Decoherence Allows Model Reduction in Nonadiabatic Dynamics Simulations.
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
Dynamical system modeling via signal reduction and neural network simulation
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.
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
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
Structured building model reduction toward parallel simulation
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.
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.
Process simulation of aluminum reduction cells
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.
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.
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.
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
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.
Cantera Aerosol Dynamics Simulator
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.
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.
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.
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.
Molecular dynamics simulations
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.
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
Simulation of dose reduction in tomosynthesis
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
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.
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.
Validation of CT dose-reduction simulation.
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
Validation of CT dose-reduction simulation
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
Domain reduction method for atomistic simulations
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.
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.
Dynamic simulation of voltage collapses
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.
Floating orbital molecular dynamics simulations.
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
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).
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.
Dynamic stiffness removal for direct numerical simulations
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)
Simulation visualization through dynamic instrumentation
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.
Dose reduction using a dynamic, piecewise-linear attenuator
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
Dose reduction using a dynamic, piecewise-linear attenuator
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
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
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...
Accelerated dynamics simulations of nanotubes.
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.
Radiation in molecular dynamic simulations
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.
Methods and systems for combustion dynamics reduction
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.
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.
Dynamic simulations of tissue welding
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.
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
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.
Improving computational efficiency of Monte Carlo simulations with variance reduction
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)
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
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.
Risk Reduction and Training using Simulation Based Tools - 12180
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
Dynamics of riboswitches: Molecular simulations.
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
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.
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.
A multicomb variance reduction scheme for Monte Carlo semiconductor simulators
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.
Magnetotail dynamics: MHD simulations of driven and spontaneous dynamic changes
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.
Molecular dynamics simulations of large macromolecular complexes
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
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.
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.
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.
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)
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.
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.
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.
Observing dynamical SUSY breaking with lattice simulation
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.
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.
Molecular dynamics simulations: advances and applications
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.
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.
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.
DUVFEL PHOTOINJECTOR DYNAMICS: MEASUREMENT AND SIMULATION.
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.
Simulation of wetlands forest vegetation dynamics
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.
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.
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.
Spin dynamics simulations at AGS
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.
Peptide crystal simulations reveal hidden dynamics
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
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
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.
Multibody dynamic simulation of knee contact mechanics
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
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.
Approximate Bisimulation-Based Reduction of Power System Dynamic Models
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.
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.
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.
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 %.
Buckybomb: Reactive Molecular Dynamics Simulation.
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
Dynamic procedure for filtered gyrokinetic simulations
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.
Computer simulation of microstructural dynamics
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.
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.
Dynamic Fracture Simulations of Explosively Loaded Cylinders
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.
Dynamic simulation recalls condensate piping event
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.
Molecular dynamic simulations of ocular tablet dissolution.
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
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.
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.
Fully dynamical simulation of central nuclear collisions.
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
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.
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.
Dynamic simulation of a reverse Brayton refrigerator
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.
ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*
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
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.
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.
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.
Geometric reduction of dynamical nonlocality in nanoscale quantum circuits
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
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.
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.
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.
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.
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.
Dynamic Simulation of a Helium Liquefier
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.
Thermostability of Enzymes from Molecular Dynamics Simulations.
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
Reduction of dynamical biochemical reactions networks in computational biology
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
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.
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.
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.
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.
Simulation of counterflow pedestrian dynamics using spheropolygons.
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
Electronic continuum model for molecular dynamics simulations.
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
Integrated computer simulation on FIR FEL dynamics
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.
Molecular dynamics simulation of liquid sulfur dioxide.
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
Simulating stochastic dynamics using large time steps.
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
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.
Exploiting Enzymatic Dynamic Reductive Kinetic Resolution (DYRKR) in Stereocontrolled Synthesis
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
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.
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.
Dynamic simulator for PEFC propulsion plant
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.
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.
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).
INCORPORATING DYNAMIC 3D SIMULATION INTO PRA
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.
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.
Stress Reduction in Adjacent Level Discs via Dynamic Instrumentation: A Finite Element Analysis
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
Monoamine transporters: insights from molecular dynamics simulations
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
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.
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.
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.
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.
Molecular Dynamics Simulations of Graphene Oxide Frameworks
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.
Finite element simulation of pipe dynamic response
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.
Molecular dynamics simulations of weak detonations.
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
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.
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..
Isotropic MD simulations of dynamic brittle fracture
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}.
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.
Molecular dynamics simulations of dense plasmas
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.
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.
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.
Molecular dynamics simulation of amorphous indomethacin.
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
Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations.
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
Atomistic molecular dynamic simulations of multiferroics.
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
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.
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.
Quantum molecular dynamics simulations of dense matter
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.
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.
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
Dynamics simulations for engineering macromolecular interactions
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
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.
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
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
CADS:Cantera Aerosol Dynamics Simulator.
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.
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.
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.
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
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
Simulations of Operation Dynamics of Different Type GaN Particle Sensors
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
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
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.
Numerical simulation of tulip flame dynamics
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.
Numerical simulation of tulip flame dynamics
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.
Molecular dynamics simulations of microscale fluid transport
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.
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.
Consequence modeling using the fire dynamics simulator.
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
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.
Erbium Implantation in Silica Studied by Molecular Dynamics Simulations
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.
Dynamic Shade and Irradiance Simulation of Aquatic Landscapes and Watersheds
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...
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.
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.
Studying Interactions by Molecular Dynamics Simulations at High Concentration
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
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
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.
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.
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
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
Rotational Brownian Dynamics simulations of clathrin cage formation
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.
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.
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
Molecular Dynamics Simulation of Disordered Zircon
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.
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.
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
Simulation of chemical isomerization reaction dynamics on a NMR quantum simulator.
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
Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition.
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.
Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition
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.
Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition
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
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
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.
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.
Kinetic simulations of plasmoid chain dynamics
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.
Molecular Dynamics Simulations of Coulomb Explosion
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.
Annual Report 1999 Environmental Dynamics and Simulation
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.
Expansion techniques for collisionless stellar dynamical simulations
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.
Nanoscale deicing by molecular dynamics simulation.
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
Dynamic Simulation over Long Time Periods with 100% Solar Generation.
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.
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.
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.
Molecular Dynamics Simulations of Glycerol Monooleate Confined between Mica Surfaces.
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
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.
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.
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…
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.
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.
A note on simulation and dynamical hierarchies
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.
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.
Kinetic distance and kinetic maps from molecular dynamics simulation.
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
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.
Molecular dynamics simulations of He bubble nucleation at grain boundaries
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.
Thermal Transport in Fullerene Derivatives Using Molecular Dynamics Simulations
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
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.
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…
Binary-fluid turbulence: Signatures of multifractal droplet dynamics and dissipation reduction.
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
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.
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.
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.
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.
A POLLUTION REDUCTION METHODOLOGY FOR CHEMICAL PROCESS SIMULATORS
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...
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.
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.
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.
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
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
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.
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.
Self-organization and dynamics reduction in recurrent networks: stimulus presentation and learning.
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
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.
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.
An electro-fluid-dynamic simulator for the cardiovascular system.
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
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.
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.
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.
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.
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.
Perspective: Computer simulations of long time dynamics.
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
Perspective: Computer simulations of long time dynamics
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
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.
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.
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.
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.
Simulating food web dynamics along a gradient: quantifying human influence.
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
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Flow Dynamics and Nutrient Reduction in Rain Gardens
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...
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.
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.
Large-eddy simulation of a turbulent flow over a heavy vehicle with drag reduction devices
NASA Astrophysics Data System (ADS)
Lee, Sangseung; Kim, Myeongkyun; You, Donghyun
2015-11-01
Aerodynamic drag contributes to a considerable amount of energy loss of heavy vehicles. To reduce the energy loss, drag reduction devices such as side skirts and boat tails, are often installed to the side and the rear of a heavy vehicle. In the present study, turbulent flow around a heavy vehicle with realistic geometric details is simulated using large-eddy simulation (LES), which is capable of providing unsteady flow physics responsible for aerodynamic in sufficient detail. Flow over a heavy vehicle with and without a boat tail and side skirts as drag reduction devices is simulated. The simulation results are validated against accompanying in-house experimental measurements. Effects of a boat tail and side skirts on drag reduction are discussed in detail. Supported by the Korea Agency for Infrastructure Technology Advancement (KAIA) Grant NTIS 1615007940.
Brownian dynamics simulation for modeling ion permeation across bionanotubes.
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
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.
3-D simulation of posterior fossa reduction in Chiari I.
Fernandes, Yvens Barbosa; Perestrelo, Pedro Fábio Mendonça; Noritomi, Pedro Yoshito; Mathias, Roger Neves; Silva, Jorge Vicente Lopes da; Joaquim, Andrei Fernandes
2016-05-01
We proposed a 3D model to evaluate the role of platybasia and clivus length in the development of Chiari I (CI). Using a computer aided design software, two DICOM files of a normal CT scan and MR were used to simulate different clivus lengths (CL) and also different basal angles (BA). The final posterior fossa volume (PFV) was obtained for each variation and the percentage of the volumetric change was acquired with the same method. The initial normal values of CL and BA were 35.65 mm and 112.66º respectively, with a total PFV of 209 ml. Ranging the CL from 34.65 to 29.65 - 24.65 - 19.65, there was a PFV decrease of 0.47% - 1.12% - 1.69%, respectively. Ranging the BA from 122.66º to 127.66º - 142.66º, the PFV decreased 0.69% - 3.23%, respectively. Our model highlights the importance of the basal angle and clivus length to the development of CI. PMID:27191237
Simulation analysis of dynamic working performance for star trackers.
Shen, Juan; Zhang, Guangjun; Wei, Xinguo
2010-12-01
The elongated imaging track pertaining to a star spot recorded in the image sensor of a star tracker will diffuse over several pixels at a high angular velocity, leading to an inaccurate, even false, attitude value. A computer simulation of the attitude determination from a dynamic star tracker is developed first, based on a dynamic mathematical model of the star-spot imaging and an efficiency validation of the star centroiding algorithm in the dynamic condition. Then major error sources affecting the attitude accuracy in the dynamic condition are analyzed and discussed systematically based on the simulation results. A mathematical model calculating the average star number detected in the field of view is also deduced, using simulation results and signal processing theory, with image trailing ranging from 0 to 20 pixels during exposure. The summarized regularity is helpful in the system design and accuracy evaluation of a star tracker. PMID:21119749
SSME-HAS dynamic load simulators
NASA Technical Reports Server (NTRS)
1975-01-01
The space shuttle main engine propellant valve actuators (SSME) were designed to simulate the loads reflected into the SSME by the chamber coolant valve, the fuel preburner, and the oxidizer. The design, and functional description are included along with a list of the drawings. The load fixture control transform, friction torque, and flow calculations are reported.
Programmable quantum simulation by dynamic Hamiltonian engineering
NASA Astrophysics Data System (ADS)
Hayes, David; Flammia, Steven T.; Biercuk, Michael J.
2014-08-01
Quantum simulation is a promising near term application for quantum information processors with the potential to solve computationally intractable problems using just a few dozen interacting qubits. A range of experimental platforms have recently demonstrated the basic functionality of quantum simulation applied to quantum magnetism, quantum phase transitions and relativistic quantum mechanics. However, in all cases, the physics of the underlying hardware restricts the achievable inter-particle interactions and forms a serious constraint on the versatility of the simulators. To broaden the scope of these analog devices, we develop a suite of pulse sequences that permit a user to efficiently realize average Hamiltonians that are beyond the native interactions of the system. Specifically, this approach permits the generation of all symmetrically coupled translation-invariant two-body Hamiltonians with homogeneous on-site terms, a class which includes all spin-1/2 XYZ chains, but generalized to include long-range couplings. Our work builds on previous work proving that universal simulation is possible using both entangling gates and single-qubit unitaries. We show that determining the appropriate ‘program’ of unitary pulse sequences which implements an arbitrary Hamiltonian transformation can be formulated as a linear program over functions defined by those pulse sequences, running in polynomial time and scaling efficiently in hardware resources. Our analysis extends from circuit model quantum information to adiabatic quantum evolutions, representing an important and broad-based success in applying functional analysis to the field of quantum information.
SIMULATING FISH ASSEMBLAGE DYNAMICS IN RIVER NETWORKS
My recently retired colleague, Joan Baker, and I have developed a prototype computer simulation model for studying the effects of human and non-human alterations of habitats and species availability on fish assemblage populations. The fish assemblage model, written in R, is a sp...
Dynamic Process Simulation for Analysis and Design.
ERIC Educational Resources Information Center
Nuttall, Herbert E., Jr.; Himmelblau, David M.
A computer program for the simulation of complex continuous process in real-time in an interactive mode is described. The program is user oriented, flexible, and provides both numerical and graphic output. The program has been used in classroom teaching and computer aided design. Typical input and output are illustrated for a sample problem to…
Computational Models of Protein Kinematics and Dynamics: Beyond Simulation
Gipson, Bryant; Hsu, David; Kavraki, Lydia E.; Latombe, Jean-Claude
2016-01-01
Physics-based simulation represents a powerful method for investigating the time-varying behavior of dynamic protein systems at high spatial and temporal resolution. Such simulations, however, can be prohibitively difficult or lengthy for large proteins or when probing the lower-resolution, long-timescale behaviors of proteins generally. Importantly, not all questions about a protein system require full space and time resolution to produce an informative answer. For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger, domain-level picture of protein dynamics can be revealed. The purpose of this review is to highlight the growing body of complementary work that goes beyond simulation. In particular, this review focuses on methods that address kinematics and dynamics, as well as those that address larger organizational questions and can quickly yield useful information about the long-timescale behavior of a protein. PMID:22524225
Simulations of Energetic Particles Interacting with Dynamical Magnetic Turbulence
NASA Astrophysics Data System (ADS)
Hussein, M.; Shalchi, A.
2016-02-01
We explore the transport of energetic particles in interplanetary space by using test-particle simulations. In previous work such simulations have been performed by using either magnetostatic turbulence or undamped propagating plasma waves. In the current paper we simulate for the first time particle transport in dynamical turbulence. To do so we employ two models, namely the damping model of dynamical turbulence and the random sweeping model. We compute parallel and perpendicular diffusion coefficients and compare our numerical findings with solar wind observations. We show that good agreement can be found between simulations and the Palmer consensus range for both dynamical turbulence models if the ratio of turbulent magnetic field and mean field is δB/B0 = 0.5.
Multi-petaflop/s quantum and reactive molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Nakano, Aiichiro
We have developed a divide-conquer-recombine algorithmic framework for large quantum molecular dynamics (QMD) and reactive molecular dynamics (RMD) simulations. The algorithms have achieved parallel efficiency over 0.98 on 786,432 IBM Blue Gene/Q processors for 39.8 trillion electronic degrees-of-freedom QMD in the framework of density functional theory and 67.6 billion-atom RMD. We will discuss several applications including (1) 16,616-atom QMD simulation of rapid hydrogen production from water using metallic alloy nanoparticles, (2) 6,400-atom nonadiabatic QMD simulation of exciton dynamics for efficient solar cells, and (3) 112 million-atom RMD simulation of nanocarbon synthesis by high temperature oxidation of SiC nanoparticles.
Dynamic simulation of chemical industry wastewater treatment plants.
Bury, S J; Groot, C K; Huth, C; Hardt, N
2002-01-01
High variability, stringent effluent permits, and often extreme operating conditions define the practice of wastewater treatment in the chemical industry. This paper reviews the benefits and challenges of applying dynamic simulation to chemical-industry wastewater treatment plants by describing case studies at full-scale wastewater treatment plants (WWTP). The applications range from process troubleshooting to optimization and control. The applications have been valuable and useful in developing a deeper understanding of the plants as integrated systems. However there still remains substantial work to implement the dynamic simulations for daily real-time use by plant engineers and operators. This opportunity to improve plant operations is still largely untapped and will remain so until dynamic state estimation and data reconciliation are incorporated into simulation packages for use in developing the on-line simulations. PMID:11936653
NASA Astrophysics Data System (ADS)
Johnson, Todd; Bartol, Tom; Sejnowski, Terrence; Mjolsness, Eric
2015-07-01
A stochastic reaction network model of Ca2+ dynamics in synapses (Pepke et al PLoS Comput. Biol. 6 e1000675) is expressed and simulated using rule-based reaction modeling notation in dynamical grammars and in MCell. The model tracks the response of calmodulin and CaMKII to calcium influx in synapses. Data from numerically intensive simulations is used to train a reduced model that, out of sample, correctly predicts the evolution of interaction parameters characterizing the instantaneous probability distribution over molecular states in the much larger fine-scale models. The novel model reduction method, ‘graph-constrained correlation dynamics’, requires a graph of plausible state variables and interactions as input. It parametrically optimizes a set of constant coefficients appearing in differential equations governing the time-varying interaction parameters that determine all correlations between variables in the reduced model at any time slice.
Johnson, Todd; Bartol, Tom; Sejnowski, Terrence; Mjolsness, Eric
2015-01-01
Astochastic reaction network model of Ca2+ dynamics in synapses (Pepke et al PLoS Comput. Biol. 6 e1000675) is expressed and simulated using rule-based reaction modeling notation in dynamical grammars and in MCell. The model tracks the response of calmodulin and CaMKII to calcium influx in synapses. Data from numerically intensive simulations is used to train a reduced model that, out of sample, correctly predicts the evolution of interaction parameters characterizing the instantaneous probability distribution over molecular states in the much larger fine-scale models. The novel model reduction method, ‘graph-constrained correlation dynamics’, requires a graph of plausible state variables and interactions as input. It parametrically optimizes a set of constant coefficients appearing in differential equations governing the time-varying interaction parameters that determine all correlations between variables in the reduced model at any time slice. PMID:26086598
Simulating the dynamic response of magnesium alloys
NASA Astrophysics Data System (ADS)
Lloyd, Jeffrey; Becker, Richard
Unlike several conventional metals, the mechanical response of magnesium is severely anisotropic for quasistatic and dynamic loading conditions. In this work we present a crystal-based strength model that is the same order of magnitude in computational cost as rate-dependent isotropic strength models, yet is able to capture essential features exhibited by textured magnesium polycrystals. The model demarcates plastic deformation into contributions from basal slip, extension twinning, and non-basal slip mechanisms. Comparisons are made between model predictions and experiments for two magnesium alloys with differing processing histories. The model is then used to explore and quantify the dependence of metallurgical and processing variations for several dynamic experiments that probe propensity for localization and failure under complex loading conditions.
Dynamics Modeling and Simulation of Large Transport Airplanes in Upset Conditions
NASA Technical Reports Server (NTRS)
Foster, John V.; Cunningham, Kevin; Fremaux, Charles M.; Shah, Gautam H.; Stewart, Eric C.; Rivers, Robert A.; Wilborn, James E.; Gato, William
2005-01-01
As part of NASA's Aviation Safety and Security Program, research has been in progress to develop aerodynamic modeling methods for simulations that accurately predict the flight dynamics characteristics of large transport airplanes in upset conditions. The motivation for this research stems from the recognition that simulation is a vital tool for addressing loss-of-control accidents, including applications to pilot training, accident reconstruction, and advanced control system analysis. The ultimate goal of this effort is to contribute to the reduction of the fatal accident rate due to loss-of-control. Research activities have involved accident analyses, wind tunnel testing, and piloted simulation. Results have shown that significant improvements in simulation fidelity for upset conditions, compared to current training simulations, can be achieved using state-of-the-art wind tunnel testing and aerodynamic modeling methods. This paper provides a summary of research completed to date and includes discussion on key technical results, lessons learned, and future research needs.
Quantum dynamics simulation with classical oscillators
NASA Astrophysics Data System (ADS)
Briggs, John S.; Eisfeld, Alexander
2013-12-01
In a previous paper [J. S. Briggs and A. Eisfeld, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.052111 85, 052111 (2012)] we showed that the time development of the complex amplitudes of N coupled quantum states can be mapped by the time development of positions and velocities of N coupled classical oscillators. Here we examine to what extent this mapping can be realized to simulate the “quantum,” properties of entanglement and qubit manipulation. By working through specific examples, e.g., of quantum gate operation, we seek to illuminate quantum and classical differences which hitherto have been treated more mathematically. In addition, we show that important quantum coupled phenomena, such as the Landau-Zener transition and the occurrence of Fano resonances can be simulated by classical oscillators.
Chain networking revealed by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing
Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)
Molecular dynamics simulation of propagating cracks
NASA Technical Reports Server (NTRS)
Mullins, M.
1982-01-01
Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.
Simulation in a dynamic prototyping environment: Petri nets or rules?
NASA Technical Reports Server (NTRS)
Moore, Loretta A.; Price, Shannon; Hale, Joseph P.
1994-01-01
An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.
Simulation in a dynamic prototyping environment: Petri nets or rules?
NASA Technical Reports Server (NTRS)
Moore, Loretta A.; Price, Shannon W.; Hale, Joseph P.
1994-01-01
An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are normally delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.
Simulating Dynamics Of The Gamma-Ray Observatory Satellite
NASA Technical Reports Server (NTRS)
Stark, M.
1991-01-01
GRODY developed alongside GROSS computer program (GSC-13147), a FORTRAN dynamics-simulator program performing same functions. GRODY conceived for use in case study to assess feasibility and effectiveness of Ada programming language for development of flight-dynamics software. Designed for those familiar with analysis of attitudes of spacecraft. Supports planning of maneuvers as well as analytical testing and evaluation of attitude-determination and -control system used on board Gamma-Ray Observatory (GRO) satellite. Simulates computer and control processor electronics aboard GRO satellite. Enables analyst to check and update commands sent from ground and values of parameters, obtain displays of status of simulation, interrupt simulation, analyze previous runs, and obtain printed output of simulation runs. Written mainly in Ada (99 percent) with remainder in FORTRAN.
A reduced basis method for molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Vincent-Finley, Rachel Elisabeth
In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D. Kühn, Oliver
2015-06-28
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Executive Summary: Special Section on Credible Computational Fluid Dynamics Simulations
NASA Technical Reports Server (NTRS)
Mehta, Unmeel B.
1998-01-01
This summary presents the motivation for the Special Section on the credibility of computational fluid dynamics (CFD) simulations, its objective, its background and context, its content, and its major conclusions. Verification and validation (V&V) are the processes for establishing the credibility of CFD simulations. Validation assesses whether correct things are performed and verification assesses whether they are performed correctly. Various aspects of V&V are discussed. Progress is made in verification of simulation models. Considerable effort is still needed for developing a systematic validation method that can assess the credibility of simulated reality.
GRODY - GAMMA RAY OBSERVATORY DYNAMICS SIMULATOR IN ADA
NASA Technical Reports Server (NTRS)
Stark, M.
1994-01-01
Analysts use a dynamics simulator to test the attitude control system algorithms used by a satellite. The simulator must simulate the hardware, dynamics, and environment of the particular spacecraft and provide user services which enable the analyst to conduct experiments. Researchers at Goddard's Flight Dynamics Division developed GRODY alongside GROSS (GSC-13147), a FORTRAN simulator which performs the same functions, in a case study to assess the feasibility and effectiveness of the Ada programming language for flight dynamics software development. They used popular object-oriented design techniques to link the simulator's design with its function. GRODY is designed for analysts familiar with spacecraft attitude analysis. The program supports maneuver planning as well as analytical testing and evaluation of the attitude determination and control system used on board the Gamma Ray Observatory (GRO) satellite. GRODY simulates the GRO on-board computer and Control Processor Electronics. The analyst/user sets up and controls the simulation. GRODY allows the analyst to check and update parameter values and ground commands, obtain simulation status displays, interrupt the simulation, analyze previous runs, and obtain printed output of simulation runs. The video terminal screen display allows visibility of command sequences, full-screen display and modification of parameters using input fields, and verification of all input data. Data input available for modification includes alignment and performance parameters for all attitude hardware, simulation control parameters which determine simulation scheduling and simulator output, initial conditions, and on-board computer commands. GRODY generates eight types of output: simulation results data set, analysis report, parameter report, simulation report, status display, plots, diagnostic output (which helps the user trace any problems that have occurred during a simulation), and a permanent log of all runs and errors. The
PSF halo reduction in adaptive optics using dynamic pupil masking.
Osborn, James; Myers, Richard M; Love, Gordon D
2009-09-28
We describe a method to reduce residual speckles in an adaptive optics system which add to the halo of the point spread function (PSF). The halo is particularly problematic in astronomical applications involving the detection of faint companions. Areas of the pupil are selected where the residual wavefront aberrations are large and these are masked using a spatial light modulator. The method is also suitable for smaller telescopes without adaptive optics as a relatively simple method to increase the resolution of the telescope. We describe the principle of the technique and show simulation results. PMID:19907514
Monte Carlo simulations of surface reactions: NO reduction by CO or H{sub 2}
Álvarez-Falcón, L.; Vicente, L.
