduce the dimensionality of the problem. The approach is tested on a quasi-geostrophic 2-layer baroclinic model of planetary atmospheres by comparison to the traditional approach of accumulating statistics via numerical simulation, and to zonal averaged CE2. Supported in part by NSF DMR-1306806 and NSF CCF-1048701.

  16. Simulating food web dynamics along a gradient: quantifying human influence.

    PubMed

    Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M

    2012-01-01

    Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics

  17. Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.

    SciTech Connect

    Lau, E Y; Krishnan, V V

    2007-07-18

    The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.

  18. Optimized reduction of uncertainty in bursty human dynamics

    NASA Astrophysics Data System (ADS)

    Jo, Hang-Hyun; Moon, Eunyoung; Kaski, Kimmo

    2012-01-01

    Human dynamics is known to be inhomogeneous and bursty but the detailed understanding of the role of human factors in bursty dynamics is still lacking. In order to investigate their role we devise an agent-based model, where an agent in an uncertain situation tries to reduce the uncertainty by communicating with information providers while having to wait time for responses. Here the waiting time can be considered as cost. We show that the optimal choice of the waiting time under uncertainty gives rise to the bursty dynamics, characterized by the heavy tailed distribution of optimal waiting time. We find that in all cases the efficiency for communication is relevant to the scaling behavior of the optimal waiting time distribution. On the other hand, the cost turns out in some cases to be irrelevant depending on the degree of uncertainty and efficiency.

  19. Simulation of dynamic interface fracture using spectral boundary integral method

    NASA Astrophysics Data System (ADS)

    Harish, Ajay Bangalore

    Simulation of three-dimensional dynamic fracture events constitutes one of the most challenging topics in the field of computational mechanics. Spontaneous dynamic fracture along the interface of two elastic solids is of great importance and interest to a number of disciplines in engineering and science. Applications include dynamic fractures in aircraft structures, earthquakes, thermal shocks in nuclear containment vessels and delamination in layered composite materials.

  20. A Process for Comparing Dynamics of Distributed Space Systems Simulations

    NASA Technical Reports Server (NTRS)

    Cures, Edwin Z.; Jackson, Albert A.; Morris, Jeffery C.

    2009-01-01

    The paper describes a process that was developed for comparing the primary orbital dynamics behavior between space systems distributed simulations. This process is used to characterize and understand the fundamental fidelities and compatibilities of the modeling of orbital dynamics between spacecraft simulations. This is required for high-latency distributed simulations such as NASA s Integrated Mission Simulation and must be understood when reporting results from simulation executions. This paper presents 10 principal comparison tests along with their rationale and examples of the results. The Integrated Mission Simulation (IMSim) (formerly know as the Distributed Space Exploration Simulation (DSES)) is a NASA research and development project focusing on the technologies and processes that are related to the collaborative simulation of complex space systems involved in the exploration of our solar system. Currently, the NASA centers that are actively participating in the IMSim project are the Ames Research Center, the Jet Propulsion Laboratory (JPL), the Johnson Space Center (JSC), the Kennedy Space Center, the Langley Research Center and the Marshall Space Flight Center. In concept, each center participating in IMSim has its own set of simulation models and environment(s). These simulation tools are used to build the various simulation products that are used for scientific investigation, engineering analysis, system design, training, planning, operations and more. Working individually, these production simulations provide important data to various NASA projects.

  1. Dynamics of a compound vesicle: numerical simulations

    NASA Astrophysics Data System (ADS)

    Veerapaneni, Shravan; Young, Yuan-Nan; Vlahovska, Petia; Blawzdziewicz, Jerzy

    2010-11-01

    Vesicles (self-enclosing lipid membranes) in simple linear flows are known to exhibit rich dynamics such as tank-treading, tumbling, trembling (swinging), and vacillating breathing. Recently, vesicles have been used as a multi-functional platform for drug-delivery. In this work, the dynamics of simplified models for such compound vesicles is investigated numerically using a state-of-the-art boundary-integral code that has been validated with high accuracy and efficiency. Results show that for a vesicle enclosing a rigid particle in a simple shear flow, transition from tank-treading to tumbling is possible even in the absence of viscosity mismatch in the interior and exterior fluids. We will discuss the shape transformations, multiple particle interactions and the flow properties. Comparison with results from analytical modeling gives insights to the underlying physics for such novel dynamics.