2014-01-14
The development of surface science has given an opportunity to investigate the process of heterogeneous catalysis at a molecular level. In this way there has been a great progress in understanding the mechanism in NO decomposition. Modeling has been an very important tool in this goal. In this work we analyze the reactions NO+H{sub 2} and NO+CO. The extremely narrow production peak of N{sub 2} and CO{sub 2} which occurs in the reaction of NO+CO on Pt(100), a phenomenon known as “surface explosion,” is studied using a dynamic Monte Carlo method on a square lattice at low pressure under isothermal conditions. The catalytic reduction of nitric oxide by hydrogen over a Pt surface is also studied by using a dynamic Monte Carlo. Using a Langmuir-Hinshelwod mechanism of reaction, a simplified model with only four adsorbed species (NO, H, O, and N) is constructed. The effect on NO dissociation rate, the limiting step in the whole reaction, is inhibited by coadsorbed NO and H{sub 2} molecules, and is enhanced both by the presence of empty sites and adsorbed N atoms as nearest-neighbors. In these simulations experimental parameters values are included, such as: adsorption, desorption and diffusion of the reactants. The phenomenon is studied changing the temperature in the range of 300–550 K. The modeling reproduces well observed TPD and TPR experimental results and allows a visualization of the spatial development of the surface explosion.
Simulating Timescale Dynamics of Network Traffic Using Homogeneous Modeling
Yuan, Jian; Mills, Kevin L.
2006-01-01
Simulating and understanding traffic dynamics in large networks are difficult and challenging due to the complexity of such networks and the limitations inherent in simulation modeling. Typically, simulation models used to study traffic dynamics include substantial detail representing protocol mechanisms across several layers of functionality. Such models must be restricted in space and time in order to be computationally tractable. We propose an alternative simulation approach that uses homogeneous modeling with an increased level of abstraction, in order to explore networks at larger space-time scales than otherwise feasible and to develop intuition and insight about the space-time dynamics of large networks. To illustrate the utility of our approach, we examine some current understandings of the timescale dynamics of network traffic, and we discuss some speculative results obtained with homogeneous modeling. Using a wavelet-based technique, we show correlation structures, and changes in correlation structures, of network traffic under variations in traffic sources, transport mechanisms, and network structure. Our simulation results justify further investigation of our approach, which might benefit from cross-verifications against more detailed simulation models. PMID:27274931
Solar simulator for solar dynamic space power system testing
NASA Technical Reports Server (NTRS)
Jefferies, Kent S.
1993-01-01
Planned vacuum tank testing of a solar dynamic space power system requires a solar simulator. Several solar simulators were previously built and used for vacuum tank testing of various space systems. However, the apparent solar subtense angle, i.e., the angular size of the apparent sun as viewed from the experiment, of these solar simulators is too large to enable testing of solar dynamic systems. A new design was developed to satisfy the requirements of the solar dynamic testing. This design provides 1.8 kW/m(sup 2) onto a 4.5M diameter test area from a source that subtends only 1 deg, full cone angle. Key features that enable this improved performance are (1) elimination of the collimating mirror commonly used in solar simulators to transform the diverging beam into a parallel beam; (2) a redesigned lamp module that has increased efficiency; and (3) the use of a segmented reflective surface to combine beams from several individual lamp modules at the pseudosun. Each segment of this reflective surface has complex curvature to control the distribution of light. By developing a new solar simulator design for testing of the solar dynamic system instead of modifying current designs, the initial cost was cut in half, the efficiency was increased by 50 percent reducing the operating costs by one-third, and the volume occupied by the solar simulator was reduced by a factor of 10.
Multiscale Simulation of Microbe Structure and Dynamics
Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.
2012-01-01
A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin. PMID:21802438
Dynamic stall simulation including turbulence modeling
Allet, A.; Halle, S.; Paraschivoiu, I.
1995-09-01
The objective of this study is to investigate the two-dimensional unsteady flow around an airfoil undergoing a Darrieus motion in dynamic stall conditions. For this purpose, a numerical solver based on the solution of the Reynolds-averaged Navier-Stokes equations expressed in a streamfunction-vorticity formulation in a non-inertial frame of reference was developed. The governing equations are solved by the streamline upwind Petrov-Galerkin finite element method (FEM). Temporal discretization is achieved by second-order-accurate finite differences. The resulting global matrix system is linearized by the Newton method and solved by the generalized minimum residual method (GMRES) with an incomplete triangular factorization preconditioning (ILU). Turbulence effects are introduced in the solver by an eddy viscosity model. The investigation centers on an evaluation of the possibilities of several turbulence models, including the algebraic Cebeci-Smith model (CSM) and the nonequilibrium Johnson-King model (JKM). In an effort to predict dynamic stall features on rotating airfoils, first the authors present some testing results concerning the performance of both turbulence models for the flat plate case. Then, computed flow structure together with aerodynamic coefficients for a NACA 0015 airfoil in Darrieus motion under stall conditions are presented.
Gas dynamic simulations of galaxy formation
NASA Technical Reports Server (NTRS)
Evrard, August E.
1993-01-01
Results are presented from a simulation modeling the formation of a group of galaxies in a 'standard' cold, dark matter universe with delta = 1, h sub 0 = 50 km/(s(Mpc)), baryon fraction omega sub b = 0.1 and spectrum normalization sigma sub 8 = 0.6 (bias parameter b = 1.7). Initial conditions are generated within a periodic box with comoving length 16 Mpc in a manner constrained to produce a small cluster of total mass approximately 10 exp 14 solar mass. Two sets of 643 particles are used to model the dark matter and baryon fluids. Each gas particle represents 1.08 x 10 exp -8 solar mass, implying an L* galaxy is resolved by approximately 1000 particles. The system is evolved self-consistently in three dimensions using the combined N-body/hydrodynamic scheme P3MSPH up to a final redshift z = 1. Evolving to the present is prohibited by the fact that the mean density in the simulated volume is above critical and the entire volume would be going nonlinear beyond this point, We are currently analyzing another run with somewhat poorer mass resolution which was evolved to the present.
Distortion and flow of nematics simulated by dissipative particle dynamics.
Zhao, Tongyang; Wang, Xiaogong
2014-05-14
In this study, we simulated distortion and flow of nematics by dissipative particle dynamics (DPD). The nematics were modeled by a binary mixture that contained rigid rods composed of DPD particles as mesogenic units and normal DPD particles as solvent. Elastic distortions were investigated by monitoring director orientation in space under influences of boundary anchoring and external fields. Static distortion demonstrated by the simulation is consistent with the prediction of Frank elastic theory. Spatial distortion profile of the director was examined to obtain static elastic constants. Rotational motions of the director under influence of the external field were simulated to understand the dynamic process. The rules revealed by the simulation are in a good agreement with those obtained from dynamical experiments and classical theories for nematics. Three Miesowicz viscosities were obtained by using external fields to hold the orientation of the rods in shear flows. The simulation showed that the Miesowicz viscosities have the order of ηc > ηa > ηb and the rotational viscosity γ1 is about two orders larger than the Miesowicz viscosity ηb. The DPD simulation correctly reproduced the non-monotonic concentration dependence of viscosity, which is a unique property of lyotropic nematic fluids. By comparing simulation results with classical theories for nematics and experiments, the DPD nematic fluids are proved to be a valid model to investigate the distortion and flow of lyotropic nematics. PMID:24832301
Distortion and flow of nematics simulated by dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Zhao, Tongyang; Wang, Xiaogong
2014-05-01
In this study, we simulated distortion and flow of nematics by dissipative particle dynamics (DPD). The nematics were modeled by a binary mixture that contained rigid rods composed of DPD particles as mesogenic units and normal DPD particles as solvent. Elastic distortions were investigated by monitoring director orientation in space under influences of boundary anchoring and external fields. Static distortion demonstrated by the simulation is consistent with the prediction of Frank elastic theory. Spatial distortion profile of the director was examined to obtain static elastic constants. Rotational motions of the director under influence of the external field were simulated to understand the dynamic process. The rules revealed by the simulation are in a good agreement with those obtained from dynamical experiments and classical theories for nematics. Three Miesowicz viscosities were obtained by using external fields to hold the orientation of the rods in shear flows. The simulation showed that the Miesowicz viscosities have the order of ηc > ηa > ηb and the rotational viscosity γ1 is about two orders larger than the Miesowicz viscosity ηb. The DPD simulation correctly reproduced the non-monotonic concentration dependence of viscosity, which is a unique property of lyotropic nematic fluids. By comparing simulation results with classical theories for nematics and experiments, the DPD nematic fluids are proved to be a valid model to investigate the distortion and flow of lyotropic nematics.
Development of semiclassical molecular dynamics simulation method.
Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi
2016-04-28
Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383
Simulation of plume dynamics using particle graphics
NASA Astrophysics Data System (ADS)
Tourtellott, John; Coker, Charles F.; Crow, Dennis R.
2000-07-01
To enhance the fidelity of numerical flow field (plume) imagery in hardware-in-the-loop (HIL) systems, new methods using particle system graphics have been developed. To render infrared (IR) images that are consistent with the underlying physical phenomenology, techniques for particle placement, pixel rasterization and drawing were developed and implemented in computer software. The software was integrated into an existing HIL scene generator and used to demonstrate several new capabilities. Moving particle systems were used to depict the internal flow and turbulence common to plumes. Persistent particle systems were used to depict the trail of hot gas and particulates left behind typical plumes. The addition of plume dynamic behaviors such as these can potentially improve HIL systems and, as a result, improve the testing of seekers and other weapon systems.
Dynamic Discharge Arc Driver. [computerized simulation
NASA Technical Reports Server (NTRS)
Dannenberg, R. E.; Slapnicar, P. I.
1975-01-01
A computer program using nonlinear RLC circuit analysis was developed to accurately model the electrical discharge performance of the Ames 1-MJ energy storage and arc-driver system. Solutions of circuit parameters are compared with experimental circuit data and related to shock speed measurements. Computer analysis led to the concept of a Dynamic Discharge Arc Driver (DDAD) capable of increasing the range of operation of shock-driven facilities. Utilization of mass addition of the driver gas offers a unique means of improving driver performance. Mass addition acts to increase the arc resistance, which results in better electrical circuit damping with more efficient Joule heating, producing stronger shock waves. Preliminary tests resulted in an increase in shock Mach number from 34 to 39 in air at an initial pressure of 2.5 torr.
Expansion techniques for collisionless stellar dynamical simulations
NASA Astrophysics Data System (ADS)
Meiron, Yohai
2016-02-01
We present ETICS, a collisionless N-body code based on two kinds of series expansions of the Poisson equation, implemented for graphics processing units (GPUs). The code is publicly available and can be used as a standalone program or as a library (an AMUSE plugin is included). One of the two expansion methods available is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other 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.
Modeling and simulation of consumer response to dynamic pricing.
Valenzuela, J.; Thimmapuram, P.; Kim, J
2012-08-01
Assessing the impacts of dynamic-pricing under the smart grid concept is becoming extremely important for deciding its full deployment. In this paper, we develop a model that represents the response of consumers to dynamic pricing. In the model, consumers use forecasted day-ahead prices to shift daily energy consumption from hours when the price is expected to be high to hours when the price is expected to be low while maintaining the total energy consumption as unchanged. We integrate the consumer response model into the Electricity Market Complex Adaptive System (EMCAS). EMCAS is an agent-based model that simulates restructured electricity markets. We explore the impacts of dynamic-pricing on price spikes, peak demand, consumer energy bills, power supplier profits, and congestion costs. A simulation of an 11-node test network that includes eight generation companies and five aggregated consumers is performed for a period of 1 month. In addition, we simulate the Korean power system.
Simulation of ceramics fracture due to high rate dynamic impact
NASA Astrophysics Data System (ADS)
Kazarinov, N. A.; Bratov, V. A.; Petrov, Y. V.
2015-11-01
In this paper dynamic fracture process due to high-speed impact of steel plunger into ceramic sample is simulated. The developed numerical model is based on finite element method and a concept of incubation time criterion, which is proven applicable in order to predict brittle fracture under high-rate deformation. Simulations were performed for ZrO2(Y2O3) ceramic plates. To characterize fracture process quantitatively fracture surface area parameter is introduced and controlled. This parameter gives the area of new surface created during dynamic fracture of a sample and is essentially connected to energetic peculiarities of fracture process. Multiple simulations with various parameters made it possible to explore dependencies of fracture area on plunger velocity and material properties. Energy required to create unit of fracture area at fracture initiation (dynamic analogue of Griffith surface energy) was evaluated and was found to be an order of magnitude higher as comparing to its static value.
Molecular dynamics simulation of interfacial adhesion
Yarovsky, I.; Chaffee, A.L.
1996-12-31
Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.
Analytical Dynamics and Nonrigid Spacecraft Simulation
NASA Technical Reports Server (NTRS)
Likins, P. W.
1974-01-01
Application to the simulation of idealized spacecraft are considered both for multiple-rigid-body models and for models consisting of combination of rigid bodies and elastic bodies, with the elastic bodies being defined either as continua, as finite-element systems, or as a collection of given modal data. Several specific examples are developed in detail by alternative methods of analytical mechanics, and results are compared to a Newton-Euler formulation. The following methods are developed from d'Alembert's principle in vector form: (1) Lagrange's form of d'Alembert's principle for independent generalized coordinates; (2) Lagrange's form of d'Alembert's principle for simply constrained systems; (3) Kane's quasi-coordinate formulation of D'Alembert's principle; (4) Lagrange's equations for independent generalized coordinates; (5) Lagrange's equations for simply constrained systems; (6) Lagrangian quasi-coordinate equations (or the Boltzmann-Hamel equations); (7) Hamilton's equations for simply constrained systems; and (8) Hamilton's equations for independent generalized coordinates.
Molecular dynamics simulations of heme reorientational motions in myoglobin.
Henry, E R
1993-01-01
Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes
Use of MODIS Data in Dynamic SPARROW Analysis of Watershed Loading Reductions
NASA Astrophysics Data System (ADS)
Smith, R. A.; Schwarz, G. E.; Brakebill, J. W.; Hoos, A.; Moore, R. B.; Nolin, A. W.; Shih, J. S.; Journey, C. A.; Macauley, M.
2014-12-01
Predicting the temporal response of stream water quality to a proposed reduction in contaminant loading is a major watershed management problem due to temporary storage of contaminants in groundwater, vegetation, snowpack, etc. We describe the response of dynamically calibrated SPARROW models of total nitrogen (TN) flux to hypothetical reductions in reactive nitrogen inputs in three sub-regional watersheds: Potomac River Basin (Chesapeake Bay drainage), Long Island Sound drainage, and South Carolina coastal drainage. The models are based on seasonal water quality and watershed input data from 170 monitoring stations for the period 2002 to 2008.The spatial reference frames of the three models are stream networks containing an average 38,000 catchments and the time step is seasonal. We use MODIS Enhanced Vegetation Index (EVI) and snow/ice cover data to parameterize seasonal uptake and release of nitrogen from vegetation and snowpack. The model accounts for storage of total nitrogen inputs from fertilized cropland, pasture, urban land, and atmospheric deposition. Model calibration is by non-linear regression. Model source terms based on previous season export allow for recursive simulation of stream flux and can be used to estimate the approximate residence times of TN in the watersheds. Catchment residence times in the Long Island Sound Basin are shorter (typically < 1 year) than in the Potomac or South Carolina Basins (typically > 1 year), in part, because a significant fraction of nitrogen flux derives from snowmelt and occurs within one season of snowfall. We use the calibrated models to examine the response of TN flux to hypothetical step reductions in source inputs at the beginning of the 2002-2008 period and the influence of observed fluctuations in precipitation, temperature, vegetation growth and snow melt over the period. Following non-point source reductions of up to 100%, stream flux was found to continue to vary greatly for several years as a function of
Robotic Simulation of Flexible-Body Spacecraft Dynamics
NASA Technical Reports Server (NTRS)
Brannan, Justin C.; Carignan, Craig R.
2016-01-01
A robotic testbed has been developed to conduct hardware-in-the-loop simulations of a robotic servicer interacting with a client satellite on-orbit. By creating an analytical model of a satellite with flexible appendages, it is possible to simulate the system response to external force and torque inputs and compare the predicted system motion to a robot mass simulator outfitted with physical appendages. This validation effort includes multiple test cases that encompass the types of interaction forces a satellite might experience during a nominal on-orbit servicing mission and aims to show the simulation's ability to capture the physical system response. After incorporating the flexible-body dynamics into the robotic mass simulator at NASA Goddard Space Flight Center (GSFC), a hardware-in-the-loop simulation can be used to characterize the potential impact of structural flexibility on an end-to-end satellite servicing mission.
Combined molecular dynamics-spin dynamics simulations of bcc iron
Perera, Meewanage Dilina N; Yin, Junqi; Landau, David P; Nicholson, Don M; Stocks, George Malcolm; Eisenbach, Markus; Brown, Greg
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Dynamic Multiscale Quantum Mechanics/Electromagnetics Simulation Method.
Meng, Lingyi; Yam, ChiYung; Koo, SiuKong; Chen, Quan; Wong, Ngai; Chen, GuanHua
2012-04-10
A newly developed hybrid quantum mechanics and electromagnetics (QM/EM) method [Yam et al. Phys. Chem. Chem. Phys.2011, 13, 14365] is generalized to simulate the real time dynamics. Instead of the electric and magnetic fields, the scalar and vector potentials are used to integrate Maxwell's equations in the time domain. The TDDFT-NEGF-EOM method [Zheng et al. Phys. Rev. B2007, 75, 195127] is employed to simulate the electronic dynamics in the quantum mechanical region. By allowing the penetration of a classical electromagnetic wave into the quantum mechanical region, the electromagnetic wave for the entire simulating region can be determined consistently by solving Maxwell's equations. The transient potential distributions and current density at the interface between quantum mechanical and classical regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. Charge distribution, current density, and potentials at different temporal steps and spatial scales are integrated seamlessly within a unified computational framework. PMID:26596737
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
Vashishta, Priya; Kalia, Rajiv
2005-02-24
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report.
Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems
Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus
2014-01-01
Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171
Study of simulating dynamic polarization laser echo signal
NASA Astrophysics Data System (ADS)
Yang, Di; Liu, Qing; Zhan, Yong-hong; Zeng, Chang-e.
2014-12-01
In the test for the laser seeker in the hardware-in-loop simulation, acquiring the effect of polarization laser echo wave to optical stress polarization of the seeker and to the polarization guidance performance was not considered. A new method to generating the dynamic polarization laser echo signal was provided based on the scene model; furthermore, the method to adding the polarization characters to the energy scene was introduced. At last, the insufficient of the method to generating and simulating the dynamic polarization signal was analyzed.
Simulation: A tool for steam plant dynamic analysis
NASA Astrophysics Data System (ADS)
Anneveld, H.
Stringent requirements of combined cycles makes design and operation of process plants increasingly complex. The behavior of the complete controlled process is studied by way of simulation. By utilizing this method, process conditions can be optimized with reduced risk. This will lead to greater financial benefits. There is a large range of simulation programs which make it possible to study realistically the dynamic behavior of a wide range of complex process conditions and problematic interactions. The steam generation and distribution, the pressure limitation controls, and the dynamic behavior of a steam plant are discussed.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
NASA Technical Reports Server (NTRS)
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
LINAC BEAM DYNAMICS SIMULATIONS WITH PY-ORBIT
Shishlo, Andrei P
2012-01-01
Linac dynamics simulation capabilities of the PyORBIT code are discussed. PyORBIT is an open source code and a further development of the original ORBIT code that was created and used for design, studies, and commissioning of the SNS ring. The PyORBIT code, like the original one, has a two-layer structure. C++ is used to perform time-consuming computations, and the program flow is controlled from a Python language shell. The flexible structure makes it possible to use PyORBIT also for linac dynamics simulations. A benchmark of PyORBIT with Parmila and the XAL Online model is presented.
Turbulent Simulation of the Dynamics of the Magnetotail
NASA Technical Reports Server (NTRS)
Wu, Cheng-Chin
2003-01-01
In situ observations indicate that the dynamical processes in the geoplasma environment generally entail localized intermittent processes and anomalous global transports. It was suggested by T. Chang that instead of considering the turbulence as a mixture of interacting waves, such type of patchy intermittency could be more easily understood in terms of the development, interaction, merging, preferential acceleration and evolution of coherent magnetic structures. In this three-year project, we have used direct numerical MHD simulations to study some aspects of the MHD dynamics in Chang's model. Our large-scale numerical calculations and simulations have been supplemented by and coordinated with theoretical studies conducted by Chang and his colleagues.
Numerical simulation of dynamic fracture and failure in solids
Chen, E.P.
1994-05-01
Numerical simulation of dynamic fracture and failure processes in solid continua using Lagrangian finite element techniques is the subject of discussion in this investigation. The specific configurations in this study include penetration of steel projectiles into aluminum blocks and concrete slabs. The failure mode in the aluminum block is excessive deformation while the concrete slab fails by hole growth, spallation, and scabbing. The transient dynamic finite element code LS-DYNA2D was used for the numerical analysis. The erosion capability in LS-DYNA2D was exercised to carry out the fracture and failure simulations. Calculated results were compared to the experimental data. Good correlations were obtained.
Exploiting Sparse Dynamics For Bandwidth Reduction In Cooperative Sensing Systems
NASA Astrophysics Data System (ADS)
Ganapathy, Harish; Caramanis, Constantine; Ying, Lei
2013-07-01
Recently, there has been a significant interest in developing cooperative sensing systems for certain types of wireless applications. In such systems, a group of sensing nodes periodically collect measurements about the signals being observed in the given geographical region and transmit these measurements to a central node, which in turn processes this information to recover the signals. For example, in cognitive radio networks, the signals of interest are those generated by the primary transmitters and the sensing nodes are the secondary users. In such networks, it is critically important to be able to reliably determine the presence or absence of primary transmitters in order to avoid causing interference. The standard approach to transmit these measurements from sensor the nodes to the fusion center has been to use orthogonal channels. Such an approach quickly places a burden on the control-channel-capacity of the network that would scale linearly in the number of cooperating sensing nodes. In this paper, we show that as long as one condition is satisfied: the dynamics of the observed signals are sparse, i.e., the observed signals do not change their values very rapidly in relation to the time-scale at which the measurements are collected, we can significantly reduce the control bandwidth of the system while achieving the full (linear) bandwidth performance.
Nonlinear model order reduction of jointed structures for dynamic analysis
NASA Astrophysics Data System (ADS)
Festjens, H.; Chevallier, G.; Dion, J. L.
2014-03-01
Assembled structures generally show weak nonlinearity, thus it is rather commonplace to assume that their modes are both linear and uncoupled. At small to modest amplitude, the linearity assumption remains correct in terms of stiffness but, on the contrary, the dissipation in joints is strongly amplitude-dependent. Besides, the modes of any large structure may be LOCALLY collinear in the localized region of a joint. As a result the projection of the structure on normal modes is not appropriate since the corresponding generalized coordinates may be strongly coupled. Instead of using this global basis, the present paper deals with the use of a local basis to reduce the size of the problem without losing the nonlinear physics. Under an appropriate set of assumptions, the method keeps the dynamic properties of joints, even for large amplitude, which include coupling effects, nonlinear damping and softening effects. The formulation enables us to take into account FE models of any realistic geometry. It also gives a straightforward process for experimental identification. The formulation is detailed and investigated on a jointed structure.
Simulating aggregate dynamics in ocean biogeochemical models
NASA Astrophysics Data System (ADS)
Jackson, George A.; Burd, Adrian B.
2015-04-01
The dynamics of elements in the water column is complex, depending on multiple biological and physical processes operating at very different physical scales. Coagulation of particulate material is important for transforming particles and moving them in the water column. Mechanistic models of coagulation processes provide a means to predict these processes, help interpret observations, and provide insight into the processes occurring. However, most model applications have focused on describing simple marine systems and mechanisms. We argue that further model development, in close collaboration with field and experimental scientists, is required in order to extend the models to describe the large-scale elemental distributions and interactions being studied as part of GEOTRACES. Models that provide a fundamental description of trace element-particle interactions are required as are experimental tests of the mechanisms involved and the predictions arising from models. However, a comparison between simple and complicated models of aggregation and trace metal provides a means for understanding the implications of simplifying assumptions and providing guidance as to which simplifications are needed.
Improving the performance of molecular dynamics simulations on parallel clusters.
Borstnik, Urban; Hodoscek, Milan; Janezic, Dusanka
2004-01-01
In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds. PMID:15032512
Dynamic simulation of coronal mass ejections
NASA Technical Reports Server (NTRS)
Steinolfson, R. S.; Wu, S. T.
1980-01-01
A model is developed for the formation and propagation through the lower corona of the loop-like coronal transients in which mass is ejected from near the solar surface to the outer corona. It is assumed that the initial state for the transient is a coronal streamer. The initial state for the streamer is a polytropic, hydrodynamic solution to the steady-state radial equation of motion coupled with a force-free dipole magnetic field. The numerical solution of the complete time-dependent equations then gradually approaches a stationary coronal streamer configuration. The streamer configuration becomes the initial state for the coronal transient. The streamer and transient simulations are performed completely independent of each other. The transient is created by a sudden increase in the pressure at the base of the closed-field region in the streamer configuration. Both coronal streamers and coronal transients are calculated for values of the plasma beta (the ratio of thermal to magnetic pressure) varying from 0.1 to 100.
Error and efficiency of replica exchange molecular dynamics simulations
Rosta, Edina; Hummer, Gerhard
2009-01-01
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977
Error and efficiency of replica exchange molecular dynamics simulations.
Rosta, Edina; Hummer, Gerhard
2009-10-28
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977
Simulating spin dynamics in organic solids under heteronuclear decoupling.
Frantsuzov, Ilya; Ernst, Matthias; Brown, Steven P; Hodgkinson, Paul
2015-09-01
Although considerable progress has been made in simulating the dynamics of multiple coupled nuclear spins, predicting the evolution of nuclear magnetisation in the presence of radio-frequency decoupling remains challenging. We use exact numerical simulations of the spin dynamics under simultaneous magic-angle spinning and RF decoupling to determine the extent to which numerical simulations can be used to predict the experimental performance of heteronuclear decoupling for the CW, TPPM and XiX sequences, using the methylene group of glycine as a model system. The signal decay times are shown to be strongly dependent on the largest spin order simulated. Unexpectedly large differences are observed between the dynamics with and without spin echoes. Qualitative trends are well reproduced by modestly sized spin system simulations, and the effects of finite spin-system size can, in favourable cases, be mitigated by extrapolation. Quantitative prediction of the behaviour in complex parameter spaces is found, however, to be very challenging, suggesting that there are significant limits to the role of numerical simulations in RF decoupling problems, even when specialist techniques, such as state-space restriction, are used. PMID:26073419
Molecular dynamics simulations: Parameter evaluation, application and development
NASA Astrophysics Data System (ADS)
Zhou, Jin
Molecular dynamics (MD) simulation is a theoretical technique for investigating the physical properties of a wide variety of molecules. This dissertation contains my studies on three important parts of the MD simulation: evaluation of parameters in empirical energy functions widely used in MD simulations, application of MD simulation on experimentally interested biological molecules and development of new methods for constraint dynamics simulations. All the work in this thesis made use of CHARMM as an MD simulation tool. The MD simulation uses empirical energy functions parameterized by a set of parameters. These parameters play an important role in the quality of the simulations. I evaluated nine parameter sets from Harvard University and Molecular Simulations, Inc. for protein simulations by the MD simulations of hydrated form of carboxy- myoglobin and interleukin-1/beta, which are rich in two typical protein structure motifs, helix and β sheet structures respectively. It is found that some sets are good at representing helical structure proteins while others are good at β sheet proteins. But all of them need improvement on representing motions at low temperature. Experimental evidence indicates that the 1A coiled-coil domains of the Intermediate Filament (IF) proteins consisting of coiled human keratins 1 and 10 (K1 and K10) are 'hot spots' for substitutional mutations. Some of these mutations are correlated to the human skin diseases-epidermolytic hyperkeratiosis (EH) and epidermolysis bullosa simplex (EBS). The MD simulation technique is used here for the first time to model and simulate these proteins to elucidate the molecular-level effects of these mutations. Lacking the experimental crystal structures, the initial structure of 1A domain of the wild type Intermediate Filament protein and its mutants were modeled from scratch to reproduce the well- known properties of the proteins of this kind followed by identical MD simulations. The important result is
Repetition-Related Reductions in Neural Activity during Emotional Simulations of Future Events
2015-01-01
Simulations of future experiences are often emotionally arousing, and the tendency to repeatedly simulate negative future outcomes has been identified as a predictor of the onset of symptoms of anxiety. Nonetheless, next to nothing is known about how the healthy human brain processes repeated simulations of emotional future events. In this study, we present a paradigm that can be used to study repeated simulations of the emotional future in a manner that overcomes phenomenological confounds between positive and negative events. The results show that pulvinar nucleus and orbitofrontal cortex respectively demonstrate selective reductions in neural activity in response to frequently as compared to infrequently repeated simulations of negative and positive future events. Implications for research on repeated simulations of the emotional future in both non-clinical and clinical populations are discussed. PMID:26390294
Papaleo, Elena
2015-01-01
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210
Efficient dynamic simulation for multiple chain robotic mechanisms
NASA Technical Reports Server (NTRS)
Lilly, Kathryn W.; Orin, David E.
1989-01-01
An efficient O(mN) algorithm for dynamic simulation of simple closed-chain robotic mechanisms is presented, where m is the number of chains, and N is the number of degrees of freedom for each chain. It is based on computation of the operational space inertia matrix (6 x 6) for each chain as seen by the body, load, or object. Also, computation of the chain dynamics, when opened at one end, is required, and the most efficient algorithm is used for this purpose. Parallel implementation of the dynamics for each chain results in an O(N) + O(log sub 2 m+1) algorithm.
Leaf transmission reduction using moving jaws for dynamic MLC IMRT
Schmidhalter, D.; Fix, M. K.; Niederer, P.; Mini, R.; Manser, P.
2007-09-15
The aim of this work is to investigate to what extent it is possible to use the secondary collimator jaws to reduce the transmitted radiation through the multileaf collimator (MLC) during an intensity modulated radiation therapy (IMRT). A method is developed and introduced where the jaws follow the open window of the MLC dynamically (dJAW method). With the aid of three academic cases (Closed MLC, Sliding-gap, and Chair) and two clinical cases (prostate and head and neck) the feasibility of the dJAW method and the influence of this method on the applied dose distributions are investigated. For this purpose the treatment planning system Eclipse and the Research-Toolbox were used as well as measurements within a solid water phantom were performed. The transmitted radiation through the closed MLC leads to an inhomogeneous dose distribution. In this case, the measured dose within a plane perpendicular to the central axis differs up to 40% (referring to the maximum dose within this plane) for 6 and 15 MV. The calculated dose with Eclipse is clearly more homogeneous. For the Sliding-gap case this difference is still up to 9%. Among other things, these differences depend on the depth of the measurement within the solid water phantom and on the application method. In the Chair case, the dose in regions where no dose is desired is locally reduced by up to 50% using the dJAW method instead of the conventional method. The dose inside the chair-shaped region decreased up to 4% if the same number of monitor units (MU) as for the conventional method was applied. The undesired dose in the volume body minus the planning target volume in the clinical cases prostate and head and neck decreased up to 1.8% and 1.5%, while the number of the applied MU increased up to 3.1% and 2.8%, respectively. The new dJAW method has the potential to enhance the optimization of the conventional IMRT to a further step.
Dynamic risk simulation to assess risk along roads
NASA Astrophysics Data System (ADS)
Voumard, Jérémie; Caspar, Olivier; Derron, Marc-Henri; Jaboyedoff, Michel
2013-04-01
Risk generated through natural hazards on roads is usually calculated with an equation which integrates various parameters of hazard and traffic. These are static variables as hazard frequency and number of vehicles crossing the dangerous section. This traditional methodology cannot take into account the dynamic variations of traffic and interactions between vehicles such as speeds modifications due to the section sinuosity, slowdowns resulting saturated traffic or creation of vehicles columns in front of traffic lights. The influence of traffic dynamics on the risk estimation is not addressed with the standard methodologies. Here we show, with the help of a dynamic traffic simulator specially developed for this project, that the variations of traffic greatly influence the risk results. Several sections of an alpine road in Switzerland were analyzed with the method of dynamic risk and compared with the results of the conventional method of risk calculation. It was possible to demonstrate that risk significantly increases on sinuous sections with the decreasing of vehicles speed. It has been highlighted that well positioned traffic lights, outside the risk area, can prevent a risk increase during a construction site, while a column of vehicles located within the danger zone greatly increases the risk. These results demonstrate the importance to consider the traffic in a dynamic way to assess risk to the closest field reality. Thus, recommendations to reduce risk on the roads can be given using a dynamic traffic simulator, modeling interactions between vehicles. Eventually, dynamic risk assessment can also be integrated into existing methodologies that consider only static parameters.
Validating clustering of molecular dynamics simulations using polymer models
2011-01-01
Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the
Selection of Solar Simulator for Solar Dynamic Ground Test
NASA Technical Reports Server (NTRS)
Tolbert, Carol M.
1994-01-01
The 2 kWe Solar Dynamic (SD) Ground Test Demonstration (GTD) experiment will be conducted in 1995 at NASA Lewis Research Center (LeRC). This solar dynamic power system test will be conducted in a simulated space environment and will require an artificial sun. To address the solar simulator requirements for the GTD, Arnold Engineering Development Center (AEDC) was hired under contract to review and visit four existing solar simulator facilities. The four facilities included, AEDC's Mark 1 Chamber, NASA-JSC Chamber A, AEDC's 12V Chamber, and NASA-JPL Space Simulator Chamber. Two design concepts were considered following several months of evaluating existing solar simulator facilities throughout the United States. To satisfy system requirements for the SD GTD experiment the solar simulator needs to provide a uniform light flux to the SD concentrator, provide the light within a subtense angle of one degree, and provide an intensity of one solar constant (1.37 kW/sq m) at airmass zero. Most solar simulators are designed for supplying heat loads to spacecraft where a cone angle as large as 3 degrees is acceptable. It was also concluded that a solar simulator, such like these considered in the AEDC study, would require major facility modifications for NASA LeRC and result in significant impacts to the program. The advanced solar simulator concept developed by NASA LeRC will meet the system requirements for the SD GTD experiment Since SD GTD solar simulator requirements could not be addressed by existing simulator, an advanced concept was considered.
The Simulation of an Oxidation-Reduction Titration Curve with Computer Algebra
ERIC Educational Resources Information Center
Whiteley, Richard V., Jr.
2015-01-01
Although the simulation of an oxidation/reduction titration curve is an important exercise in an undergraduate course in quantitative analysis, that exercise is frequently simplified to accommodate computational limitations. With the use of readily available computer algebra systems, however, such curves for complicated systems can be generated…
Assessment of methods for methyl iodide emission reduction and pest control using a simulation model
Technology Transfer Automated Retrieval System (TEKTRAN)
Various methods have been developed to reduce atmospheric emissions from the agricultural use of highly volatile pesticides and mitigate their adverse environmental effects. The effectiveness of various methods on emissions reduction and pest control was assessed using simulation model in this study...
Simulation of Pedestrian Dynamic Using a Vector Floor Field Model
NASA Astrophysics Data System (ADS)
Yang, Jun; Hou, Zhongsheng; Zhan, Minghui
2013-04-01
Simulation of complex scenarios and multi-direction pedestrian flow is a main challenge to microscopic model of pedestrian movement. It is an issue to simulate real pedestrian traffic with great fidelity while keeping its computational cost at an acceptable level. This paper reports on an improved floor field model called vector floor field model to simulate pedestrian flows in some basic scenarios. In this model, vectorization of static floor field and dynamic floor field are used to indicate preference directions and the pedestrian flow tendency, respectively. Pedestrian transition depends on both their preference directions and tendency. The simulations in some basic scenarios are conducted, quantitative comparison to the record of practical experiments and standard floor field model is given as well, and the results indicate the effectivity of this model. An adjusted static vector floor field is also proposed to simulate pedestrian flow in turning scenario. The vector floor field model is also sufficient to simulate some essential features in pedestrian dynamic, such as lane formation. This model can be widely used in the simulation of multi-direction pedestrian at turning, crossing and other junctions.
Reduction in overvoltages and dynamic power losses in power switches of multilevel voltage inverters
NASA Astrophysics Data System (ADS)
Voronin, P. A.; Voronin, I. P.; Panfilov, D. I.; Rozhkov, D. V.
2014-12-01
A number of the circuit and design decisions that provide a reduction in overvoltage and dynamic power losses in power switches of multilevel voltage inverters with clamping diodes is considered. It is shown that the integral or unpackaged version is the most effective method for a reduction in the stray inductance in the multilevel circuit, which is the general cause for occurrence of dynamic overvoltage. To reduce dynamic losses of power, a method for resonant commutation on fronts, which provides commutation of switches in the multilevel circuit at zero voltage (SZV) and zero current (SZC), is proposed. The resonant switching method as applied to the multilevel circuit simultaneously solves a problem of dynamic overvoltage by means of limitation for the rate of voltage rise in the SZV mode or the mode of preliminary fault of energy stored in the inductance of the switching circuit in the SZC mode.
Hg2+ reduction and re-emission from simulated wet flue gas desulfurization liquors.
Wo, Jingjing; Zhang, Meng; Cheng, Xiaoya; Zhong, Xiaohang; Xu, Jiang; Xu, Xinhua
2009-12-30
In this study, considering that Hg(2+) in wet flue gas desulfurization (FGD) systems can easily be reduced and then released into atmosphere, causing secondary pollution, the researches about Hg(2+) reduction and Hg(0) re-emission mechanism were carried out. The effects of several experimental parameters on the reduction were studied, including initial pH, temperature, and concentrations of Cl(-) and S(IV). Our experimental results indicated that Cl(-) had a restraining effect on the Hg(2+) reduction and Hg(0) re-emission, after 24h reaction, only 20.5% of Hg(2+) was reduced with 100mM Cl(-) in simulated desulfurization solution. Cl(-) can slow Hg(2+) reduction and Hg(0) re-emissions dramatically through changing reaction mechanism, with formation of new intermediate: ClHgSO(3)(-), which can decompose to Hg(0), but much more slowly than Hg(SO(3))(2)(2-) or HgSO(3). Simulating the conditions of the practical application (initial pH 5, T=50 degrees C, S(IV)=5 mM, Cl(-)=100 mM), we also found that Ca(2+), NO(3)(-), F(-), etc. all had obvious effects on reduction rates. Based on the material balance and characteristic of the reactants, the reduction emission mechanism of Hg(2+) has been established, providing theoretical basis for industrial application of mercury control in wet FGD systems. PMID:19699584
Simulations of laminar flow past a superhydrophobic sphere with drag reduction and separation delay
NASA Astrophysics Data System (ADS)
Gruncell, Brian R. K.; Sandham, Neil D.; McHale, Glen
2013-04-01
Superhydrophobic surfaces have potential for reducing hydrodynamic drag by combining a structured surface and hydrophobicity to retain a lubricating air layer (plastron) at the surface. In the present contribution, numerical simulations of laminar flow past a superhydrophobic sphere are conducted using a two-phase flow representation. The results show drag reductions in Stokes flow of up to 19% for an air-water system, in agreement with previous analytic work, and demonstrate an increased effect as the Reynolds number is increased to 100. Drag reductions of up to 50% are achieved due to reduction in viscous drag and suppression of separation by the plastron, resulting in a narrower wake. To explore a less idealised model of the plastron, baffles have also been introduced to simulate the support of a plastron by roughness elements. The baffles lead to the attached vortex regime no longer being suppressed, but separation is delayed and drag reductions are evident in comparison to a solid sphere. Increasing the area solid fraction results in a diminished drag reduction due to the plastron, however drag reductions of up to 15% can still be achieved with solid fractions of 10%.
Dynamic materials response at multiscales: Experiments and simulations
NASA Astrophysics Data System (ADS)
Luo, Sheng-Nian
One of the grand challenges in materials physics is dynamic responses to impulsive loading, including shock waves, radiation, and pulsed fields, due to their highly transient nature and extremely complex microstructure effects. Dynamic responses, such as plasticity, damage, cavitation, phase changes, and chemical reactions, are inherently multiscale and heavily dependent on microstructure. One has to resort to a suite of tools, including experiments, modeling and simulations, and theory. However, the gaps in spatial or temporal scales between experiments and simulations are still wide, while cross-scale theories are still in early development. To this end, we exploit large-scale molecular dynamics simulations, electron microscopy, and ultrafast synchrotron X-ray imaging and scattering, to probe materials response at length scales ranging from lattice to micron, and time scales, from picosecond to second. For examples, simultaneous, high-speed, X-ray imaging (mesoscale strain-field mapping) and diffraction measurements along with macroscopic measurements have been achieved. Based on classical nucleation theory and large-scale molecular dynamics simulations, we demonstrate the equivalence between length and time scales for nucleation events, which provides a framework to bridge different scales. Certainly, advancing multiscale science requires sustained, concerted, experimental, modeling and theoretical efforts. We have benefited from the colleagues at the Advanced Photon Source, and the Peac Institute of Multiscales Sciences.
Simulating field-scale soil organic carbon dynamics using EPIC
Technology Transfer Automated Retrieval System (TEKTRAN)
Simulation models integrate our understanding of soil organic C (SOC) dynamics and are useful tools for evaluating impacts of crop management on soil C sequestration, yet, they require local calibration. Our objectives were to calibrate the Environmental Policy Integrated Climate (EPIC) model, and e...
The 3-axis Dynamic Motion Simulator (DMS) system
NASA Technical Reports Server (NTRS)
1975-01-01
A three-axis dynamic motion simulator (DMS) consisting of a test table with three degrees of freedom and an electronics control system was designed, constructed, delivered, and tested. Documentation, as required in the Data Requirements List (DRL), was also provided.
Diffusion of Particle in Hyaluronan Solution, a Brownian Dynamics Simulation
NASA Astrophysics Data System (ADS)
Takasu, Masako; Tomita, Jungo
2004-04-01
Diffusion of a particle in hyaluronan solution is investigated using Brownian dynamics simulation. The slowing down of diffusion is observed, in accordance with the experimental results. The temperature dependence of the diffusion is calculated, and a turnover is obtained when the temperature is increased.
Simulating Poverty and Inequality Dynamics in Developing Countries
ERIC Educational Resources Information Center
Ansoms, An; Geenen, Sara
2012-01-01
This article considers how the simulation game of DEVELOPMENT MONOPOLY provides insight into poverty and inequality dynamics in a development context. It first discusses how the game is rooted in theoretical and conceptual frameworks on poverty and inequality. Subsequently, it reflects on selected playing experiences, with special focus on the…
Generating dynamic simulations of movement using computed muscle control.
Thelen, Darryl G; Anderson, Frank C; Delp, Scott L
2003-03-01
Computation of muscle excitation patterns that produce coordinated movements of muscle-actuated dynamic models is an important and challenging problem. Using dynamic optimization to compute excitation patterns comes at a large computational cost, which has limited the use of muscle-actuated simulations. This paper introduces a new algorithm, which we call computed muscle control, that uses static optimization along with feedforward and feedback controls to drive the kinematic trajectory of a musculoskeletal model toward a set of desired kinematics. We illustrate the algorithm by computing a set of muscle excitations that drive a 30-muscle, 3-degree-of-freedom model of pedaling to track measured pedaling kinematics and forces. Only 10 min of computer time were required to compute muscle excitations that reproduced the measured pedaling dynamics, which is over two orders of magnitude faster than conventional dynamic optimization techniques. Simulated kinematics were within 1 degrees of experimental values, simulated pedal forces were within one standard deviation of measured pedal forces for nearly all of the crank cycle, and computed muscle excitations were similar in timing to measured electromyographic patterns. The speed and accuracy of this new algorithm improves the feasibility of using detailed musculoskeletal models to simulate and analyze movement. PMID:12594980
Modeling and Dynamic Simulation of a Large Scale Helium Refrigerator
NASA Astrophysics Data System (ADS)
Lv, C.; Qiu, T. N.; Wu, J. H.; Xie, X. J.; Li, Q.
In order to simulate the transient behaviors of a newly developed 2 kW helium refrigerator, a numerical model of the critical equipment including a screw compressor with variable-frequency drive, plate-fin heat exchangers, a turbine expander, and pneumatic valves wasdeveloped. In the simulation,the calculation of the helium thermodynamic properties arebased on 32-parameter modified Benedict-Webb-Rubin (MBWR) state equation.The start-up process of the warm compressor station with gas management subsystem, and the cool-down process of cold box in an actual operation, were dynamically simulated. The developed model was verified by comparing the simulated results with the experimental data.Besides, system responses of increasing heat load were simulated. This model can also be used to design and optimize other large scale helium refrigerators.
Evaluating the Accuracy of Hessian Approximations for Direct Dynamics Simulations.
Zhuang, Yu; Siebert, Matthew R; Hase, William L; Kay, Kenneth G; Ceotto, Michele
2013-01-01
Direct dynamics simulations are a very useful and general approach for studying the atomistic properties of complex chemical systems, since an electronic structure theory representation of a system's potential energy surface is possible without the need for fitting an analytic potential energy function. In this paper, recently introduced compact finite difference (CFD) schemes for approximating the Hessian [J. Chem. Phys.2010, 133, 074101] are tested by employing the monodromy matrix equations of motion. Several systems, including carbon dioxide and benzene, are simulated, using both analytic potential energy surfaces and on-the-fly direct dynamics. The results show, depending on the molecular system, that electronic structure theory Hessian direct dynamics can be accelerated up to 2 orders of magnitude. The CFD approximation is found to be robust enough to deal with chaotic motion, concomitant with floppy and stiff mode dynamics, Fermi resonances, and other kinds of molecular couplings. Finally, the CFD approximations allow parametrical tuning of different CFD parameters to attain the best possible accuracy for different molecular systems. Thus, a direct dynamics simulation requiring the Hessian at every integration step may be replaced with an approximate Hessian updating by tuning the appropriate accuracy. PMID:26589009
Westermann, P.; Ahring, B.K.
1987-10-01
The dynamics of sulfate reduction, methane production, and denitrification were investigated in a permanently waterlogged alder swamp. Molybdate, an inhibitor of sulfate reduction, stimulated methane production in soil slurries, thus suggesting competition for common substrates between sulfate-reducing and methane-producing bacteria. Acetate, hydrogen, and methanol were found to stimulate both sulfate reduction and methane production, while trimethylamine mainly stimulated methane production. Nitrate addition reduced both methane production and sulfate reduction, either as a consequence of competition of poisoning of the bacteria. Sulfate-reducing bacteria were only slightly limited by the availability of electron acceptors, while denitrifying bacteria were seriously limited by low nitrate concentrations. Arrhenius plots of the three processes revealed different responses to temperature changes in the slurries. Methane production was most sensitive to temperature changes, followed by denitrification and sulfate reduction. No significant differences between slope patterns were observed when comparing summer and winter measurements, indicating similar populations regarding temperature responses.
Westermann, Peter; Ahring, Birgitte Kiær
1987-01-01
The dynamics of sulfate reduction, methane production, and denitrification were investigated in a permanently waterlogged alder swamp. Molybdate, an inhibitor of sulfate reduction, stimulated methane production in soil slurries, thus suggesting competition for common substrates between sulfate-reducing and methane-producing bacteria. Acetate, hydrogen, and methanol were found to stimulate both sulfate reduction and methane production, while trimethylamine mainly stimulated methane production. Nitrate addition reduced both methane production and sulfate reduction, either as a consequence of competition or poisoning of the bacteria. Sulfate-reducing bacteria were only slightly limited by the availability of electron acceptors, while denitrifying bacteria were seriously limited by low nitrate concentrations. Arrhenius plots of the three processes revealed different responses to temperature changes in the slurries. Methane production was most sensitive to temperature changes, followed by denitrification and sulfate reduction. No significant differences between slope patterns were observed when comparing summer and winter measurements, indicating similar populations regarding temperature responses. PMID:16347472
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter
2015-12-07
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.