  2. Further Reductions of Normal Forms for Dynamical Systems

    NASA Astrophysics Data System (ADS)

    Chen, Guoting; Della Dora, Jean

    2000-09-01

    We propose in this paper a method for obtaining a significant refinement of normal forms for dynamical systems or vector fields, with concrete and interesting applications. We use lower order nonlinear terms in the normal form for the simplifications of higher order terms. Our approach is applicable for both the non nilpotent and the nilpotent cases. For dynamical systems of dimensions 2 and 3 we give an algorithm that leads to interesting finite order normal forms which are optimal (or unique) with respect to equivalence by formal near identity transformations. We can compute at the same time a formal diffeormorphism that realizes the normalization. Comparisons with other methods are given for several examples.

  3. Dynamics Simulation Model for Space Tethers

    NASA Technical Reports Server (NTRS)

    Levin, E. M.; Pearson, J.; Oldson, J. C.

    2006-01-01

    This document describes the development of an accurate model for the dynamics of the Momentum Exchange Electrodynamic Reboost (MXER) system. The MXER is a rotating tether about 100-km long in elliptical Earth orbit designed to catch payloads in low Earth orbit and throw them to geosynchronous orbit or to Earth escape. To ensure successful rendezvous between the MXER tip catcher and a payload, a high-fidelity model of the system dynamics is required. The model developed here quantifies the major environmental perturbations, and can predict the MXER tip position to within meters over one orbit.

  4. A Landing Gear Noise Reduction Study Based on Computational Simulations

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Lockard, David P.

    2006-01-01

    Landing gear is one of the more prominent airframe noise sources. Techniques that diminish gear noise and suppress its radiation to the ground are highly desirable. Using a hybrid computational approach, this paper investigates the noise reduction potential of devices added to a simplified main landing gear model without small scale geometric details. The Ffowcs Williams and Hawkings equation is used to predict the noise at far-field observer locations from surface pressure data provided by unsteady CFD calculations. Because of the simplified nature of the model, most of the flow unsteadiness is restricted to low frequencies. The wheels, gear boxes, and oleo appear to be the primary sources of unsteadiness at these frequencies. The addition of fairings around the gear boxes and wheels, and the attachment of a splitter plate on the downstream side of the oleo significantly reduces the noise over a wide range of frequencies, but a dramatic increase in noise is observed at one frequency. The increased flow velocities, a consequence of the more streamlined bodies, appear to generate extra unsteadiness around other parts giving rise to the additional noise. Nonetheless, the calculations demonstrate the capability of the devices to improve overall landing gear noise.

  5. Stochastic simulation of patterns using ISOMAP for dimensionality reduction of training images

    NASA Astrophysics Data System (ADS)

    Zhang, Ting; Du, Yi; Huang, Tao; Yang, Jiaqing; Li, Xue

    2015-06-01

    Most data in the real world are normally nonlinear or difficult to determine whether they are linear or not beforehand. Some linear dimensionality reduction algorithms, e.g., principal component analysis (PCA) and multi-dimensional scaling (MDS) are only suitable for linear dimensionality reduction of spatial data. The patterns extracted from training images (TIs) used in MPS simulation mostly are probably nonlinear, so for some MPS simulation methods based on dimensionality reduction, e.g., FILTERSIM using some filters created via the idea of PCA and DisPAT using MDS as a tool of dimensionality reduction, those linear methods for dimensionality reduction are not appropriate when realizing the dimensionality reduction of nonlinear data of patterns. Therefore, isometric mapping (ISOMAP) working as a nonlinear dimensionality reduction method used in manifold learning is introduced to map those patterns, regardless of being linear or nonlinear, into low-dimensional space. However, because the original ISOMAP has some disadvantages in computing speed and accuracy, landmark points of patterns are selected to improve the speed and neighborhoods of patterns are set to guarantee the quality of dimensionality reduction. Next, the sequential simulation similar to FILTERSIM is performed after low-dimensional data of patterns are classified by a density-based clustering algorithm. The comparisons with FILTERSIM and DisPAT show the improvement of pattern reproductivity and computing speed of our method for both continuous and categorical variables.