Large Dynamic Range Simulations of Galaxies Hosting Supermassive Black Holes
NASA Astrophysics Data System (ADS)
Levine, Robyn
2011-08-01
The co-evolution of supermassive black holes (SMBHs) and their host galaxies is a rich problem, spanning a large-dynamic range and depending on many physical processes. Simulating the transport of gas and angular momentum from super-galactic scales all the way down to the outer edge of the black hole's accretion disk requires sophisticated numerical techniques with extensive treatment of baryonic physics. We use a hydrodynamic adaptive mesh refinement simulation to follow the growth and evolution of a typical disk galaxy hosting an SMBH, in a cosmological context (covering a dynamical range of 10 million!). We have adopted a piecemeal approach, focusing our attention on the gas dynamics in the central few hundred parsecs of the simulated galaxy (with boundary conditions provided by the larger cosmological simulation), and beginning with a simplified picture (no mergers or feedback). In this scenario, we find that the circumnuclear disk remains marginally stable against catastrophic fragmentation, allowing stochastic fueling of gas into the vicinity of the SMBH. I will discuss the successes and the limitations of these simulations, and their future direction.
Reactive Molecular Dynamics Simulations at the Petascale (Invited)
NASA Astrophysics Data System (ADS)
Nakano, A.
2013-12-01
We are developing a divide-conquer-recombine algorithmic framework into a metascalable (or 'design once, scale on new architectures') parallelization scheme to perform large spatiotemporal-scale reactive molecular dynamics simulations. The scheme has achieved parallel efficiency well over 0.9 on 786,432 IBM BlueGene/Q processors for 8.5 trillion-atom molecular dynamics and 1.9 trillion electronic degrees-of-freedom quantum molecular dynamics in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic alloy nanoparticles; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; and (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets.
Dynamics simulation and controller interfacing for legged robots
Reichler, J.A.; Delcomyn, F.
2000-01-01
Dynamics simulation can play a critical role in the engineering of robotic control code, and there exist a variety of strategies both for building physical models and for interacting with these models. This paper presents an approach to dynamics simulation and controller interfacing for legged robots, and contrasts it to existing approaches. The authors describe dynamics algorithms and contact-resolution strategies for multibody articulated mobile robots based on the decoupled tree-structure approach, and present a novel scripting language that provides a unified framework for control-code interfacing, user-interface design, and data analysis. Special emphasis is placed on facilitating the rapid integration of control algorithms written in a standard object-oriented language (C++), the production of modular, distributed, reusable controllers, and the use of parameterized signal-transmission properties such as delay, sampling rate, and noise.
Quantum Dynamics Simulations for Modeling Experimental Pump-Probe Measurements
NASA Astrophysics Data System (ADS)
Pearson, Brett; Nayyar, Sahil; Liss, Kyle; Weinacht, Thomas
2016-05-01
Time-resolved studies of quantum dynamics have benefited greatly from developments in ultrafast table-top and free electron lasers. Advances in computer software and hardware have lowered the barrier for performing calculations such that relatively simple simulations allow for direct comparison with experimental results. We describe here a set of quantum dynamics calculations in low-dimensional molecular systems. The calculations incorporate coupled electronic-nuclear dynamics, including two interactions with an applied field and nuclear wave packet propagation. The simulations were written and carried out by undergraduates as part of a senior research project, with the specific goal of allowing for detailed interpretation of experimental pump-probe data (in additional to the pedagogical value).
Dose reduction in CT using bismuth shielding: measurements and Monte Carlo simulations
Chang, Kyung-Hwan; Lee, Wonho; Choo, Dong-Myung; Lee, Choon-Sik; Kim, Youhyun
2010-01-01
In this research, using direct measurements and Monte Carlo calculations, the potential dose reduction achieved by bismuth shielding in computed tomography was evaluated. The patient dose was measured using an ionisation chamber in a polymethylmethacrylate (PMMA) phantom that had five measurement points at the centre and periphery. Simulations were performed using the MCNPX code. For both the bare and the bismuth-shielded phantom, the differences of dose values between experiment and simulation were within 9 %. The dose reductions due to the bismuth shielding were 1.2–55 % depending on the measurement points, X-ray tube voltage and the type of shielding. The amount of dose reduction was significant for the positions covered by the bismuth shielding (34 − 46 % for head and 41 − 55 % for body phantom on average) and negligible for other peripheral positions. The artefact on the reconstructed images were minimal when the distance between the shielding and the organs was >1 cm, and hence the shielding should be selectively located to protect critical organs such as the eye lens, thyroid and breast. The simulation results using the PMMA phantom was compared with those using a realistically voxelised phantom (KTMAN-2). For eye and breast, the simulation results using the PMMA and KTMAN-2 phantoms were similar with each other, while for thyroid the simulation results were different due to the discrepancy of locations and the sizes of the phantoms. The dose reductions achieved by bismuth and lead shielding were compared with each other and the results showed that the difference of the dose reductions achieved by the two materials was less than 2–3 %. PMID:19959602
Dose reduction in CT using bismuth shielding: measurements and Monte Carlo simulations.
Chang, Kyung-Hwan; Lee, Wonho; Choo, Dong-Myung; Lee, Choon-Sik; Kim, Youhyun
2010-03-01
In this research, using direct measurements and Monte Carlo calculations, the potential dose reduction achieved by bismuth shielding in computed tomography was evaluated. The patient dose was measured using an ionisation chamber in a polymethylmethacrylate (PMMA) phantom that had five measurement points at the centre and periphery. Simulations were performed using the MCNPX code. For both the bare and the bismuth-shielded phantom, the differences of dose values between experiment and simulation were within 9%. The dose reductions due to the bismuth shielding were 1.2-55% depending on the measurement points, X-ray tube voltage and the type of shielding. The amount of dose reduction was significant for the positions covered by the bismuth shielding (34 - 46% for head and 41 - 55% for body phantom on average) and negligible for other peripheral positions. The artefact on the reconstructed images were minimal when the distance between the shielding and the organs was >1 cm, and hence the shielding should be selectively located to protect critical organs such as the eye lens, thyroid and breast. The simulation results using the PMMA phantom was compared with those using a realistically voxelised phantom (KTMAN-2). For eye and breast, the simulation results using the PMMA and KTMAN-2 phantoms were similar with each other, while for thyroid the simulation results were different due to the discrepancy of locations and the sizes of the phantoms. The dose reductions achieved by bismuth and lead shielding were compared with each other and the results showed that the difference of the dose reductions achieved by the two materials was less than 2-3%. PMID:19959602
The dynamical influences of cloud shading on simulated supercell thunderstorms
NASA Astrophysics Data System (ADS)
Frame, Jeffrey
2008-10-01
Numerical simulations of supercell thunderstorms which include parameterized radiative transfer and surface fluxes are performed using the Advanced Regional Prediction System (ARPS) model. The tilted independent column approximation (TICA) is adopted for use in the ARPS model because the existing method of parameterized radiative transfer, the independent column approximation (ICA), permits only the vertical transfer of shortwave radiation. The computed radiative fluxes from both the TICA and ICA are compared to output from a three-dimensional Monte Carlo radiative transfer solver and it is determined that the TICA fluxes more closely match those from the Monte Carlo model than do those from the ICA. Additionally, the TICA is able to capture the extensions of shadows that occur when the solar zenith angle deviates significantly from zero, which cannot be captured by the ICA. The maximum low-level air temperature deficits within the modeled cloud shadows is 1.5 to 2.0 K, which is only about half that previously observed. The loss of strong solar heating of the model surface within the shaded regions cools the surface temperatures, and changes the sign of the sensible heat flux near the edge of the shadow. This stabilizes the model surface layer and suppresses vertical mixing at low levels within the shaded area. This reduction in vertical mixing means that higher momentum air from aloft is prevented from mixing with air near the surface that has lost momentum to surface friction. The net result of this is a shallower, but more intense vertically-sheared layer near the surface. As the supercell's rear-flank gust front propagates into this modified shear layer, the layer of cold outflow air becomes shallower and it accelerates eastward. In the case of a stationary storm, the cold outflow undercuts the updraft and mesocyclone, depriving them of warm and moist inflow, and ultimately weakening the storm. These results are not likely applicable to all simulations of
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
Wei Gu; Garcia, A.E.; Schoenborn, B.P.
1994-12-31
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.
Ultrascale simulations of non-smooth granular dynamics
NASA Astrophysics Data System (ADS)
Preclik, Tobias; Rüde, Ulrich
2015-06-01
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their micro-dynamics and thus to extend the time and length scales that can be simulated. The global multi-contact problem is solved using a non-linear block Gauss-Seidel method that is conforming to the subdomain structure. The parallel algorithms employ a sophisticated protocol between processors that delegate algorithmic tasks such as contact treatment and position integration uniquely and robustly to the processors. Communication overhead is minimized through aggressive message aggregation, leading to excellent strong and weak scaling. The robustness and scalability is assessed on three clusters including two peta-scale supercomputers with up to 458,752 processor cores. The simulations can reach unprecedented resolution of up to ten billion () non-spherical particles and contacts.
Simulation of the dynamic inefficiency of the CMS pixel detector
NASA Astrophysics Data System (ADS)
Bartók, M.
2015-05-01
The Pixel Detector is the innermost part of the CMS Tracker. It therefore has to prevail in the harshest environment in terms of particle fluence and radiation. There are several mechanisms that may decrease the efficiency of the detector. These are mainly caused by data acquisition (DAQ) problems and/or Single Event Upsets (SEU). Any remaining efficiency loss is referred to as the dynamic inefficiency. It is caused by various mechanisms inside the Readout Chip (ROC) and depends strongly on the data occupancy. In the 2012 data, at high values of instantaneous luminosity the inefficiency reached 2% (in the region closest to the interaction point) which is not negligible. In the 2015 run higher instantaneous luminosity is expected, which will result in lower efficiencies; therefore this effect needs to be understood and simulated. A data-driven method has been developed to simulate dynamic inefficiency, which has been shown to successfully simulate the effects.
ParaDiS-FEM dislocation dynamics simulation code primer
Tang, M; Hommes, G; Aubry, S; Arsenlis, A
2011-09-27
The ParaDiS code is developed to study bulk systems with periodic boundary conditions. When we try to perform discrete dislocation dynamics simulations for finite systems such as thin films or cylinders, the ParaDiS code must be extended. First, dislocations need to be contained inside the finite simulation box; Second, dislocations inside the finite box experience image stresses due to the free surfaces. We have developed in-house FEM subroutines to couple with the ParaDiS code to deal with free surface related issues in the dislocation dynamics simulations. This primer explains how the coupled code was developed, the main changes from the ParaDiS code, and the functions of the new FEM subroutines.
Molecular dynamics simulations of a lithium/sodium carbonate mixture.
Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo
2016-03-01
The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates. PMID:26897519
Molecular dynamics simulations of detonation on the roadrunner supercomputer
NASA Astrophysics Data System (ADS)
Mniszewski, Susan; Cawkwell, Marc; Germann, Timothy C.
2012-03-01
The temporal and spatial scales intrinsic to a real detonating explosive are extremely difficult to capture using molecular dynamics (MD) simulations. Nevertheless, MD remains very attractive since it allows for the resolution of dynamic phenomena at the atomic scale. Large-scale reactive MD simulations in three dimensions require immense computational resources even when simple reactive force fields are employed. We focus on the REBO force field for 'AB' since it has been shown to support a detonation while being simple, analytic, and short-ranged. The transition from two-to three- dimensional simulations is being facilitated by the port of the REBO force field in the parallel MD code SPaSM to LANL's petaflop supercomputer 'Roadrunner'. We provide a detailed discussion of the challenges associated with computing interatomic forces on a hybrid Opteron/Cell BE computational architecture.
Software life cycle dynamic simulation model: The organizational performance submodel
NASA Technical Reports Server (NTRS)
Tausworthe, Robert C.
1985-01-01
The submodel structure of a software life cycle dynamic simulation model is described. The software process is divided into seven phases, each with product, staff, and funding flows. The model is subdivided into an organizational response submodel, a management submodel, a management influence interface, and a model analyst interface. The concentration here is on the organizational response model, which simulates the performance characteristics of a software development subject to external and internal influences. These influences emanate from two sources: the model analyst interface, which configures the model to simulate the response of an implementing organization subject to its own internal influences, and the management submodel that exerts external dynamic control over the production process. A complete characterization is given of the organizational response submodel in the form of parameterized differential equations governing product, staffing, and funding levels. The parameter values and functions are allocated to the two interfaces.
Quantum simulation of the dynamical Casimir effect with trapped ions
NASA Astrophysics Data System (ADS)
Trautmann, N.; Hauke, P.
2016-04-01
Quantum vacuum fluctuations are a direct manifestation of Heisenberg’s uncertainty principle. The dynamical Casimir effect (DCE) allows for the observation of these vacuum fluctuations by turning them into real, observable photons. However, the observation of this effect in a cavity QED experiment would require the rapid variation of the length of a cavity with relativistic velocities, a daunting challenge. Here, we propose a quantum simulation of the DCE using an ion chain confined in a segmented ion trap. We derive a discrete model that enables us to map the dynamics of the multimode radiation field inside a variable-length cavity to radial phonons of the ion crystal. We perform a numerical study comparing the ion-chain quantum simulation under realistic experimental parameters to an ideal Fabry–Perot cavity, demonstrating the viability of the mapping. The proposed quantum simulator, therefore, allows for probing the photon (respectively phonon) production caused by the DCE on the single photon level.
Molecular Dynamics Simulation of Electrophoresis of a Telehelic Polymer Chain
NASA Astrophysics Data System (ADS)
Bhattacharya, Aniket
2002-08-01
We report the conformational and the dynamical properties of an end-labeled polymer chain embedded in a porous medium made of randomly distributed immobile spherical obstacles using a stochastic Molecular Dynamic(MD) simulation method for several obstacle densities and for various bias strenghts applied only to one end of the chain. First, various properties of the chain are studied when the external bias is set to zero. We then extend the stochastic MD simulation to study the electrophresis of a polymer chain driven by (i) a steady and (ii) a time dependent electric field. These studies are relevant for various time dependent gel electrophoresis methods widely used to separate DNA molecules. The qualitative features are compared with experiments, analytic theories, and recent Monte Carlo Simulation results.
McGroddy, K A; Brady, J W; Oswald, R E
1994-01-01
Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED. Images FIGURE 1 FIGURE 2 PMID:8161685
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.
Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A
2016-01-01
Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics. PMID:26013419
Dynamic simulations for the Terrestrial Planet Finder interferometer
NASA Astrophysics Data System (ADS)
Li, Ying-Yong; Hamlin, Louise A.; Wirz, Richie; Adams, Douglas; Moore, Greg; Coppolino, Robert; Peng, Chia-Yen; Levine, Marie
2005-08-01
The Terrestrial Planet Finder Interferometer (TPF-I) mission requires a set of formation-flying collector telescopes that direct the incoming light to a beam combiner where the beams are combined and detected to identify habitable planets. A baseline TPF collector design, using a primary mirror of 4.2 meters in diameter, is used here to conduct a dynamic study. The objective is to investigate the effects of dynamic response of the spacecraft on the system optical performance at the presence of disturbances that arise from the reaction wheel assembly and thruster loading, respectively. Frequency responses where the frequency is associated with the flywheel speed are presented in the paper. The results focus on the surface oscillation of the primary mirror and the point at which the secondary mirror is located. Transient response simulations under the baseline four thruster-assembly configuration were conducted using various duty cycles and thrust levels determined by the TPF formation rotation requirements. This paper will also describe an investigation conducted using new IMOS (Integrated Modeling of Optical Systems), which is an open, multi-disciplinary, and Matlab-based dynamic/optical system simulation code. A pre-processor that is able to generate the sub-structure modal models required by ISYSD (Integrated System Dynamics) was developed in new IMOS. ISYSD is used to develop a high-fidelity system dynamic model by integrating the sub-structure modal models. Finally, the paper will summarize current and future work in order to meet the TPF dynamic requirements.
Dynamic risk simulation to assess risk along roads
NASA Astrophysics Data System (ADS)
Voumard, J.; Caspar, O.; Derron, M.-H.; Jaboyedoff, M.
2013-04-01
Risk generated by natural hazards on roads is usually calculated with equations integrating various parameters related to hazard and traffic. These are static variables, like a rockfall hazard estimation for a road section or the average number of vehicles crossing this section every day. This methodology cannot take into account dynamic variations of traffic and interactions between vehicles such as speed modifications due to the sinuosity, slowdowns resulting of saturated traffic or vehicles columns forming in front of traffic lights. The influence of traffic dynamics on the risk estimation is not assessed with standard methodologies. Here we show, by mean of a dynamic traffic simulator, that the traffic variations may greatly influence the risk estimation over time. The risk is analysed on several alpine road sections in Switzerland using a dynamic vehicles approach and compared with the results of the static methodology. It demonstrates that risk significantly increases on sinuous sections because of the decreasing of vehicles speed. A more realistic risk can be obtained from a dynamic approach especially on mountain roads. A dynamic traffic simulator, modelling interactions between vehicles is a helpful tool to support decision making to reduce risk on roads.
Simulation of screw dislocation motion in iron by molecular dynamics simulations.
Domain, Christophe; Monnet, Ghiath
2005-11-18
Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations. PMID:16384158
NASA Astrophysics Data System (ADS)
Ghatee, Mohammad Hadi; Zolghadr, Amin Reza; Moosavi, Fatemeh; Ansari, Younes
2012-03-01
Bulk and surface properties of the ionic liquids 1-alkyl-3-methyl-imidazolium iodides ([Cnmim]I) were simulated by classical molecular dynamics using all atom non-polarizable force field (n = 4, butyl; 6, hexyl; 8, octyl). The structure of ionic liquids were initially optimized by density functional theory and atomic charges obtained by CHELPG method. Reduction of partial atomic charges (by 20% for simulation of density and surface tension, and by 10% for viscosity) found to improve the accuracy, while a non-polarizable force field was applied. Additionally, the simulation ensembles approach the equilibrium faster when the charge reduction is applied. By these refined force field parameters, simulated surface tensions in the range of 323-393 k are quite in agreement with the experiments. Simulation of temperature dependent surface tension of [C4mim]I well beyond room temperature (up to 700 K) permits prediction of the critical temperature in agreement with that predicted from experimental surface tension data. Simulated densities in the range of 298-450 K for the three ionic liquids are within 0.8% of the experimental data. Structural properties for [C4mim]I were found to be in agreement with the results of Car-Parrinello molecular dynamics simulation we performed, which indicates a rather well-structured cation-anion interaction and occurs essentially through the imidazolium ring cation. Diffusion coefficient changes with alkyl chain length in the order of [C8mim]I > [C6mim]I > [C4mim]I for the cation and the anion. Formation of a dense domain in subsurface region is quite evident, and progressively becomes denser as the alkyl chain length increases. Bivariate orientational analysis was used to determine the average orientation of molecule in ionic liquids surface, subsurface, and bulk regions. Dynamic bisector-wise and side-wise movement of the imodazolium ring cation in the surface region can be deduced from the bivariate maps. Atom-atom density profile and
Blöchliger, Nicolas; Caflisch, Amedeo; Vitalis, Andreas
2015-11-10
Data mining techniques depend strongly on how the data are represented and how distance between samples is measured. High-dimensional data often contain a large number of irrelevant dimensions (features) for a given query. These features act as noise and obfuscate relevant information. Unsupervised approaches to mine such data require distance measures that can account for feature relevance. Molecular dynamics simulations produce high-dimensional data sets describing molecules observed in time. Here, we propose to globally or locally weight simulation features based on effective rates. This emphasizes, in a data-driven manner, slow degrees of freedom that often report on the metastable states sampled by the molecular system. We couple this idea to several unsupervised learning protocols. Our approach unmasks slow side chain dynamics within the native state of a miniprotein and reveals additional metastable conformations of a protein. The approach can be combined with most algorithms for clustering or dimensionality reduction. PMID:26574336
Simulating Field-Scale Soil Organic Carbon Dynamics Using EPIC
Causarano, Hector J.; Shaw, Joey N.; Franzluebbers, A. J.; reeves, D. W.; Raper, Randy L.; Balkcom, Kipling S.; Norfleet, M. L.; Izaurralde, R Cesar
2007-07-01
Simulation models integrate our knowledge of soil organic C (SOC) dynamics and are useful tools for evaluating impacts of crop management on soil C sequestration; yet, they require local calibration. Our objectives were to calibrate the Environmental Policy Integrated Climate (EPIC) model, and evaluate its performance for simulating SOC fractions as affected by soil landscape and management. An automated parameter optimization procedure was used to calibrate the model for a site-specific experiment in the Coastal Plain of central Alabama. The ability of EPIC to predict corn (Zea mays L.) and cotton (Gossypium hirsutum L.) yields and SOC dynamics on different soil landscape positions (summit, sideslope and drainageway) during the initial period of conservation tillage adoption (5 years) was evaluated using regression and mean squared deviations. Simulated yield explained 88% of measured yield variation, with greatest disagreement on the sideslope position and highest agreement in the drainageway. Simulations explained approximately 1, 34 and 40% of the total variation in microbial biomass C (MBC), particulate organic C (POC) and total organic C (TOC), respectively. Lowest errors on TOC simulations (0-20 cm) were found on the sideslope and summit. We conclude that the automated parameterization was generally successful, although further work is needed to refine the MBC and POC fractions, and to improve EPIC predictions of SOC dynamics with depth. Overall, EPIC was sensitive to spatial differences in C fractions that resulted from differing soil landscape positions. The model needs additional refinement for accurate simulations of field-scale SOC dynamics affected by short-term management decisions.
Multiscale Simulations of the Structure and Dynamics of the Magnetopause
NASA Astrophysics Data System (ADS)
Berchem, Jean; Lapenta, Giovanni; Ashour-Abdalla, Maha
2016-04-01
Ongoing observations by the spacecraft of NASA's Magnetospheric Multiscale Mission are revealing a very complex structure and dynamics of the low-latitude magnetopause. One of the main difficulties to comprehend physical processes occurring at the magnetopause is that it requires following both the evolution of the large-scale interaction of the solar wind with the dayside magnetosphere, and the details of the kinetic processes that enable transport of energy and mass in localized regions of the magnetospheric boundary. To address this multiscale problem, we have carried out particle-in-cell (PIC) simulations of the dayside magnetopause. These simulations employ domains that are large enough to include large-scale features of the solar wind interaction with the geomagnetic field (e.g., field curvature and plasma asymmetries). The numerical challenge is dealt with by using the implicit iPic3d simulation code together with the results of global magnetohydrodynamic (MHD) simulations. We discuss the results of the PIC simulations in the context of the global MHD states that provide initial and boundary conditions, and local spacecraft observations at the magnetopause. In particular, we analyze the evolution of electromagnetic fields and particle distributions in different regions of the simulations to determine how reconnection processes affect the structure and dynamics of the magnetospheric boundary.
The molecular dynamics simulation of ion-induced ripple growth
Suele, P.; Heinig, K.-H.
2009-11-28
The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength ({lambda}) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths ({lambda}<35 nm) the adatom yield drops hence no surface diffusion takes place which is sufficient for ripple growth. The MD simulations predict that the growth of ripples with {lambda}>35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in {lambda} long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for {lambda}>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.
Dynamic Simulation of a Wave Rotor Topped Turboshaft Engine
NASA Technical Reports Server (NTRS)
Greendyke, R. B.; Paxson, D. E.; Schobeiri, M. T.
1997-01-01
The dynamic behavior of a wave rotor topped turboshaft engine is examined using a numerical simulation. The simulation utilizes an explicit, one-dimensional, multi-passage, CFD based wave rotor code in combination with an implicit, one-dimensional, component level dynamic engine simulation code. Transient responses to rapid fuel flow rate changes and compressor inlet pressure changes are simulated and compared with those of a similarly sized, untopped, turboshaft engine. Results indicate that the wave rotor topped engine responds in a stable, and rapid manner. Furthermore, during certain transient operations, the wave rotor actually tends to enhance engine stability. In particular, there is no tendency toward surge in the compressor of the wave rotor topped engine during rapid acceleration. In fact, the compressor actually moves slightly away from the surge line during this transient. This behavior is precisely the opposite to that of an untopped engine. The simulation is described. Issues associated with integrating CFD and component level codes are discussed. Results from several transient simulations are presented and discussed.
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics
2016-01-01
Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886
Synthesis of recurrent neural networks for dynamical system simulation.
Trischler, Adam P; D'Eleuterio, Gabriele M T
2016-08-01
We review several of the most widely used techniques for training recurrent neural networks to approximate dynamical systems, then describe a novel algorithm for this task. The algorithm is based on an earlier theoretical result that guarantees the quality of the network approximation. We show that a feedforward neural network can be trained on the vector-field representation of a given dynamical system using backpropagation, then recast it as a recurrent network that replicates the original system's dynamics. After detailing this algorithm and its relation to earlier approaches, we present numerical examples that demonstrate its capabilities. One of the distinguishing features of our approach is that both the original dynamical systems and the recurrent networks that simulate them operate in continuous time. PMID:27182811
Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control
Zhang, Xingwu; Chen, Xuefeng; You, Shangqin; He, Zhengjia; Li, Bing
2012-01-01
In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC) is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results. PMID:22666072
Generic solar photovoltaic system dynamic simulation model specification.
Ellis, Abraham; Behnke, Michael Robert; Elliott, Ryan Thomas
2013-10-01
This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intended to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.
Interactive simulation and analysis of emission reduction systems in commercial boilers
Diachin, D.; Freitag, L.; Heath, D.; Herzog, J.; Plassmann, P.; Michels, W.
1996-12-31
In this paper the authors describe an interactive virtual environment developed to model an emission reduction system for commercial boilers. The interactive environment is used to optimize the performance of the reduction system through the spatial adjustment and spray reconfiguration of reagent injectors. They describe the three principal components of the system: a computational model for the particle dynamics, a three-dimensional display device and graphics environment, and the communication layer that allows the interaction of the user in the visualization environment with the computational model. Timing results for each component are given for three hardware configurations that demonstrate the real-time performance of this tool.
A description of Lax type integrable dynamical systems via the Marsden-Weinstein reduction method
NASA Astrophysics Data System (ADS)
Prykarpatsky, Yarema A.
2013-09-01
A Lie-algebraic approach to constructing nonlinear Lax type integrable dynamical systems of modern mathematical and theoretical physics, based on the Marsden-Weinstein reduction method on canonically symplectic manifolds with group symmetry, is proposed. Its natural relationship with the well known Adler-Kostant-Souriau-Berezin-Kirillov method and the associated R-matrix approach is analyzed.
Noe, F; Diadone, Isabella; Lollmann, Marc; Sauer, Marcus; Chondera, John D; Smith, Jeremy C
2011-01-01
There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is dynamical fingerprints which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.
Dynamical Effects and Product Distributions in Simulated CN + Methane Reactions.
Preston, Thomas J; Hornung, Balázs; Pandit, Shubhrangshu; Harvey, Jeremy N; Orr-Ewing, Andrew J
2016-07-14
Dynamics of collisions between structured molecular species quickly become complex as molecules become large. Reactions of methane with halogen and oxygen atoms serve as model systems for polyatomic molecule chemical dynamics, and replacing the atomic reagent with a diatomic radical affords further insights. A new, full-dimensional potential energy surface for collisions between CN + CH4 to form HCN + CH3 is developed and then used to perform quasi-classical simulations of the reaction. Coupled-cluster energies serve as input to an empirical valence bonding (EVB) model, which provides an analytical function for the surface. Efficient sampling permits simulation of velocity-map ion images and exploration of dynamics over a range of collision energies. Reaction populates HCN vibration, and energy partitioning changes with collision energy. The reaction cross-section depends on the orientation of the diatomic CN radical. A two-dimensional extension of the cone of acceptance for an atom in the line-of-centers model appropriately describes its reactivity. The simulation results foster future experiments and diatomic extensions to existing atomic models of chemical collisions and reaction dynamics. PMID:26812395
Frank, Martin; Gutbrod, Peter; Hassayoun, Chokri; von Der Lieth, Claus-W
2003-10-01
Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions at an atomic level. The "Dynamic Molecules" approach is the first internet portal that provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The aim is to open molecular dynamics techniques to a broader range of users including undergraduate students, teachers and scientists outside the bioinformatics field. The time-limiting factors are the availability of free capacity on the computing server to run the simulations and the time required to transport the history file through the internet for the animation mode. The interactive access mode of the portal is acceptable for animations of molecules having up to about 500 atoms. PMID:12908101
Wang, Shaobu; Lu, Shuai; Zhou, Ning; Lin, Guang; Elizondo, Marcelo A.; Pai, M. A.
2014-09-04
In interconnected power systems, dynamic model reduction can be applied on generators outside the area of interest to mitigate the computational cost with transient stability studies. This paper presents an approach of deriving the reduced dynamic model of the external area based on dynamic response measurements, which comprises of three steps, dynamic-feature extraction, attribution and reconstruction (DEAR). In the DEAR approach, a feature extraction technique, such as singular value decomposition (SVD), is applied to the measured generator dynamics after a disturbance. Characteristic generators are then identified in the feature attribution step for matching the extracted dynamic features with the highest similarity, forming a suboptimal ‘basis’ of system dynamics. In the reconstruction step, generator state variables such as rotor angles and voltage magnitudes are approximated with a linear combination of the characteristic generators, resulting in a quasi-nonlinear reduced model of the original external system. Network model is un-changed in the DEAR method. Tests on several IEEE standard systems show that the proposed method gets better reduction ratio and response errors than the traditional coherency aggregation methods.
Climate Simulations with an Isentropic Finite Volume Dynamical Core
Chen, Chih-Chieh; Rasch, Philip J.
2012-04-15
This paper discusses the impact of changing the vertical coordinate from a hybrid pressure to a hybrid-isentropic coordinate within the finite volume dynamical core of the Community Atmosphere Model (CAM). Results from a 20-year climate simulation using the new model coordinate configuration are compared to control simulations produced by the Eulerian spectral and FV dynamical cores of CAM which both use a pressure-based ({sigma}-p) coordinate. The same physical parameterization package is employed in all three dynamical cores. The isentropic modeling framework significantly alters the simulated climatology and has several desirable features. The revised model produces a better representation of heat transport processes in the atmosphere leading to much improved atmospheric temperatures. We show that the isentropic model is very effective in reducing the long standing cold temperature bias in the upper troposphere and lower stratosphere, a deficiency shared among most climate models. The warmer upper troposphere and stratosphere seen in the isentropic model reduces the global coverage of high clouds which is in better agreement with observations. The isentropic model also shows improvements in the simulated wintertime mean sea-level pressure field in the northern hemisphere.
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.
2000-10-10
Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.
A dynamic traffic simulator for roads affected by natural hasards
NASA Astrophysics Data System (ADS)
Voumard, J.; Jaboyedoff, M.; Derron, M.-H.
2012-04-01
This work focuses on the issue of natural hazards threatening roads. Nowadays, risk estimations of rock falls or landslides affecting whole sections of road are generally quite accurate and under relatively good control. Mitigation measures provide intervention means to reduce the hazards along roads. However, as classical models of risk calculation on communication routes do not take into account the dynamic traffic parameters, little is known on the way of reducing the risk at road level. It is not known precisely what really happens on the road when an event occurs and how vehicles interact. A dynamic traffic simulator in development provides information on factors having an impact on the risk level related to the road. Variables such as visibility, curvature radius of turns or vehicle type were included in the model. Varying these variables within dynamic traffic simulations can suggest solutions to minimize the risks for road users. These simulations can provide answers to various questions, such as: does speed have a significant impact on the risk incurred by drivers? Is it possible to significantly reduce the risk with appropriate speeds? The simulation is performed with the MATLAB © software. The model is yet to be calibrated and validated through in situ tests.
NETIMIS: Dynamic Simulation of Health Economics Outcomes Using Big Data.
Johnson, Owen A; Hall, Peter S; Hulme, Claire
2016-02-01
Many healthcare organizations are now making good use of electronic health record (EHR) systems to record clinical information about their patients and the details of their healthcare. Electronic data in EHRs is generated by people engaged in complex processes within complex environments, and their human input, albeit shaped by computer systems, is compromised by many human factors. These data are potentially valuable to health economists and outcomes researchers but are sufficiently large and complex enough to be considered part of the new frontier of 'big data'. This paper describes emerging methods that draw together data mining, process modelling, activity-based costing and dynamic simulation models. Our research infrastructure includes safe links to Leeds hospital's EHRs with 3 million secondary and tertiary care patients. We created a multidisciplinary team of health economists, clinical specialists, and data and computer scientists, and developed a dynamic simulation tool called NETIMIS (Network Tools for Intervention Modelling with Intelligent Simulation; http://www.netimis.com ) suitable for visualization of both human-designed and data-mined processes which can then be used for 'what-if' analysis by stakeholders interested in costing, designing and evaluating healthcare interventions. We present two examples of model development to illustrate how dynamic simulation can be informed by big data from an EHR. We found the tool provided a focal point for multidisciplinary team work to help them iteratively and collaboratively 'deep dive' into big data. PMID:26879667
Molecular-dynamics simulation of a ceramide bilayer
NASA Astrophysics Data System (ADS)
Pandit, Sagar A.; Scott, H. Larry
2006-01-01
Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368K (5° above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall "dipole potential," when ceramide is compared to sphingomyelin.
A dynamic simulation tool for hydrogen fuel cell vehicles
NASA Astrophysics Data System (ADS)
Moore, R. M.; Hauer, K. H.; Friedman, D.; Cunningham, J.; Badrinarayanan, P.; Ramaswamy, S.; Eggert, A.
This paper describes a dynamic fuel cell vehicle simulation (FCVSim) tool for the load-following direct-hydrogen (DH) fuel cell vehicle. The emphasis is on simulation of the direct-hydrogen fuel cell system (FC System) within the vehicle simulation tool. This paper is focused on the subsystems that are specific to the load-following direct-hydrogen model. The four major subsystems discussed are the fuel cell stack, the air supply, the water and thermal management (WTM), and the hydrogen supply. The discussion provides the details of these subsystem simulations. The basic vehicle configuration has been previously outlined by Hauer [An Analysis Tool For Fuel Cell Vehicle Hardware and Software (Controls) with an Application to Fuel Economy Comparisons of Alternative System Designs, Dissertation, UC California, Davis, USA, 2001] and Hauer and Moore [Fuel Cells for Automotive Applications, Professional Engineering Publishing, 2003, pp. 157-177, ISBN 1860584233] and is only briefly reviewed in this paper.
Molecular Dynamics Simulations of Carbon Nanotubes in Water
NASA Technical Reports Server (NTRS)
Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.
2000-01-01
We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.
Advanced beam-dynamics simulation tools for RIA.
Garnett, R. W.; Wangler, T. P.; Billen, J. H.; Qiang, J.; Ryne, R.; Crandall, K. R.; Ostroumov, P.; York, R.; Zhao, Q.; Physics; LANL; LBNL; Tech Source; Michigan State Univ.
2005-01-01
We are developing multi-particle beam-dynamics simulation codes for RIA driver-linac simulations extending from the low-energy beam transport (LEBT) line to the end of the linac. These codes run on the NERSC parallel supercomputing platforms at LBNL, which allow us to run simulations with large numbers of macroparticles. The codes have the physics capabilities needed for RIA, including transport and acceleration of multiple-charge-state beams, beam-line elements such as high-voltage platforms within the linac, interdigital accelerating structures, charge-stripper foils, and capabilities for handling the effects of machine errors and other off-normal conditions. This year will mark the end of our project. In this paper we present the status of the work, describe some recent additions to the codes, and show some preliminary simulation results.
Novel procedure for thermal equilibration in molecular dynamics simulation.
Gallo, Marco T; Grant, Barry J; Teodoro, Miguel L; Melton, Julia; Cieplak, Piotr; Phillips, George N; Stec, Boguslaw
2009-04-01
We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797
Novel procedure for thermal equilibration in molecular dynamics simulation
Gallo, Marco T.; Grant, Barry J.; Teodoro, Miguel L.; Melton, Julia; Cieplak, Piotr; Phillips, George N.; Stec, Boguslaw
2014-01-01
We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797
Spotting the difference in molecular dynamics simulations of biomolecules.
Sakuraba, Shun; Kono, Hidetoshi
2016-08-21
Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (LDA-ITER) to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the "difference" between two trajectories. PMID:27544096
Insights into Buforin II Membrane Translocation from Molecular Dynamics Simulations
Elmore, Donald E.
2012-01-01
Buforin II is a histone-derived antimicrobial peptide that readily translocates across lipid membranes without causing significant membrane permeabilization. Previous studies showed that mutating the sole proline of buforin II dramatically decreases its translocation. As well, researchers have proposed that the peptide crosses membranes in a cooperative manner through forming transient toroidal pores. This paper reports molecular dynamics simulations designed to investigate the structure of buforin II upon membrane entry and evaluate whether the peptide is able to form toroidal pore structures. These simulations showed a relationship between protein-lipid interactions and increased structural deformations of the buforin N-terminal region promoted by proline. Moreover, simulations with multiple peptides show how buforin II can embed deeply into membranes and potentially form toroidal pores. Together, these simulations provide structural insight into the translocation process for buforin II in addition to providing more general insight into the role proline can play in antimicrobial peptides. PMID:23022591
Survey of Dynamic Simulation Programs for Nuclear Fuel Reprocessing
Troy J. Tranter; Daryl R. Haefner
2008-06-01
The absence of any industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other industries. Modeling programs to simulate the dynamic behavior of nuclear fuel separations and processing were originally developed to support the US government’s mission of weapons production and defense fuel recovery. Consequently there has been little effort is the US devoted towards improving this specific process simulation capability during the last two or three decades. More recent work has been focused on elucidating chemical thermodynamics and developing better models of predicting equilibrium in actinide solvent extraction systems. These equilibrium models have been used to augment flowsheet development and testing primarily at laboratory scales. The development of more robust and complete process models has not kept pace with the vast improvements in computational power and user interface and is significantly behind simulation capability in other chemical processing and separation fields.
Computational Fluid Dynamics (CFD) simulation of the Madison Dynamo Experiment.
NASA Astrophysics Data System (ADS)
Haehn, N. S.; Forest, C. B.; Weber, C. R.; Kendrick, R. D.; Taylor, N. Z.; Oakley, J. G.; Bonazza, R.; Spence, Erik
2007-11-01
The Madison Dynamo Experiment is designed to study a self-generated magnetic field called a dynamo. The flow characteristics of a water experiment that is dimensionally similar to the liquid sodium experiment has been modeled using the Computational Fluid Dynamics (CFD) software Fluent. Results from the CFD simulations are used to confirm flow characteristics measured experimentally by both Laser Doppler Velocimetry (LDV) and Particle Imaging Velocimetry (PIV). Simulations can also give insight into the flow characteristics in regions of the experiment which are not accessible via the LDV and PIV systems. The results from the simulations are also used as input for a MHD code to predict the threshold for Dynamo onset. The CFD simulations -- in conjunction with the MHD dynamo prediction code -- can be used to design modifications to the experiment to minimize costly changes. The CFD code has shown that the addition of an equatorial baffle along with several poloidal baffles can lower the threshold for Dynamo onset.
Analysis of utilization of desert habitats with dynamic simulation
Williams, B.K.
1986-01-01
The effects of climate and herbivores on cool desert shrubs in north-western Utah were investigated with a dynamic simulation model. Cool desert shrublands are extensively managed as grazing lands, and are defoliated annually by domestic livestock. A primary production model was used to simulate harvest yields and shrub responses under a variety of climatic regimes and defoliation patterns. The model consists of six plant components, and it is based on equations of growth analysis. Plant responses were simulated under various combinations of 20 annual weather patterns and 14 defoliation strategies. Results of the simulations exhibit some unexpected linearities in model behavior, and emphasize the importance of both the pattern of climate and the level of plant vigor in determining optimal harvest strategies. Model behaviors are interpreted in terms of shrub morphology, physiology and ecology.
Method for inserting noise in digital mammography to simulate reduction in radiation dose
NASA Astrophysics Data System (ADS)
Borges, Lucas R.; de Oliveira, Helder C. R.; Nunes, Polyana F.; Vieira, Marcelo A. C.
2015-03-01
The quality of clinical x-ray images is closely related to the radiation dose used in the imaging study. The general principle for selecting the radiation is ALARA ("as low as reasonably achievable"). The practical optimization, however, remains challenging. It is well known that reducing the radiation dose increases the quantum noise, which could compromise the image quality. In order to conduct studies about dose reduction in mammography, it would be necessary to acquire repeated clinical images, from the same patient, with different dose levels. However, such practice would be unethical due to radiation related risks. One solution is to simulate the effects of dose reduction in clinical images. This work proposes a new method, based on the Anscombe transformation, which simulates dose reduction in digital mammography by inserting quantum noise into clinical mammograms acquired with the standard radiation dose. Thus, it is possible to simulate different levels of radiation doses without exposing the patient to new levels of radiation. Results showed that the achieved quality of simulated images generated with our method is the same as when using other methods found in the literature, with the novelty of using the Anscombe transformation for converting signal-independent Gaussian noise into signal-dependent quantum noise.
Evaluation of Airframe Noise Reduction Concepts via Simulations Using a Lattice Boltzmann Approach
NASA Technical Reports Server (NTRS)
Fares, Ehab; Casalino, Damiano; Khorrami, Mehdi R.
2015-01-01
Unsteady computations are presented for a high-fidelity, 18% scale, semi-span Gulfstream aircraft model in landing configuration, i.e. flap deflected at 39 degree and main landing gear deployed. The simulations employ the lattice Boltzmann solver PowerFLOW® to simultaneously capture the flow physics and acoustics in the near field. Sound propagation to the far field is obtained using a Ffowcs Williams and Hawkings acoustic analogy approach. In addition to the baseline geometry, which was presented previously, various noise reduction concepts for the flap and main landing gear are simulated. In particular, care is taken to fully resolve the complex geometrical details associated with these concepts in order to capture the resulting intricate local flow field thus enabling accurate prediction of their acoustic behavior. To determine aeroacoustic performance, the farfield noise predicted with the concepts applied is compared to high-fidelity simulations of the untreated baseline configurations. To assess the accuracy of the computed results, the aerodynamic and aeroacoustic impact of the noise reduction concepts is evaluated numerically and compared to experimental results for the same model. The trends and effectiveness of the simulated noise reduction concepts compare well with measured values and demonstrate that the computational approach is capable of capturing the primary effects of the acoustic treatment on a full aircraft model.
Shafique, Neha; Kennedy, Kiley E; Douglas, Jack F; Starr, Francis W
2016-06-16
Heterogeneity of dynamics plays a vital role in membrane function, but the methods for quantifying this heterogeneity are still being developed. Here we examine membrane dynamical heterogeneity via molecular simulations of a single-component dipalmitoylphosphatidylcholine (DPPC) lipid bilayer using the MARTINI force field. We draw upon well-established analysis methods developed in the study of glass-forming fluids and find significant changes in lipid dynamics between the fluid (Lα), and gel (Lβ) phases. In particular, we distinguish two mobility groups in the more ordered Lβ phase: (i) lipids that are transiently trapped by their neighbors and (ii) lipids with displacements on the scale of the intermolecular spacing. These distinct mobility groups spatially segregate, forming dynamic clusters that have characteristic time (1-2 μs) and length (1-10 nm) scales comparable to those of proteins and other biomolecules. We suggest that these dynamic clusters could couple to biomolecules within the membrane and thus may play a role in many membrane functions. In the equilibrium membrane, lipid molecules dynamically exchange between the mobility groups, and the resulting clusters are not associated with a thermodynamic phase separation. Dynamical clusters having similar characteristics arise in many other condensed phase materials, placing membranes in a broad class of materials with strong intermolecular interactions. PMID:27223339
Molecular dynamics simulations of solvated yeast tRNA(Asp).
Auffinger, P; Louise-May, S; Westhof, E
1999-01-01
Transfer RNA molecules are involved in a variety of biological processes, implying complex recognition events with proteins and other RNAs. From a structural point of view, tRNAs constitute a reference system for studying RNA folding and architecture. A deeper understanding of their structural and functional properties will derive from our ability to model accurately their dynamical behavior. We present the first dynamical model of a fully neutralized and solvated tRNA molecule over a 500-ps time scale. Starting from the crystallographic structure of yeast tRNA(Asp), the 75-nucleotide molecule was modeled with 8055 water molecules and 74 NH4+ counterions, using the AMBER4.1 program and the particle mesh Ewald (PME) method for the treatment of long-range electrostatic interactions. The calculations led to a dynamically stable model of the tRNA molecule. During the simulation, all secondary and tertiary base pairs are maintained while a certain lability of base triples in the tRNA core is observed. This lability was interpreted as resulting from intrinsic factors associated with the "weaker" hydrogen bonding patterns seen in these base triples and from an altered ionic environment of the tRNA molecule. Calculated thermal factors are used to compare the dynamics of the tRNA in solution and in the crystal. The present molecular dynamics simulation of a complex and highly charged nucleic acid molecule attests to the fact that simulation methods are now able to investigate not only the dynamics of proteins, but also that of large RNA molecules. Thus they also provide a basis for further investigations on the structural and functional effects of chemical and posttranscriptionally modified nucleotides as well as on ionic environmental effects. PMID:9876122
Spectral Element Simulations of Rupture Dynamics along kinked faults
NASA Astrophysics Data System (ADS)
Vilotte, J.; Festa, G.; Madariaga, R.
2005-12-01
Numerical simulation of earthquake source dynamics provides key elements for ground-motion prediction and insights into the physics of dynamic rupture propagation. Faulting is controlled by non-linear frictional interactions and damage within the fault zone. Important features of the earthquakes dynamics, such as rupture velocity, arrest phase and high-frequency radiation are believed to be strongly influenced by the geometry of the faults (kinks, jogs and forks). Data analysis as well as kinematic inversions have pointed out potential links between super-shear and geometry, as in the case of the Denali and Izmit earthquakes. Finally, recent laboratory experiments of sub- and super-shear rupture propagation along kink interfaces have shed new lights on these phenomena. We present here spectral element simulations of the dynamic rupture propagation along kinked and curved fault interfaces, a problem that has been experimentally investigated by Rousseau and Rosakis (2003). Depending on the state of the initial stress, we numerically analyze the mechanics of the dynamical fault branching for sub- and super-shear rupture propagation. Special interest is devoted to source directivity effects and high frequency generation related to the branching process. Implications for strong motion analysis will be discussed. This work was supported by the SPICE - Research and Training project
Numerical Simulation of High Drag Reduction in a Turbulent Channel Flow with Polymer Additives
NASA Technical Reports Server (NTRS)
Dubief, Yves
2003-01-01
The addition of small amounts of long chain polymer molecules to wall-bounded flows can lead to dramatic drag reduction. Although this phenomenon has been known for about fifty years, the action of the polymers and its effect on turbulent structures are still unclear. Detailed experiments have characterized two distinct regimes (Warholic et al. 1999), which are referred to as low drag reduction (LDR) and high drag reduction (HDR). The first regime exhibits similar statistical trends as Newtonian flow: the log-law region of the mean velocity profile remains parallel to that of the Newtonian ow but its lower bound moves away from the wall and the upward shift of the log-region is a function of drag reduction, DR. Although streamwise fluctuations are increased and transverse ones are reduced, the shape of the rms velocity profiles is not qualitatively modified. At higher drag reductions, of the order of 40-50%, the ow enters the HDR regime for which the slope of the log-law is dramatically augmented and the Reynolds shear stress is small (Warholic et al. 1999; Ptasinski et al. 2001). The drag reduction is eventually bounded by a maximum drag reduction (MDR) (Virk & Mickley 1970) which is a function of the Reynolds number. While several experiments report mean velocity profiles very close to the empirical profile of Virk & Mickley (1970) for MDR conditions, the observations regarding the structure of turbulence can differ significantly. For instance, Warholic et al. (1999) measured a near-zero Reynolds shear stress, whereas a recent experiment (Ptasinski et al. 2001) shows evidence of non-negligible Reynolds stress in their MDR flow. To the knowledge of the authors, only the LDR regime has been documented in numerical simulations (Sureshkumar et al. 1997; Dimitropoulos et al. 1998; Min et al. 2001; Dubief & Lele 2001; Sibilla & Baron 2002). This paper discusses the simulation of polymer drag reduced channel ow at HDR using the FENE-P (Finite Elastic non
Multi-Scale Dynamics, Control, and Simulation of Granular Spacecraft
NASA Technical Reports Server (NTRS)
Quadrelli, Marco B.; Basinger, Scott; Swartzlander, Grover
2013-01-01
In this paper, we present some ideas regarding the modeling, dynamics and control aspects of granular spacecraft. Granular spacecraft are complex multibody systems composed of a spatially disordered distribution of a large number of elements, for instance a cloud of grains in orbit. An example of application is a spaceborne observatory for exoplanet imaging, where the primary aperture is a cloud instead of a monolithic aperture. A model is proposed of a multi-scale dynamics of the grains and cloud in orbit, as well as a control approach for cloud shape maintenance and alignment, and preliminary simulation studies are carried out for the representative imaging system.
Identifying the mechanisms of polymer friction through molecular dynamics simulation.