  6. Particle dynamics simulations of Turing patterns

    NASA Astrophysics Data System (ADS)

    Dziekan, P.; Lemarchand, A.; Nowakowski, B.

    2012-08-01

    The direct simulation Monte Carlo method is used to reproduce Turing patterns at the microscopic level in reaction-diffusion systems. In order to satisfy the basic condition for the development of such a spatial structure, we propose a model involving a solvent, which allows for disparate diffusivities of individual reactive species. One-dimensional structures are simulated in systems of various lengths. Simulation results agree with the macroscopic predictions obtained by integration of the reaction-diffusion equations. Additional effects due to internal fluctuations are observed, such as temporal transitions between structures of different wavelengths in a confined system. For a structure developing behind a propagating wave front, the fluctuations suppress the induction period and accelerate the formation of the Turing pattern. These results support the ability of reaction-diffusion models to robustly reproduce axial segmentation including the formation of early vertebrae or somites in noisy biological environments.

  7. Flow Dynamics and Nutrient Reduction in Rain Gardens

    EPA Science Inventory

    The hydrological dynamics and changes in stormwater nutrient concentrations within rain gardens were studied by introducing captured stormwater runoff to rain gardens at EPA’s Urban Water Research Facility in Edison, New Jersey. The runoff used in these experiments was collected...

  8. Gamma ray observatory dynamics simulator in Ada (GRODY)

    NASA Technical Reports Server (NTRS)

    1990-01-01

    This experiment involved the parallel development of dynamics simulators for the Gamma Ray Observatory in both FORTRAN and Ada for the purpose of evaluating the applicability of Ada to the NASA/Goddard Space Flight Center's flight dynamics environment. The experiment successfully demonstrated that Ada is a viable, valuable technology for use in this environment. In addition to building a simulator, the Ada team evaluated training approaches, developed an Ada methodology appropriate to the flight dynamics environment, and established a baseline for evaluating future Ada projects.

  9. Brownian dynamics simulation for modeling ion permeation across bionanotubes.

    PubMed

    Krishnamurthy, Vikram; Chung, Shin-Ho

    2005-03-01

    The principles underlying Brownian dynamics (BD), its statistical consistency, and algorithms for practical implementation are outlined here. The ability to compute current flow across ion channels confers a distinct advantage to BD simulations compared to other simulation techniques. Thus, two obvious applications of BD ion channels are in calculation of the current-voltage and current-concentration curves, which can be directly compared to the physiological measurements to assess the reliability of the model and predictive power of the method. We illustrate how BD simulations are used to unravel the permeation dynamics in two biological ion channels-the KcsA K+ channel and CIC Cl- channel. PMID:15816176

  10. Computer simulation of multigrid body dynamics and control

    NASA Technical Reports Server (NTRS)

    Swaminadham, M.; Moon, Young I.; Venkayya, V. B.

    1990-01-01

    The objective is to set up and analyze benchmark problems on multibody dynamics and to verify the predictions of two multibody computer simulation codes. TREETOPS and DISCOS have been used to run three example problems - one degree-of-freedom spring mass dashpot system, an inverted pendulum system, and a triple pendulum. To study the dynamics and control interaction, an inverted planar pendulum with an external body force and a torsional control spring was modeled as a hinge connected two-rigid body system. TREETOPS and DISCOS affected the time history simulation of this problem. System state space variables and their time derivatives from two simulation codes were compared.