Dai, Ling; Minn, M; Satyanarayana, N; Sinha, Sujeet K; Tan, V B C
2011-12-20
Mechanisms governing the tribological behavior of polymer-on-polymer sliding were investigated by molecular dynamics simulations. Three main mechanisms governing frictional behavior were identified. Interfacial "brushing" of molecular chain ends over one another was observed as the key contribution to frictional forces. With an increase of the sliding speed, fluctuations in frictional forces reduced in both magnitude and periodicity, leading to dynamic frictional behavior. While "brushing" remained prevalent, two additional irreversible mechanisms, "combing" and "chain scission", of molecular chains were observed when the interfaces were significantly diffused. PMID:22044344
Beam Dynamics Design and Simulation in Ion Linear Accelerators (
Energy Science and Technology Software Center (ESTSC)
2006-08-01
Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modernmore » ion linear accelerators and beam transport systems.« less
Beam Dynamics Design and Simulation in Ion Linear Accelerators (
Ostroumov, Peter N.; Asseev, Vladislav N.; Mustapha, and Brahim
2006-08-01
Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modern ion linear accelerators and beam transport systems.
Analysis of motion features for molecular dynamics simulation of proteins
NASA Astrophysics Data System (ADS)
Kamada, Mayumi; Toda, Mikito; Sekijima, Masakazu; Takata, Masami; Joe, Kazuki
2011-01-01
Recently, a new method for time series analysis using the wavelet transformation has been proposed by Sakurai et al. We apply it to molecular dynamics simulation of Thermomyces lanuginosa lipase (TLL). Introducing indexes to characterize collective motion of the protein, we have obtained the following two results. First, time evolution of the collective motion involves not only the dynamics within a single potential well but also takes place wandering around multiple conformations. Second, correlation of the collective motion between secondary structures shows that collective motion exists involving multiple secondary structures. We discuss future prospects of our study involving 'disordered proteins'.
Molecular dynamical simulations of melting behaviors of metal clusters
Hamid, Ilyar; Fang, Meng; Duan, Haiming
2015-04-15
The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures.
Simulation of Ionic Aggregation and Ion Dynamics in Model Ionomers
NASA Astrophysics Data System (ADS)
Frischknecht, Amalie L.
2012-02-01
Ionomers, polymers containing a small fraction of covalently bound ionic groups, are of interest as possible electrolytes in batteries. A single-ion conducting polymer electrolyte would be safer and have higher efficiency than the currently-used liquid electrolytes. However, to date ionomeric materials do not have sufficiently high conductivities for practical application. This is most likely because the ions tend to form aggregates, leading to slow ion transport. A key question is therefore how molecular structure affects the ionic aggregation and ion dynamics. To probe these structure-property relationships, we have performed molecular simulations of a set of recently synthesized poly(ethylene-co-acrylic acid) copolymers and ionomers, with a focus on the morphology of the ionic aggregates. The ionomers have a precise, constant spacing of charged groups, making them ideal for direct comparisons with simulations. Ab initio calculations give insight into the expected coordination of cations with fragments of the ionomers. All-atom molecular dynamics (MD) simulations of the ionomer melt show aggregation of the ionic groups into extended string-like clusters. An extensive set of coarse-grained molecular dynamics simulations extend the results to longer times and larger length scales. The structure factors calculated from the MD simulations compare favorably with x-ray scattering data. Furthermore, the simulations give a detailed picture of the sizes, shapes, and composition of the ionic aggregates, and how they depend on polymer architecture. Implications for ion transport will be discussed. [Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2015-01-28
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
Process Modeling and Dynamic Simulation for EAST Helium Refrigerator
NASA Astrophysics Data System (ADS)
Lu, Xiaofei; Fu, Peng; Zhuang, Ming; Qiu, Lilong; Hu, Liangbing
2016-06-01
In this paper, the process modeling and dynamic simulation for the EAST helium refrigerator has been completed. The cryogenic process model is described and the main components are customized in detail. The process model is controlled by the PLC simulator, and the realtime communication between the process model and the controllers is achieved by a customized interface. Validation of the process model has been confirmed based on EAST experimental data during the cool down process of 300–80 K. Simulation results indicate that this process simulator is able to reproduce dynamic behaviors of the EAST helium refrigerator very well for the operation of long pulsed plasma discharge. The cryogenic process simulator based on control architecture is available for operation optimization and control design of EAST cryogenic systems to cope with the long pulsed heat loads in the future. supported by National Natural Science Foundation of China (No. 51306195) and Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, CAS (No. CRYO201408)
Setting up and running molecular dynamics simulations of membrane proteins.
Kandt, Christian; Ash, Walter L; Tieleman, D Peter
2007-04-01
Molecular dynamics simulations have become a popular and powerful technique to study lipids and membrane proteins. We present some general questions and issues that should be considered prior to embarking on molecular dynamics simulation studies of membrane proteins and review common simulation methods. We suggest a practical approach to setting up and running simulations of membrane proteins, and introduce two new (related) methods to embed a protein in a lipid bilayer. Both methods rely on placing lipids and the protein(s) on a widely spaced grid and then 'shrinking' the grid until the bilayer with the protein has the desired density, with lipids neatly packed around the protein. When starting from a grid based on a single lipid structure, or several potentially different lipid structures (method 1), the bilayer will start well-packed but requires more equilibration. When starting from a pre-equilibrated bilayer, either pure or mixed, most of the structure of the bilayer stays intact, reducing equilibration time (method 2). The main advantages of these methods are that they minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins. PMID:17367719
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2015-01-01
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
Fan, Weiyi; Zhu, Tianle; Sun, Yifei; Lv, Dong
2014-10-01
The effects of gas compositions on NOx reduction and NH3 slip by selective non-catalytic reduction (SNCR) with NH3 were investigated in a simulated cement precalciner atmosphere. The results show that the presence of H2O improves NOx reduction and widens the reduction temperature window significantly. O2 is indispensable for reducing NOx. The optimum reduction temperature decreases and the temperature window widens to a lower temperature with the increase of O2 content. In addition, the increase of O2 content also results in a decrease of the maximum NOx reduction efficiency. The effect of SO2 on NOx reduction is negligible in the simulated precalciner atmosphere. To increase CO concentration makes NO reduction take place at relatively low temperatures. However, NH3 will tend to be oxidized into NO instead of reducing NO after entering the stream containing O2 at high temperatures if it is initially blended with a high concentration of CO in an oxygen-free environment. The increase of H2O, O2, SO2 or CO concentration is helpful to reduce NH3 slip in the temperature region below 900°C. These effects are resulted from the fact that the generation and consumption of O and OH radicals which are crucial to NO reduction and formation can be influenced by the four gas compositions. In industrial operation of SNCR for cement precalciner, these effects should be taken into account to increase NOx reduction efficiency and avoid NH3 slip. PMID:25065808
Generation of linear dynamic models from a digital nonlinear simulation
NASA Technical Reports Server (NTRS)
Daniele, C. J.; Krosel, S. M.
1979-01-01
The results and methodology used to derive linear models from a nonlinear simulation are presented. It is shown that averaged positive and negative perturbations in the state variables can reduce numerical errors in finite difference, partial derivative approximations and, in the control inputs, can better approximate the system response in both directions about the operating point. Both explicit and implicit formulations are addressed. Linear models are derived for the F 100 engine, and comparisons of transients are made with the nonlinear simulation. The problem of startup transients in the nonlinear simulation in making these comparisons is addressed. Also, reduction of the linear models is investigated using the modal and normal techniques. Reduced-order models of the F 100 are derived and compared with the full-state models.
Rare event simulation of the chaotic Lorenz 96 dynamical system
NASA Astrophysics Data System (ADS)
Wouters, Jeroen; Bouchet, Freddy
2015-04-01
The simulation of rare events is becoming increasingly important in the climate sciences. Several sessions are devoted to rare and extreme events at this meeting and the IPCC has devoted a special report to risk management of extreme events (SREX). Brute force simulation of rare events can however be very costly. To obtain satisfactory statistics on a 1/1000y event, one needs to perform simulations over several thousands of years. Recently, a class of rare event simulation algorithms has been introduced that could yield significant increases in performance with respect to brute force simulations (see e.g. [1]). In these algorithms an ensemble of simulations is evolved in parallel, while at certain interaction times ensemble members are killed and cloned so as to have better statistics in the region of phase space that is relevant to the rare event of interest. We will discuss the implementational issues and performance gains for these algorithms. We also present results on a first application of a rare event simulation algorithm to a toy model for chaos in the atmosphere, the Lorenz 96 model. We demonstrate that for the estimation of the histogram tail of the energy observable, the algorithm gives a significant error reduction. We will furthermore discuss first results and an outlook on the application of rare event simulation algorithms to study blocking atmospheric circulation and heat wave events in the PlaSim climate model [2]. [1] Del Moral, P. & Garnier, J. Genealogical particle analysis of rare events. The Annals of Applied Probability 15, 2496-2534 (2005). [2] http://www.mi.uni-hamburg.de/Planet-Simul.216.0.html
Using collective variables to drive molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme
2013-12-01
A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.
Molecular dynamics simulation of threshold displacement energies in zircon
Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.
2009-10-15
Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different interatomic potentials. For each sublattice, the simulation was repeated from different initial conditions to estimate the uncertainty in the calculated value of Ed. The displacement threshold energies vary considerably with crystallographic direction and sublattice. The average displacement energy calculated with a recently developed transferable potential is about 120 and 60 eV for cations and anions, respectively. The oxygen displacement energy shows good agreement with experimental estimates in ceramics.
The very local Hubble flow: Computer simulations of dynamical history
NASA Astrophysics Data System (ADS)
Chernin, A. D.; Karachentsev, I. D.; Valtonen, M. J.; Dolgachev, V. P.; Domozhilova, L. M.; Makarov, D. I.
2004-02-01
The phenomenon of the very local (≤3 Mpc) Hubble flow is studied on the basis of the data of recent precision observations. A set of computer simulations is performed to trace the trajectories of the flow galaxies back in time to the epoch of the formation of the Local Group. It is found that the ``initial conditions'' of the flow are drastically different from the linear velocity-distance relation. The simulations enable one also to recognize the major trends of the flow evolution and identify the dynamical role of universal antigravity produced by the cosmic vacuum.
The architecture of Newton, a general-purpose dynamics simulator
NASA Technical Reports Server (NTRS)
Cremer, James F.; Stewart, A. James
1989-01-01
The architecture for Newton, a general-purpose system for simulating the dynamics of complex physical objects, is described. The system automatically formulates and analyzes equations of motion, and performs automatic modification of this system equations when necessitated by changes in kinematic relationships between objects. Impact and temporary contact are handled, although only using simple models. User-directed influence of simulations is achieved using Newton's module, which can be used to experiment with the control of many-degree-of-freedom articulated objects.
Simulating the Dynamic Coupling of Market and Physical System Operations
Widergren, Steven E.; Roop, Joseph M.; Guttromson, Ross T.; Huang, Zhenyu
2004-06-01
Abstract-As energy trading products cover shorter time periods and demand response programs move toward real-time pricing, financial market-based activity impacts ever more directly the physical operation of the system. To begin to understand the complex interactions between the market-driven operation signals, the engineered controlled schemes, and the laws of physics, new system modeling and simulation techniques must be explored. This discussion describes requirements for new simulation tools to address such market transaction control interactions and an approach to capture the dynamic coupling between energy markets and the physical operation of the power system appropriate for dispatcher reaction time frames.
Structural considerations for a software life cycle dynamic simulation model
NASA Technical Reports Server (NTRS)
Tausworthe, R. C.; Mckenzie, M.; Lin, C. Y.
1983-01-01
This paper presents the results of a preliminary study into the prospects for simulating the software implementation and maintenance life cycle process, with the aim of producing a computerized tool for use by management and software engineering personnel in project planning, tradeoff studies involving product, environmental, situational, and technological factors, and training. The approach taken is the modular application of a 'flow of resource' concept to the systems dynamics simulation modeling technique. The software life cycle process is represented as a number of stochastic, time-varying, interacting work tasks that each achieves one of the project milestones. Each task is characterized by the item produced, the personnel applied, and the budgetary profile.
Research of TREETOPS Structural Dynamics Controls Simulation Upgrade
NASA Technical Reports Server (NTRS)
Yates, Rose M.
1996-01-01
Under the provisions of contract number NAS8-40194, which was entitled 'TREETOPS Structural Dynamics and Controls Simulation System Upgrade', Oakwood College contracted to produce an upgrade to the existing TREETOPS suite of analysis tools. This suite includes the main simulation program, TREETOPS, two interactive preprocessors, TREESET and TREEFLX, an interactive post processor, TREEPLOT, and an adjunct program, TREESEL. A 'Software Design Document', which provides descriptions of the argument lists and internal variables for each subroutine in the TREETOPS suite, was established. Additionally, installation guides for both DOS and UNIX platforms were developed. Finally, updated User's Manuals, as well as a Theory Manual, were generated.
Simulating Hamiltonian dynamics with a truncated Taylor series.
Berry, Dominic W; Childs, Andrew M; Cleve, Richard; Kothari, Robin; Somma, Rolando D
2015-03-01
We describe a simple, efficient method for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. Our method can simulate the time evolution of a wide variety of physical systems. As in another recent algorithm, the cost of our method depends only logarithmically on the inverse of the desired precision, which is optimal. However, we simplify the algorithm and its analysis by using a method for implementing linear combinations of unitary operations together with a robust form of oblivious amplitude amplification. PMID:25793789
Dislocation dynamics simulations of plasticity at small scales
Zhou, Caizhi
2010-01-01
As metallic structures and devices are being created on a dimension comparable to the length scales of the underlying dislocation microstructures, the mechanical properties of them change drastically. Since such small structures are increasingly common in modern technologies, there is an emergent need to understand the critical roles of elasticity, plasticity, and fracture in small structures. Dislocation dynamics (DD) simulations, in which the dislocations are the simulated entities, offer a way to extend length scales beyond those of atomistic simulations and the results from DD simulations can be directly compared with the micromechanical tests. The primary objective of this research is to use 3-D DD simulations to study the plastic deformation of nano- and micro-scale materials and understand the correlation between dislocation motion, interactions and the mechanical response. Specifically, to identify what critical events (i.e., dislocation multiplication, cross-slip, storage, nucleation, junction and dipole formation, pinning etc.) determine the deformation response and how these change from bulk behavior as the system decreases in size and correlate and improve our current knowledge of bulk plasticity with the knowledge gained from the direct observations of small-scale plasticity. Our simulation results on single crystal micropillars and polycrystalline thin films can march the experiment results well and capture the essential features in small-scale plasticity. Furthermore, several simple and accurate models have been developed following our simulation results and can reasonably predict the plastic behavior of small scale materials.
Kramer, Manuel; Ellmann, Stephan; Allmendinger, Thomas; Eller, Achim; Kammerer, Ferdinand; May, Matthias S; Baigger, João F; Uder, Michael; Lell, Michael M
2015-07-01
Computed tomography angiography (CTA) of carotid arteries and vertebrobasilar system is a standardized procedure with excellent image quality, but radiation exposure remains a matter of concern. The aim of this study is to examine to what extent radiation dose can be lowered in relation to a standard protocol by simulating examinations with lower tube currents applying a dedicated software.Lower tube current was simulated by a dedicated noise insertion and reconstruction software (ReconCT). In a phantom study, true scans were performed with different dose protocols and compared to the results of simulated dose reductions of the same degree, respectively. In a patient study, 30 CTAs of supra-aortic vessels were reconstructed at a level of 100%, 75%, 50%, and 25% of the initial dose. Objective and subjective image analyses were performed.No significant noise differences between true scans and simulated scans of mimicked contrasted vessels were found. In the patient study, the quality scores of the 4 dose groups differed statistically significant; this difference vanished for the comparison of the 100% and 75% datasets after dichotomization into the categories of diagnostic and nondiagnostic image quality (P = .50).This study suggests an easy-to-implement method of simulating CTAs of carotid arteries and vertebrobasilar system with lower tube current for dose reduction by artificially adding noise to the original raw data. Lowering the radiation dose in a moderate extent to 75% of the original dose levels does not significantly alter the diagnostic image quality. PMID:26131822
Chiavazzo, Eliodoro; Karlin, Iliya V.; Gorban, Alexander N.; Boulouchos, Konstantinos
2010-10-15
A new framework of simulation of reactive flows is proposed based on a coupling between accurate reduced reaction mechanism and the lattice Boltzmann representation of the flow phenomena. The model reduction is developed in the setting of slow invariant manifold construction, and the simplest lattice Boltzmann equation is used in order to work out the procedure of coupling of the reduced model with the flow solver. Practical details of constructing slow invariant manifolds of a reaction system under various thermodynamic conditions are reported. The proposed method is validated with the two-dimensional simulation of a premixed counterflow flame in the hydrogen-air mixture. (author)
Stiffness detection and reduction in discrete stochastic simulation of biochemical systems
NASA Astrophysics Data System (ADS)
Pu, Yang; Watson, Layne T.; Cao, Yang
2011-02-01
Typical multiscale biochemical models contain fast-scale and slow-scale reactions, where "fast" reactions fire much more frequently than "slow" ones. This feature often causes stiffness in discrete stochastic simulation methods such as Gillespie's algorithm and the Tau-Leaping method leading to inefficient simulation. This paper proposes a new strategy to automatically detect stiffness and identify species that cause stiffness for the Tau-Leaping method, as well as two stiffness reduction methods. Numerical results on a stiff decaying dimerization model and a heat shock protein regulation model demonstrate the efficiency and accuracy of the proposed methods for multiscale biochemical systems.
Dislocation dynamics: simulation of plastic flow of bcc metals
Lassila, D H
2001-02-20
This is the final report for the LDRD strategic initiative entitled ''Dislocation Dynamic: Simulation of Plastic Flow of bcc Metals'' (tracking code: 00-SI-011). This report is comprised of 6 individual sections. The first is an executive summary of the project and describes the overall project goal, which is to establish an experimentally validated 3D dislocation dynamics simulation. This first section also gives some information of LLNL's multi-scale modeling efforts associated with the plasticity of bcc metals, and the role of this LDRD project in the multiscale modeling program. The last five sections of this report are journal articles that were produced during the course of the FY-2000 efforts.
Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.
Omelyan, I P
2006-09-01
A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations. PMID:17025782
Molecular dynamics simulation of radiation damage cascades in diamond
Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.
2015-06-28
Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.
Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics
NASA Astrophysics Data System (ADS)
Alekseeva, Uliana; Winkler, Roland G.; Sutmann, Godehard
2016-06-01
A new adaptive resolution technique for particle-based multi-level simulations of fluids is presented. In the approach, the representation of fluid and solvent particles is changed on the fly between an atomistic and a coarse-grained description. The present approach is based on a hybrid coupling of the multiparticle collision dynamics (MPC) method and molecular dynamics (MD), thereby coupling stochastic and deterministic particle-based methods. Hydrodynamics is examined by calculating velocity and current correlation functions for various mixed and coupled systems. We demonstrate that hydrodynamic properties of the mixed fluid are conserved by a suitable coupling of the two particle methods, and that the simulation results agree well with theoretical expectations.
Annihilation of craters: Molecular dynamic simulations on a silver surface
Henriksson, K. O. E.; Nordlund, K.; Keinonen, J.
2007-12-15
The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.
Molecular Dynamics Simulations of Phospholipid Bilayers with Cholesterol
Hofsäß, Christofer; Lindahl, Erik; Edholm, Olle
2003-01-01
To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0–40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations—corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols. PMID:12668428
Dynamic simulation of shell-and-tube heat exchangers
Correa, D.J.; Marchetti, J.L.
1987-01-01
The transient operation of a multipass shell-and-tube heat exchanger with baffles is described by a multicell dynamic model where every cell represents a specific part of the exchanger. The proposed modeling technique can be used in a digital computer for the dynamic simulation of almost any type of shell-and-tube heat exchanger. The model includes time-dependent inlet conditions for both the cold and the hot streams. Hence, a number of start-up cases can be simulated and, once the system reaches a stationary operating point, a disturbance can be introduced in the inlet temperatures or the flow rates. This particular feature makes the model very useful not only for design purposes but also for transient analysis and control system design.
Molecular dynamics simulations of dislocation instability in a stress gradient
NASA Astrophysics Data System (ADS)
Li, Ming; Selinger, Robin L.
2003-04-01
We present simulation studies of a morphological instability arising in dislocation dynamics. When an initially straight dislocation line is driven by a stress whose magnitude grows along the direction of dislocation motion, vibrational modes of the dislocation line with wavelength above a threshold value become linearly unstable. Molecular dynamics simulation studies of screw dislocations in Al demonstrate the onset of the instability during dislocation pair annihilation and annihilation at a crack tip. The wavelength of the unstable vibrational mode observed in each case agrees with the predictions of theoretical analysis. We discuss the role of temperature in nucleating the instability and speculate about how instabilities in dislocation motion could affect the density of threading dislocations during growth of heteroepitaxial thin films.
Time series analysis of molecular dynamics simulation using wavelet
NASA Astrophysics Data System (ADS)
Toda, Mikito
2012-08-01
A new method is presented to extract nonstationary features of slow collective motion toward time series data of molecular dynamics simulation for proteins. The method consists of the following two steps: (1) the wavelet transformation and (2) the singular value decomposition (SVD). The wavelet transformation enables us to characterize time varying features of oscillatory motions and SVD enables us to reduce the degrees of freedom of the movement. We apply the method to molecular dynamics simulation of various proteins such as Adenylate Kinase from Escherichia coli (AKE) and Thermomyces lanuginosa lipase (TLL). Moreover, we introduce indexes to characterize collective motion of proteins. These indexes provide us with information of nonstationary deformation of protein structures. We discuss future prospects of our study involving "intrinsically disordered proteins".
Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics.
Petsev, Nikolai D; Leal, L Gary; Shell, M Scott
2016-02-28
Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales. PMID:26931689
Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2016-02-01
Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales.
The role of dynamic simulation in pipeline field applications
Chiu, K.C.; Kakka, R.S.
1998-12-31
In gas transmission pipeline and oil/gas field applications, gas compression is a key operation. Knowledge of the behavior of a gas compression system during upset conditions is required to evaluate the proposed compressor anti-surge control system, gas relief safety system and any future expansion and modifications. Dynamic simulation is a good engineering tool for such analyses. In this paper, a gas compression system is modeled which consists of eight identical parallel export compressors cascaded to four identical parallel reinjection compressors. The results of dynamic simulation for various what if scenarios are presented., The peak pressure of each header and amount of relieved gas were evaluated for the gas relief safety system. The surge margin of each compressor and other pertinent variables were analyzed for the compressor anti-surge control system.
Description of ferrocenylalkylthiol SAMs on gold by molecular dynamics simulations.
Goujon, F; Bonal, C; Limoges, B; Malfreyt, P
2009-08-18
Molecular dynamics simulations of mixed monolayers consisting of Fc(CH2)12S-/C10S-Au SAMs are carried out to calculate structural (density profiles, angular distributions, positions of atoms) and energetic properties. The purpose of this paper is to explore the possible inhomogeneity of the neutral ferrocene moieties within the monolayer. Five systems have been studied using different grafting densities for the ferrocenylalkylthiolates. The angular distributions are described in terms of the relative contributions from isolated and clustered ferrocene moieties in the binary SAMs. It is shown that the energetic contributions strongly depend on the state of the ferrocene. The ability of molecular dynamics simulations to enable better understanding the SAM structure is illustrated in this work. PMID:19449821
A review of the analytical simulation of aircraft crash dynamics
NASA Technical Reports Server (NTRS)
Fasanella, Edwin L.; Carden, Huey D.; Boitnott, Richard L.; Hayduk, Robert J.
1990-01-01
A large number of full scale tests of general aviation aircraft, helicopters, and one unique air-to-ground controlled impact of a transport aircraft were performed. Additionally, research was also conducted on seat dynamic performance, load-limiting seats, load limiting subfloor designs, and emergency-locator-transmitters (ELTs). Computer programs were developed to provide designers with methods for predicting accelerations, velocities, and displacements of collapsing structure and for estimating the human response to crash loads. The results of full scale aircraft and component tests were used to verify and guide the development of analytical simulation tools and to demonstrate impact load attenuating concepts. Analytical simulation of metal and composite aircraft crash dynamics are addressed. Finite element models are examined to determine their degree of corroboration by experimental data and to reveal deficiencies requiring further development.
Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining
NASA Astrophysics Data System (ADS)
Khasin, M.; Kosloff, R.
2010-04-01
An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables—the elements of the spectrum-generating algebra—is simulated by a surrogate open-system dynamics, which can be interpreted as weak measurement of the target observables, performed on the evolving system. The open-system state can be represented by a mixture of pure states, localized in the phase space. The localization reduces the scaling of the computational resources with the Hilbert-space dimension n by factor n3/2(lnn)-1 compared to conventional sparse-matrix methods. The guidelines for the choice of parameters for the simulation are presented and the scaling of the computational resources with the Hilbert-space dimension of the system is estimated. The algorithm is applied to the simulation of the dynamics of systems of 2×104 and 2×106 cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.
The Dynamics of Simulated Convective Storms in Hurricane Environments.
NASA Astrophysics Data System (ADS)
McCaul, Eugene Williamson, Jr.
Numerical simulations of convection in selected hurricane environments show that supercell storms are possible, even when buoyancy is relatively small. In one simulated supercell, the dynamic pressure force is found to reach a maximum about three times as strong as that of buoyancy in the late stages of the simulation. Updrafts reach peak intensity at low levels, often around 2-3 km AGL, and may exceed magnitudes expected from consideration of moist CAPE alone. Interactions between updraft and ambient vertical shear, and, later, growing contributions from vorticity, appear to dominate the development of the dynamic pressure field. Although the weak buoyancy tends to restrict storm intensity, a favorable matching of the vertical distribution of buoyancy with that of the vertical shear allows the pressure forces to become strong enough to take up the slack. Terms in the disturbance kinetic energy budget are correspondingly more strongly influenced by pressure effects than by buoyancy. Although the simulated supercells display the very strong, organized rotation characteristic of tornadic storms, many of the multicell storms which appear in the simulations also contain local concentrations of vorticity intense enough to suggest tornado potential. Simulations with differing background rotation (Coriolis) rates "f" show that convection which was multicellular at low f can become supercellular at higher f. The enhanced vertical vorticity that develops naturally in decaying tropical cyclones when angular momentum disperses under the influence of weakening pressure gradients may, by analogy, help explain why dissipating tropical cyclones are an especially fertile breeding ground for tornadic storms. Test simulations in which surface drag and a slightly modified subgrid mixing formulation were used show that the details of storm behavior can be quite sensitive to changes in these model parameters, although updraft and vorticity statistics are not altered greatly. In general
Flexing computational muscle: modeling and simulation of musculotendon dynamics.
Millard, Matthew; Uchida, Thomas; Seth, Ajay; Delp, Scott L
2013-02-01
Muscle-driven simulations of human and animal motion are widely used to complement physical experiments for studying movement dynamics. Musculotendon models are an essential component of muscle-driven simulations, yet neither the computational speed nor the biological accuracy of the simulated forces has been adequately evaluated. Here we compare the speed and accuracy of three musculotendon models: two with an elastic tendon (an equilibrium model and a damped equilibrium model) and one with a rigid tendon. Our simulation benchmarks demonstrate that the equilibrium and damped equilibrium models produce similar force profiles but have different computational speeds. At low activation, the damped equilibrium model is 29 times faster than the equilibrium model when using an explicit integrator and 3 times faster when using an implicit integrator; at high activation, the two models have similar simulation speeds. In the special case of simulating a muscle with a short tendon, the rigid-tendon model produces forces that match those generated by the elastic-tendon models, but simulates 2-54 times faster when an explicit integrator is used and 6-31 times faster when an implicit integrator is used. The equilibrium, damped equilibrium, and rigid-tendon models reproduce forces generated by maximally-activated biological muscle with mean absolute errors less than 8.9%, 8.9%, and 20.9% of the maximum isometric muscle force, respectively. When compared to forces generated by submaximally-activated biological muscle, the forces produced by the equilibrium, damped equilibrium, and rigid-tendon models have mean absolute errors less than 16.2%, 16.4%, and 18.5%, respectively. To encourage further development of musculotendon models, we provide implementations of each of these models in OpenSim version 3.1 and benchmark data online, enabling others to reproduce our results and test their models of musculotendon dynamics. PMID:23445050
Numerical simulation on the reduction of flow heterogeneity in the biofilter media
NASA Astrophysics Data System (ADS)
Yan, Weiwei; Liu, Xingli; Wu, Jie; Wei, Yikun; Xu, Peng
2016-02-01
The biofilters are the ideal solutions for the biological treatment of air pollutants. However, there exists strong flow heterogeneity in porous media that degrades the removal efficiency of biofilters. Thus, the effects of Darcy number, Reynolds number and porosity of porous media on the reduction of flow heterogeneity in three biofilter models were numerically studied by the lattice Boltzmann method. The simulation results lead to three conclusions: (1) The Darcy number has dominant influence on the flow heterogeneity in the biofilters. The reduction of flow heterogeneity can be realized by designing a comparatively low Darcy number. (2) The Reynolds number has obvious effect on the flow heterogeneity in the biofilters. However, the reduction of flow heterogeneity cannot be effectively established by regulating the Reynolds number. (3) The property of porous media greatly influences the flow heterogeneity in the biofilters. The present results are helpful for the optimized design of practical biofilter models.
Applying Parallel Processing Techniques to Tether Dynamics Simulation
NASA Technical Reports Server (NTRS)
Wells, B. Earl
1996-01-01
The focus of this research has been to determine the effectiveness of applying parallel processing techniques to a sizable real-world problem, the simulation of the dynamics associated with a tether which connects two objects in low earth orbit, and to explore the degree to which the parallelization process can be automated through the creation of new software tools. The goal has been to utilize this specific application problem as a base to develop more generally applicable techniques.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
NASA Astrophysics Data System (ADS)
Rapaport, D. C.
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Molecular dynamics simulations on PGLa using NMR orientational constraints.
Sternberg, Ulrich; Witter, Raiker
2015-11-01
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide. PMID:26358333
Simulation of dynamic material response with the PAGOSA code
Holian, K.S.; Adams, T.F.
1993-08-01
The 3D Eulerian PAGOSA hydrocode is being run on the massively parallel Connection Machine (CM) to simulate the response of materials to dynamic loading, such as by high explosives or high velocity impact. The code has a variety of equation of state forms, plastic yield models, and fracture and fragmentation models. The numerical algorithms in PAGOSA and the implementation of material models are discussed briefly.
Simulated dynamic response of a servovalve controlled hydraulic actuator
NASA Technical Reports Server (NTRS)
Babcock, Dale A.
1990-01-01
A general purpose math model of a servovalve controlled hydraulic actuator system is derived. The system consists of a linear actuator with unequal piston areas, a single stage servovalve, a gas charged hydraulic accumulator, and the interconnecting piping. The state equations are integrated using the Advanced Continuous Simulation Language (ACSL) for determining the system's dynamic response characteristics. Using this generalized hydraulic actuator system model, response characteristics were determined for various servovalve commands.
Simulating market dynamics: interactions between consumer psychology and social networks.
Janssen, Marco A; Jager, Wander
2003-01-01
Markets can show different types of dynamics, from quiet markets dominated by one or a few products, to markets with continual penetration of new and reintroduced products. In a previous article we explored the dynamics of markets from a psychological perspective using a multi-agent simulation model. The main results indicated that the behavioral rules dominating the artificial consumer's decision making determine the resulting market dynamics, such as fashions, lock-in, and unstable renewal. Results also show the importance of psychological variables like social networks, preferences, and the need for identity to explain the dynamics of markets. In this article we extend this work in two directions. First, we will focus on a more systematic investigation of the effects of different network structures. The previous article was based on Watts and Strogatz's approach, which describes the small-world and clustering characteristics in networks. More recent research demonstrated that many large networks display a scale-free power-law distribution for node connectivity. In terms of market dynamics this may imply that a small proportion of consumers may have an exceptional influence on the consumptive behavior of others (hubs, or early adapters). We show that market dynamics is a self-organized property depending on the interaction between the agents' decision-making process (heuristics), the product characteristics (degree of satisfaction of unit of consumption, visibility), and the structure of interactions between agents (size of network and hubs in a social network). PMID:14761255
Long-time dynamics of Met-enkephalin: comparison of theory with Brownian dynamics simulations.
Kostov, K S; Freed, K F
1999-01-01
A recent theory for the long time dynamics of flexible chain molecules is applied for the first time to a peptide of biological importance, the neurotransmitter met-enkephalin. The dynamics of met-enkephalin is considerably more complicated than that of the previously studied glycine oligomers; met-enkephalin contains the interesting motions of phenyl groups and of side chains relative to the backbone, motions that are present in general flexible peptides. The theory extends the generalized Rouse (GR) model used to study the dynamics of polymers by providing a systematic procedure for including the contributions from the memory function matrices neglected in the GR theory. The new method describes the dynamics by time correlation functions instead of individual trajectories. These correlation functions are analytically expressed in terms of a set of equilibrium averages and the eigenvalues and eigenfunctions of the diffusion operator. The predictions of the theory are compared with Brownian dynamics (BD) simulations, so that both theory and simulation use identical potential functions and solvent models. The theory thus contains no adjustable parameters. Inclusion of the memory function contributions profoundly affects the dynamics. The theory produces very good agreement with the BD simulations for the global motions of met-enkephalin. It also correctly predicts the long-time relaxation rate for local motions. PMID:9876130
NASA Astrophysics Data System (ADS)
Dillon, James E.; Schildkraut, Elliot Robert; Silk, J. K.; Kitajewski, L.; Martin, Robert A.; Woolhouse, Geoffrey R.
1990-09-01
This paper addresses the development of an Infrared Scene Simulator for Hardware-in-the-loop simulation of tactical IR air-to-air missile seekers. The simulator uses infrared target and background images produced by several technologies which are optically combined, collimated, and presented to the seeker under test. The system is configured for use on an optical bench but could also be hardened for flight simulator mounting. The high radiance target images of the air-to-air engagement scenarios are generated using high temperature blackbody sources and iris targets in the form of geometric figures with the size under servo control. The targets use an X-Y translation slide and dynamic attenuator to simulate movement within the field of view, range closure and the attenuation effects of the atmosphere. These targets are used to generate the aircraft tailpipe and flare decoy images required by the simulation. The high radiance targets are combined with the image from a Multiple Dynamic Simulator-Infrared Emitter Array which produces the engine plume, aircraft fuselage and background image. The three targets are combined using two beamsplitters and the composite image is collimated and relayed to the seeker under test. A workstation-based computational system generates the array image for display in real time.
NASA Astrophysics Data System (ADS)
Kalbacher, T.; Jang, E.; He, W.; Savoy, H.; Schueth, C.; Kolditz, O.
2015-12-01
Nitrate reduction reactions, as one of the most important redox reactions in a subsurface system, are strongly influenced by various heterogeneity factors which influence transport of chemical species and spatial distribution of redox substances and consequently have an effect on overall nitrate reduction capacity. In this presented work, the influence of two heterogeneity factors, spatially heterogeneity of hydrological parameters versus spatial heterogeneity of geochemical reactive substances distribution, are discussed with a focus on nitrate transport and redox transformation processes. For this purpose, a coupling interface OGS#IPhreeqc is employed. This code combines Finite-Element groundwater flow and multi-species transport code of OpenGeoSys (OGS) with the IPhreeqc module of open source geochemical solver PHREEQC. The resulting coupled model is applied for simulation of nitrate reduction processes with a series of hypothetical aquifer systems, built using exponentially-correlated log-normal distributed hydraulic conductivity and reactive substances. The spatially heterogeneous aquifer system is realized by a RandomFields package using a statistical program R. Results show that the heterogeneous hydraulics conductivity field has larger impact on nitrate reduction capacity than heterogeneous reactive substances distribution. Moreover, nitrate reduction capacity can be increased by enhanced mixing in heterogeneous hydraulic conductivity field however its overall reduction capacity has gradually decreased as a degree of heterogeneity has increased since accessibility of the chemical species by the reactive substances may be limited. These results support that appropriate characterization of the variance of hydraulic conductivity within the aquifer is important to predict contaminant fate and transport and quantify the impact of uncertainty on numerical groundwater simulation.
Direct identification of predator-prey dynamics in gyrokinetic simulations
Kobayashi, Sumire Gürcan, Özgür D; Diamond, Patrick H.
2015-09-15
The interaction between spontaneously formed zonal flows and small-scale turbulence in nonlinear gyrokinetic simulations is explored in a shearless closed field line geometry. It is found that when clear limit cycle oscillations prevail, the observed turbulent dynamics can be quantitatively captured by a simple Lotka-Volterra type predator-prey model. Fitting the time traces of full gyrokinetic simulations by such a reduced model allows extraction of the model coefficients. Scanning physical plasma parameters, such as collisionality and density gradient, it was observed that the effective growth rates of turbulence (i.e., the prey) remain roughly constant, in spite of the higher and varying level of primary mode linear growth rates. The effective growth rate that was extracted corresponds roughly to the zonal-flow-modified primary mode growth rate. It was also observed that the effective damping of zonal flows (i.e., the predator) in the parameter range, where clear predator-prey dynamics is observed, (i.e., near marginal stability) agrees with the collisional damping expected in these simulations. This implies that the Kelvin-Helmholtz-like instability may be negligible in this range. The results imply that when the tertiary instability plays a role, the dynamics becomes more complex than a simple Lotka-Volterra predator prey.
Molecular dynamics simulation of liquid water: Hybrid density functionals
Todorova, T; Seitsonen, A; Hutter, J; Kuo, W; Mundy, C
2005-09-12
The structure, dynamical and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta functional, four gradient corrected functionals, the local density and Hartree-Fock approximation. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and under-structured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller averaged numbers of hydrogen bonds and similar hydrogen bond populations as pure density functionals. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than from the corresponding pure density functionals.
Direct identification of predator-prey dynamics in gyrokinetic simulations
NASA Astrophysics Data System (ADS)
Kobayashi, Sumire; Gürcan, Özgür D.; Diamond, Patrick H.
2015-09-01
The interaction between spontaneously formed zonal flows and small-scale turbulence in nonlinear gyrokinetic simulations is explored in a shearless closed field line geometry. It is found that when clear limit cycle oscillations prevail, the observed turbulent dynamics can be quantitatively captured by a simple Lotka-Volterra type predator-prey model. Fitting the time traces of full gyrokinetic simulations by such a reduced model allows extraction of the model coefficients. Scanning physical plasma parameters, such as collisionality and density gradient, it was observed that the effective growth rates of turbulence (i.e., the prey) remain roughly constant, in spite of the higher and varying level of primary mode linear growth rates. The effective growth rate that was extracted corresponds roughly to the zonal-flow-modified primary mode growth rate. It was also observed that the effective damping of zonal flows (i.e., the predator) in the parameter range, where clear predator-prey dynamics is observed, (i.e., near marginal stability) agrees with the collisional damping expected in these simulations. This implies that the Kelvin-Helmholtz-like instability may be negligible in this range. The results imply that when the tertiary instability plays a role, the dynamics becomes more complex than a simple Lotka-Volterra predator prey.
NETL's IGCC Dynamic Simulator Reserach and Training Center
Erbes, M.; Zitney, S.
2008-01-01
The National Energy Technology Laboratory (NETL) is collaborating with software, industry, and university partners to establish a world-class Dynamic Simulator Research and Training (DSR&T) Center dedicated to the operation and control of advanced energy plants with carbon capture capabilities. The DSR&T Center will offer a collaborative R&D program and comprehensive hands-on training built around a portfolio of non-proprietary, high-fidelity, real-time dynamic simulators. The simulators will provide full-scope operator training system (OTS) capabilities for normal and faulted operations, as well as plant start-up, shutdown, and load following. Immersive three-dimensional (3-D) virtual reality will add another dimension of realism to the dynamic OTS systems and extend the training scope to both control room and outside operators, allowing them to work as a team. The benefits of high-fidelity immersive training systems (ITS) include more realistic training scenarios, improved communication and collaboration among work crews, off-line evaluations of procedures, and training for safety-critical tasks and rare abnormal situations.
Surface Diffusion of Single Polymer Chain Using Molecular Dynamics SIMULATION*
NASA Astrophysics Data System (ADS)
Desai, Tapan; Keblinski, Pawel; Kumar, Sanat; Granick, Steve
2004-05-01
Results of recent experiments on polymer chains adsorbed from dilute solution at solid-liquid interface show the power scaling law dependence of the chain diffusivity, D, as a function of the degree of polymerization, N, D ˜ N^3/2. By contrast, DNA molecules bound to fluid cationic lipid bilayers follows Rouse dynamics with D ˜ N^1. We used molecular dynamics simulations to gain an understanding of these dissimilar scaling behaviors. Our model systems contain chains comprised of N monomers connected by anharmonic springs described by the finite extendible nonlinear elastic, FENE potential, embedded into a solvent of N=1 monomers. Two types of simulations we performed: (i) the chain is confined to two dimensions, (ii) the three dimensional chain in the solvent is confined between two solids plates. With randomly placed impenetrable obstacles on the surface, the diffusion of 2D chains exhibits, D ˜ N^3/2 behavior, when the chain radius of gyration, Rg, is larger than half the distance between obstacles, and D ˜ N^1 for shorter chains. In the presence of an athermal solvent, the scaling exponent is 0.75 due to hydrodynamic forces, for the two-dimensional system. We will also discuss the nature of dynamic adsorption transition and effects of hydrodynamics forces on chain diffusion for the three-dimensional simulations.
Simulation of flood reduction by natural river rehabilitation using a distributed hydrological model
NASA Astrophysics Data System (ADS)
Liu, Y. B.; Gebremeskel, S.; de Smedt, F.; Hoffmann, L.; Pfister, L.
The effects of river rehabilitation on flood reduction in the Steinsel sub-basin of the Alzette River basin, Grand-Duchy of Luxembourg, are discussed; the rehabilitation measures include planting and changing riparian and in-stream vegetation, and re-meandering of channelised reaches, etc. in the headwater streams. To simulate flood reduction by river rehabilitation, the streams have been classified into different orders and by assessing the response of the stream channels to the resistance or obstruction of flows. Based on this assessment, the roughness to the flow in the first and second order streams is adjusted in line with the river rehabilitation while the roughness of higher order channels downstream is unchanged. The hydrological analysis utilises the WetSpa distributed model based on spatial information on topography, soil type and land use. The increased channel roughness in the headwater channels delays the flows, so that peak discharges at the outlet of the basin are reduced. The simulation indicates that, after river naturalisation, the reduction in peak flow can be as much as 14% and the time of concentration may be delayed by as much as two hours. Also, an impact analysis has assessed the possible flood reduction for a changed climate scenario.
Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.
Tavernelli, Ivano
2015-03-17
Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics
Reweighted ensemble dynamics simulations: Theory, improvement, and application
NASA Astrophysics Data System (ADS)
Gong, Lin-Chen; Zhou, Xin; Ouyang, Zhong-Can
2015-06-01
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provide schemes on selection of basis functions, and determination of the free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enables us to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in an entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems. Project supported by the National Natural Science Foundation of China (Grant No. 11175250).
Dynamic mixing in magma bodies - Theory, simulations, and implications
NASA Technical Reports Server (NTRS)
Oldenburg, Curtis M.; Spera, Frank J.; Yuen, David A.; Sewell, Granville
1989-01-01
The magma-mixing process is different from the mantle mixing process in that the mixing components of magma are dynamically active, with the melt density depending strongly on composition. This paper describes simulations of time-dependent variable-viscosity double-diffusive convection which were carried out to investigate quantitatively the mixing dynamics of magma in melt-dominated magma bodies. Results show that the dynamics of double-diffusive convection can impart complex patterns of composition, through time and space. The mixing time depends nonlinearly on many factors, including heat flux driving convection, the rate of diffusion of chemical species, the relative importance of thermal and chemical buoyancy, the viscosities of the mixing components, and the shape of the magma body.
The dynamic response of a viscoelastic biological tissue simulant
NASA Astrophysics Data System (ADS)
Shepherd, Christopher; Appleby-Thomas, Gareth; Hazell, Paul; Allsop, Derek
2009-06-01
The development and optimisation of new projectiles requires comparative techniques to assess ballistic performance. Porcine gelatin has found a substantial niche in the ballistics community as a tissue mimic. Primarily due to its elasticity, gelatin has been shown to deform in a similar manner to biological tissues. Bullet impacts typically occur in the 350-850 m/s range and consequently, knowledge of the high strain rate dynamic properties of both the projectile constituents and target materials is desirable if simulations are to allow the optimisation of projectile design. A large body of knowledge exists on the dynamic properties of projectiles, however relatively little data exists in the literature on the dynamic response of flesh simulants. The Hugoniot for a 20 wt% porcine gelatin, which exhibits a ballistic response similar to that of human tissues at room temperature, is determined in this paper using the plate impact technique. Up-Us and Up-P relationships are determined for impact velocities in the range of 200-900 m/s. Good agreement with the limited available data from the literature for similar concentrations is found and the dynamic response established at impact stresses up to 3 times higher than that observed elsewhere. Additionally, high frequency elastic properties are investigated using ultrasound and compared to those observed elsewhere.
Detailed Multidimensional Simulations of the Structure and Dynamics of Flames
NASA Technical Reports Server (NTRS)
Patnaik, G.; Kailasanath, K.
1999-01-01
Numerical simulations in which the various physical and chemical processes can be independently controlled can significantly advance our understanding of the structure, stability, dynamics and extinction of flames. Therefore, our approach has been to use detailed time-dependent, multidimensional, multispecies numerical models to perform carefully designed computational experiments of flames on Earth and in microgravity environments. Some of these computational experiments are complementary to physical experiments performed under the Microgravity Program while others provide a fundamental understanding that cannot be obtained from physical experiments alone. In this report, we provide a brief summary of our recent research highlighting the contributions since the previous microgravity combustion workshop. There are a number of mechanisms that can cause flame instabilities and result in the formation of dynamic multidimensional structures. In the past, we have used numerical simulations to show that it is the thermo-diffusive instability rather than an instability due to preferential diffusion that is the dominant mechanism for the formation of cellular flames in lean hydrogen-air mixtures. Other studies have explored the role of gravity on flame dynamics and extinguishment, multi-step kinetics and radiative losses on flame instabilities in rich hydrogen-air flames, and heat losses on burner-stabilized flames in microgravity. The recent emphasis of our work has been on exploring flame-vortex interactions and further investigating the structure and dynamics of lean hydrogen-air flames in microgravity. These topics are briefly discussed after a brief discussion of our computational approach for solving these problems.
Two-Speed Gearbox Dynamic Simulation Predictions and Test Validation
NASA Technical Reports Server (NTRS)
Lewicki, David G.; DeSmidt, Hans; Smith, Edward C.; Bauman, Steven W.
2010-01-01
Dynamic simulations and experimental validation tests were performed on a two-stage, two-speed gearbox as part of the drive system research activities of the NASA Fundamental Aeronautics Subsonics Rotary Wing Project. The gearbox was driven by two electromagnetic motors and had two electromagnetic, multi-disk clutches to control output speed. A dynamic model of the system was created which included a direct current electric motor with proportional-integral-derivative (PID) speed control, a two-speed gearbox with dual electromagnetically actuated clutches, and an eddy current dynamometer. A six degree-of-freedom model of the gearbox accounted for the system torsional dynamics and included gear, clutch, shaft, and load inertias as well as shaft flexibilities and a dry clutch stick-slip friction model. Experimental validation tests were performed on the gearbox in the NASA Glenn gear noise test facility. Gearbox output speed and torque as well as drive motor speed and current were compared to those from the analytical predictions. The experiments correlate very well with the predictions, thus validating the dynamic simulation methodologies.
Dynamic risk simulation to assess natural hazards risk along roads
NASA Astrophysics Data System (ADS)
Voumard, J.; Caspar, O.; Derron, M.-H.; Jaboyedoff, M.
2013-11-01
Risk generated by natural hazards on roads is usually calculated with equations integrating various parameters related to hazard and traffic. These are static variables, like an average number of vehicles crossing this section every day and an average vehicle speed. This methodology cannot take into account dynamic variations of traffic and interactions between vehicles such as speed modifications due to windy roads, slowdowns resulting from saturated traffic or vehicle tailbacks forming in front of traffic lights. Here we show, by means of a dynamic traffic simulator, that traffic variations may greatly influence the risk estimation over time. The risk is analysed on several sections of an Alpine road in Switzerland using a dynamic vehicles approach, and compared with the results of the static methodology. It demonstrates that risk can significantly increase on sinuous sections because of decreasing vehicle speed. For example, along an 800 m-long section of road containing two hairpin bends, the dynamic risk is about 50% higher than the static one. Badly placed signalization, slowing down, or stopping the vehicles in a hazardous area may increase the risk by about 150% (i.e. 2.5 times higher) along a straight road section where vehicles speed is high. A more realistic risk can thus be obtained from a dynamic approach, especially on mountain roads. The dynamic traffic simulator developed for this work appears to be a helpful tool to support decision-making in reducing risk on mountain roads and it shows the importance of keeping the traffic moving as freely as possible.
Method for simulating dose reduction in digital mammography using the Anscombe transformation
Borges, Lucas R.; de Oliveira, Helder C. R.; Nunes, Polyana F.; Bakic, Predrag R.; Maidment, Andrew D. A.; Vieira, Marcelo A. C.
2016-01-01
Purpose: This work proposes an accurate method for simulating dose reduction in digital mammography starting from a clinical image acquired with a standard dose. Methods: The method developed in this work consists of scaling a mammogram acquired at the standard radiation dose and adding signal-dependent noise. The algorithm accounts for specific issues relevant in digital mammography images, such as anisotropic noise, spatial variations in pixel gain, and the effect of dose reduction on the detective quantum efficiency. The scaling process takes into account the linearity of the system and the offset of the detector elements. The inserted noise is obtained by acquiring images of a flat-field phantom at the standard radiation dose and at the simulated dose. Using the Anscombe transformation, a relationship is created between the calculated noise mask and the scaled image, resulting in a clinical mammogram with the same noise and gray level characteristics as an image acquired at the lower-radiation dose. Results: The performance of the proposed algorithm was validated using real images acquired with an anthropomorphic breast phantom at four different doses, with five exposures for each dose and 256 nonoverlapping ROIs extracted from each image and with uniform images. The authors simulated lower-dose images and compared these with the real images. The authors evaluated the similarity between the normalized noise power spectrum (NNPS) and power spectrum (PS) of simulated images and real images acquired with the same dose. The maximum relative error was less than 2.5% for every ROI. The added noise was also evaluated by measuring the local variance in the real and simulated images. The relative average error for the local variance was smaller than 1%. Conclusions: A new method is proposed for simulating dose reduction in clinical mammograms. In this method, the dependency between image noise and image signal is addressed using a novel application of the Anscombe
Numerical simulation of landfill aeration using computational fluid dynamics.
Fytanidis, Dimitrios K; Voudrias, Evangelos A
2014-04-01
The present study is an application of Computational Fluid Dynamics (CFD) to the numerical simulation of landfill aeration systems. Specifically, the CFD algorithms provided by the commercial solver ANSYS Fluent 14.0, combined with an in-house source code developed to modify the main solver, were used. The unsaturated multiphase flow of air and liquid phases and the biochemical processes for aerobic biodegradation of the organic fraction of municipal solid waste were simulated taking into consideration their temporal and spatial evolution, as well as complex effects, such as oxygen mass transfer across phases, unsaturated flow effects (capillary suction and unsaturated hydraulic conductivity), temperature variations due to biochemical processes and environmental correction factors for the applied kinetics (Monod and 1st order kinetics). The developed model results were compared with literature experimental data. Also, pilot scale simulations and sensitivity analysis were implemented. Moreover, simulation results of a hypothetical single aeration well were shown, while its zone of influence was estimated using both the pressure and oxygen distribution. Finally, a case study was simulated for a hypothetical landfill aeration system. Both a static (steadily positive or negative relative pressure with time) and a hybrid (following a square wave pattern of positive and negative values of relative pressure with time) scenarios for the aeration wells were examined. The results showed that the present model is capable of simulating landfill aeration and the obtained results were in good agreement with corresponding previous experimental and numerical investigations. PMID:24525420
Simulation laboratory for evaluating dynamic traffic management systems
Ban-Akiva, M.E.; Mishalani, R.G.; Yang, Q.; Koutsopoulos, H.N.
1997-08-01
This paper presents a simulation laboratory for performance evaluation and design refinement of dynamic traffic management systems. The laboratory consists of four integrated components: (1) a traffic management simulator, which mimics the generation of route guidance and operations of traffic signals and signs; (2) a traffic flow simulator, which models individual vehicle movements and drivers` route choice decisions in the presence of real-time traffic information; (3) a surveillance system module, which collects real-time traffic data from sensors and probe vehicles in the simulated network; and (4) a control device module, which implements control strategies and route guidance generated by the traffic management system under evaluation. The simulation laboratory has been implemented in C++ using object-oriented programming and a distributed environment. It features a graphical user interface that allows users to visualize the simulation process, including animation of vehicle movements, state of surveillance sensors, traffic signals, signs, and so on. This modeling system provides a unique tool for evaluating integrated ATIS and ATMS applications in a computer-based laboratory environment.
Stochastic Simulation of Biomolecular Networks in Dynamic Environments.
Voliotis, Margaritis; Thomas, Philipp; Grima, Ramon; Bowsher, Clive G
2016-06-01
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits. PMID:27248512
Simulated impacts of insect defoliation on forest carbon dynamics
NASA Astrophysics Data System (ADS)
Medvigy, D.; Clark, K. L.; Skowronski, N. S.; Schäfer, K. V. R.
2012-12-01
Many temperate and boreal forests are subject to insect epidemics. In the eastern US, over 41 million meters squared of tree basal area are thought to be at risk of gypsy moth defoliation. However, the decadal-to-century scale implications of defoliation events for ecosystem carbon dynamics are not well understood. In this study, the effects of defoliation intensity, periodicity and spatial pattern on the carbon cycle are investigated in a set of idealized model simulations. A mechanistic terrestrial biosphere model, ecosystem demography model 2, is driven with observations from a xeric oak-pine forest located in the New Jersey Pine Barrens. Simulations indicate that net ecosystem productivity (equal to photosynthesis minus respiration) decreases linearly with increasing defoliation intensity. However, because of interactions between defoliation and drought effects, aboveground biomass exhibits a nonlinear decrease with increasing defoliation intensity. The ecosystem responds strongly with both reduced productivity and biomass loss when defoliation periodicity varies from 5 to 15 yr, but exhibits a relatively weak response when defoliation periodicity varies from 15 to 60 yr. Simulations of spatially heterogeneous defoliation resulted in markedly smaller carbon stocks than simulations with spatially homogeneous defoliation. These results show that gypsy moth defoliation has a large effect on oak-pine forest biomass dynamics, functioning and its capacity to act as a carbon sink.
Stochastic Simulation of Biomolecular Networks in Dynamic Environments
Voliotis, Margaritis; Thomas, Philipp; Grima, Ramon; Bowsher, Clive G.
2016-01-01
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate—using decision-making by a large population of quorum sensing bacteria—that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits. PMID:27248512
How to identify dislocations in molecular dynamics simulations?
NASA Astrophysics Data System (ADS)
Li, Duo; Wang, FengChao; Yang, ZhenYu; Zhao, YaPu
2014-12-01
Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals. With the development of computational facilities and technologies, the observations of dislocations at atomic level through numerical simulations are permitted. Molecular dynamics (MD) simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects. However, the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures. Thus, it is a big challenge for the beginners in this community to choose a proper method to start their investigations. In this review, we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids. A comprehensive comparison was made between the advantages and disadvantages of these typical techniques. We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing. It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.
Massively Parallel Reactive and Quantum Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Vashishta, Priya
2015-03-01
In this talk I will discuss two simulations: Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. Quantum molecular dynamics (QMD) simulations are performed on 786,432-processor Blue Gene/Q to study on-demand production of hydrogen gas from water using Al nanoclusters. QMD simulations reveal rapid hydrogen production from water by an Al nanocluster. We find a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production. I will also discuss on-demand production of hydrogen gas from water using and LiAl alloy particles. Research reported in this lecture was carried in collaboration with Rajiv Kalia, Aiichiro Nakano and Ken-ichi Nomura from the University of Southern California, and Fuyuki Shimojo and Kohei Shimamura from Kumamoto University, Japan.
Real-time simulation of dynamic fluoroscopy of ERCP
NASA Astrophysics Data System (ADS)
Jung, Hoeryong; Lee, Doo Yong
2010-02-01
This paper discusses the methods for real-time rendering of time-varying dynamic fluoroscope images including fluid flow for the ERCP (Endoscopic Retrograde Cholangiopancreatography) simulation. A volume rendering technique is used to generate virtual fluoroscopy images. This paper develops an image-overlaying method which overlaps the timevarying images onto the constant background image. The full size fluoroscopy image is computed from the initial volume data set during the pre-processing stage, which is then saved as the background image. Only the time-varying images are computed from the time-varying volume data set during the actual simulation. This involves relatively small computation compared with the background image. The time-varying images are then overlaid onto the background image to obtain the complete images. This method reduces computational overhead by removing redundant computations. A simplified particle dynamics model is employed for fast simulation of the fluid flow. The fluid model, a collection of particles, interacts only with the ducts based on principles of a complete elastic collision. Hence, the velocity of the particles, when they collide with the duct, can be computed by using simple algebraic equations. The methods are implemented for fast simulation of the ERCP.
An undergraduate laboratory activity on molecular dynamics simulations.
Spitznagel, Benjamin; Pritchett, Paige R; Messina, Troy C; Goadrich, Mark; Rodriguez, Juan
2016-01-01
Vision and Change [AAAS, 2011] outlines a blueprint for modernizing biology education by addressing conceptual understanding of key concepts, such as the relationship between structure and function. The document also highlights skills necessary for student success in 21st century Biology, such as the use of modeling and simulation. Here we describe a laboratory activity that allows students to investigate the dynamic nature of protein structure and function through the use of a modeling technique known as molecular dynamics (MD). The activity takes place over two lab periods that are 3 hr each. The first lab period unpacks the basic approach behind MD simulations, beginning with the kinematic equations that all bioscience students learn in an introductory physics course. During this period students are taught rudimentary programming skills in Python while guided through simple modeling exercises that lead up to the simulation of the motion of a single atom. In the second lab period students extend concepts learned in the first period to develop skills in the use of expert MD software. Here students simulate and analyze changes in protein conformation resulting from temperature change, solvation, and phosphorylation. The article will describe how these activities can be carried out using free software packages, including Abalone and VMD/NAMD. PMID:26751047
Simulation of dynamic processes with adaptive neural networks.
Tzanos, C. P.
1998-02-03
Many industrial processes are highly non-linear and complex. Their simulation with first-principle or conventional input-output correlation models is not satisfactory, either because the process physics is not well understood, or it is so complex that direct simulation is either not adequately accurate, or it requires excessive computation time, especially for on-line applications. Artificial intelligence techniques (neural networks, expert systems, fuzzy logic) or their combination with simple process-physics models can be effectively used for the simulation of such processes. Feedforward (static) neural networks (FNNs) can be used effectively to model steady-state processes. They have also been used to model dynamic (time-varying) processes by adding to the network input layer input nodes that represent values of input variables at previous time steps. The number of previous time steps is problem dependent and, in general, can be determined after extensive testing. This work demonstrates that for dynamic processes that do not vary fast with respect to the retraining time of the neural network, an adaptive feedforward neural network can be an effective simulator that is free of the complexities introduced by the use of input values at previous time steps.
Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M; Benedict, L; Hau-Riege, S; Langdon, A; London, R
2008-02-14
The temperature equilibration rate in dense hydrogen (for both T{sub i} > T{sub e} and T{sub i} < T{sub e}) has been calculated with large-scale molecular dynamics simulations for temperatures between 10 and 300 eV and densities between 10{sup 20}/cc to 10{sup 24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L {approx}> 1, Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] with the sub-leading corrections and the fit of Gericke-Murillo-Schlanges [Gericke et al., PRE 65, 036418 (2003)] to the T-matrix evaluation of the collision operator, agrees with the MD data to within the error bars of the simulation. For more strongly-coupled plasmas where L {approx}< 1, our numerical results are consistent with the fit of Gericke-Murillo-Schlanges.
Dynamics in a supercooled molecular liquid: Theory and simulations
Rinaldi, Adele; Sciortino, Francesco; Tartaglia, Piero
2001-06-01
We report extensive simulations of liquid supercooled states for a simple three-site molecular model, introduced by Lewis and Wahnstrom [Phys. Rev. E >50, 3865 (1994)] to mimic the behavior of ortho-terphenyl. The large system size and the long simulation length allow us to calculate very precisely (in a large q-vector range) self-correlation and collective correlation functions, providing a clean and simple reference model for theoretical descriptions of molecular liquids in supercooled states. The time and wave-vector dependence of the site-site correlation functions are compared (neglecting the molecular constraints) with detailed ideal mode-coupling theory predictions. Except for the wave-vector region where the dynamics are controlled by the center of mass (around 9 nm{sup {minus}1}), the theoretical predictions compare very well with the simulation data.
Dynamical Simulations of Terrestrial Planet Formation During Giant Planet Migration
NASA Astrophysics Data System (ADS)
Mandell, A. M.; Raymond, S. N.; Sigurdsson, S.
2005-12-01
We present preliminary results of dynamical simulations of young planetary systems undergoing migration of a Jovian-type planet through the terrestrial region. We find that a significant fraction (10-40%) of the initial planetary embryos remain after giant planet migration, and subsequent evolution of the system results in the formation of terrestrial planets in various configurations, often including a planet in the Habitable Zone. In simulations with gas drag, 3-6 Earth mass planets are formed interior to the migrating Jovian planet, swept inward through moving resonances, and eccentricities are damped for all planets. Systematic variations are seen between simulations with and without gas drag. The presence of a second, non-migrating giant planet reduces the water content and mass of the planets formed throughout the system. This research was supported in part by the Penn State Astrobiology Research Center and the Goddard Center for Astrobiology.
Molecular Dynamics Simulation of Iron — A Review
NASA Astrophysics Data System (ADS)
Chui, C. P.; Liu, Wenqing; Xu, Yongbing; Zhou, Yan
2015-12-01
Molecular dynamics (MD) is a technique of atomistic simulation which has facilitated scientific discovery of interactions among particles since its advent in the late 1950s. Its merit lies in incorporating statistical mechanics to allow for examination of varying atomic configurations at finite temperatures. Its contributions to materials science from modeling pure metal properties to designing nanowires is also remarkable. This review paper focuses on the progress of MD in understanding the behavior of iron — in pure metal form, in alloys, and in composite nanomaterials. It also discusses the interatomic potentials and the integration algorithms used for simulating iron in the literature. Furthermore, it reveals the current progress of MD in simulating iron by exhibiting some results in the literature. Finally, the review paper briefly mentions the development of the hardware and software tools for such large-scale computations.
Simulation of Tailrace Hydrodynamics Using Computational Fluid Dynamics Models
Cook, Christopher B.; Richmond, Marshall C.
2001-05-01
This report investigates the feasibility of using computational fluid dynamics (CFD) tools to investigate hydrodynamic flow fields surrounding the tailrace zone below large hydraulic structures. Previous and ongoing studies using CFD tools to simulate gradually varied flow with multiple constituents and forebay/intake hydrodynamics have shown that CFD tools can provide valuable information for hydraulic and biological evaluation of fish passage near hydraulic structures. These studies however are incapable of simulating the rapidly varying flow fields that involving breakup of the free-surface, such as those through and below high flow outfalls and spillways. Although the use of CFD tools for these types of flow are still an active area of research, initial applications discussed in this report show that these tools are capable of simulating the primary features of these highly transient flow fields.
Molecular dynamics simulation of gold cluster growth during sputter deposition
NASA Astrophysics Data System (ADS)
Abraham, J. W.; Strunskus, T.; Faupel, F.; Bonitz, M.
2016-05-01
We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.
Lightweight computational steering of very large scale molecular dynamics simulations
Beazley, D.M.; Lomdahl, P.S.
1996-09-01
We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.
Implementation of the force decomposition machine for molecular dynamics simulations.
Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka
2012-09-01
We present the design and implementation of the force decomposition machine (FDM), a cluster of personal computers (PCs) that is tailored to running molecular dynamics (MD) simulations using the distributed diagonal force decomposition (DDFD) parallelization method. The cluster interconnect architecture is optimized for the communication pattern of the DDFD method. Our implementation of the FDM relies on standard commodity components even for networking. Although the cluster is meant for DDFD MD simulations, it remains general enough for other parallel computations. An analysis of several MD simulation runs on both the FDM and a standard PC cluster demonstrates that the FDM's interconnect architecture provides a greater performance compared to a more general cluster interconnect. PMID:23085166
An Evaluative Review of Simulated Dynamic Smart 3d Objects
NASA Astrophysics Data System (ADS)
Romeijn, H.; Sheth, F.; Pettit, C. J.
2012-07-01
Three-dimensional (3D) modelling of plants can be an asset for creating agricultural based visualisation products. The continuum of 3D plants models ranges from static to dynamic objects, also known as smart 3D objects. There is an increasing requirement for smarter simulated 3D objects that are attributed mathematically and/or from biological inputs. A systematic approach to plant simulation offers significant advantages to applications in agricultural research, particularly in simulating plant behaviour and the influences of external environmental factors. This approach of 3D plant object visualisation is primarily evident from the visualisation of plants using photographed billboarded images, to more advanced procedural models that come closer to simulating realistic virtual plants. However, few programs model physical reactions of plants to external factors and even fewer are able to grow plants based on mathematical and/or biological parameters. In this paper, we undertake an evaluation of plant-based object simulation programs currently available, with a focus upon the components and techniques involved in producing these objects. Through an analytical review process we consider the strengths and weaknesses of several program packages, the features and use of these programs and the possible opportunities in deploying these for creating smart 3D plant-based objects to support agricultural research and natural resource management. In creating smart 3D objects the model needs to be informed by both plant physiology and phenology. Expert knowledge will frame the parameters and procedures that will attribute the object and allow the simulation of dynamic virtual plants. Ultimately, biologically smart 3D virtual plants that react to changes within an environment could be an effective medium to visually represent landscapes and communicate land management scenarios and practices to planners and decision-makers.
Coupling a geodynamic seismic cycling model to rupture dynamic simulations
NASA Astrophysics Data System (ADS)
Gabriel, Alice; van Dinther, Ylona
2014-05-01
The relevance and results of dynamic rupture scenarios are implicitly linked to the geometry and pre-existing stress and strength state on a fault. The absolute stresses stored along faults during interseismic periods, are largely unquantifiable. They are, however, pivotal in defining coseismic rupture styles, near-field ground motion, and macroscopic source properties (Gabriel et al., 2012). Obtaining these in a physically consistent manner requires seismic cycling models, which directly couple long-term deformation processes (over 1000 year periods), the self-consistent development of faults, and the resulting dynamic ruptures. One promising approach to study seismic cycling enables both the generation of spontaneous fault geometries and the development of thermo-mechanically consistent fault stresses. This seismo-thermo-mechanical model has been developed using a methodology similar to that employed to study long-term lithospheric deformation (van Dinther et al., 2013a,b, using I2ELVIS of Gerya and Yuen, 2007). We will innovatively include the absolute stress and strength values along physically consistent evolving non-finite fault zones (regions of strain accumulation) from the geodynamic model into dynamic rupture simulations as an initial condition. The dynamic rupture simulations will be performed using SeisSol, an arbitrary high-order derivative Discontinuous Galerkin (ADER-DG) scheme (Pelties et al., 2012). The dynamic rupture models are able to incorporate the large degree of fault geometry complexity arising in naturally evolving geodynamic models. We focus on subduction zone settings with and without a splay fault. Due to the novelty of the coupling, we first focus on methodological challenges, e.g. the synchronization of both methods regarding the nucleation of events, the localization of fault planes, and the incorporation of similar frictional constitutive relations. We then study the importance of physically consistent fault stress, strength, and
Monte Carlo-based simulation of dynamic jaws tomotherapy
Sterpin, E.; Chen, Y.; Chen, Q.; Lu, W.; Mackie, T. R.; Vynckier, S.
2011-09-15
Purpose: Original TomoTherapy systems may involve a trade-off between conformity and treatment speed, the user being limited to three slice widths (1.0, 2.5, and 5.0 cm). This could be overcome by allowing the jaws to define arbitrary fields, including very small slice widths (<1 cm), which are challenging for a beam model. The aim of this work was to incorporate the dynamic jaws feature into a Monte Carlo (MC) model called TomoPen, based on the MC code PENELOPE, previously validated for the original TomoTherapy system. Methods: To keep the general structure of TomoPen and its efficiency, the simulation strategy introduces several techniques: (1) weight modifiers to account for any jaw settings using only the 5 cm phase-space file; (2) a simplified MC based model called FastStatic to compute the modifiers faster than pure MC; (3) actual simulation of dynamic jaws. Weight modifiers computed with both FastStatic and pure MC were compared. Dynamic jaws simulations were compared with the convolution/superposition (C/S) of TomoTherapy in the ''cheese'' phantom for a plan with two targets longitudinally separated by a gap of 3 cm. Optimization was performed in two modes: asymmetric jaws-constant couch speed (''running start stop,'' RSS) and symmetric jaws-variable couch speed (''symmetric running start stop,'' SRSS). Measurements with EDR2 films were also performed for RSS for the formal validation of TomoPen with dynamic jaws. Results: Weight modifiers computed with FastStatic were equivalent to pure MC within statistical uncertainties (0.5% for three standard deviations). Excellent agreement was achieved between TomoPen and C/S for both asymmetric jaw opening/constant couch speed and symmetric jaw opening/variable couch speed, with deviations well within 2%/2 mm. For RSS procedure, agreement between C/S and measurements was within 2%/2 mm for 95% of the points and 3%/3 mm for 98% of the points, where dose is greater than 30% of the prescription dose (gamma analysis
Modeling and Simulation of the MIDREX Shaft Furnace: Reduction, Transition and Cooling Zones
NASA Astrophysics Data System (ADS)
Shams, Alireza; Moazeni, Faegheh
2015-11-01
Metallic iron used in steel industries is mostly obtained from a direct reduction process. The focus of this study is to simulate the furnace of the MIDREX technology. MIDREX technology which is the most important gas-based direct reduced iron (DRI) process in the world, includes reduction, transition and cooling zones. The reduction zone considered as a counter current gas-solid reactor produces sponge iron from iron ore pellets. The transition zone has sufficient height to isolate the reduction zone and cooling zone from each other and the cooling zone cools the solid product down to around 50°C. Each zone has a system of reactions. Simultaneous mass and energy balances along the reduction zone lead to a set of ordinary differential equations with two points of boundary conditions. The transitions and cooling zone are investigated at the equilibrium condition leading to a set of algebraic equations. By solving these systems of equations, we determined the materials concentration, temperature, and pressure along the furnace. Our results are in a good agreement with data reported by Parisi and Laborde (2004) for a real MIDREX plant. Using this model, the effect of reactor length and cooling gas flow on the metallization and the effect of cooling gas flow on the outlet temperature of the solid phase have been studied. These new findings can be used to minimize the consumed energy.
NASA Astrophysics Data System (ADS)
Krivov, Sergei V.
2011-07-01
Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game—the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.
Towards optimum permeability reduction in porous media using biofilm growth simulations.
Pintelon, T R R; Graf von der Schulenburg, D A; Johns, M L
2009-07-01
While biological clogging of porous systems can be problematic in numerous processes (e.g., microbial enhanced oil recovery-MEOR), it is targeted during bio-barrier formation to control sub-surface pollution plumes in ground water. In this simulation study, constant pressure drop (CPD) and constant volumetric flow rate (CVF) operational modes for nutrient provision for biofilm growth in a porous system are considered with respect to optimum (minimum energy requirement for nutrient provision) permeability reduction for bio-barrier applications. Biofilm growth is simulated using a Lattice-Boltzmann (LB) simulation platform complemented with an individual-based biofilm model (IbM). A biomass detachment technique has been included using a fast marching level set (FMLS) method that models the propagation of the biofilm-liquid interface with a speed proportional to the adjacent velocity shear field. The porous medium permeability reduction is simulated for both operational modes using a range of biofilm strengths. For stronger biofilms, less biomass deposition and energy input are required to reduce the system permeability during CPD operation, whereas CVF is more efficient at reducing the permeability of systems containing weaker biofilms. PMID:19309753
Recovering position-dependent diffusion from biased molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-01
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica® package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics. Given known free energy and D, the package can also generate diffusive trajectories.
Recovering position-dependent diffusion from biased molecular dynamics simulations
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-28
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.
Recovering position-dependent diffusion from biased molecular dynamics simulations.
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-28
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica(®) package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics. Given known free energy and D, the package can also generate diffusive trajectories. PMID:24588150
MCNPX--PoliMi Variance Reduction Techniques for Simulating Neutron Scintillation Detector Response
NASA Astrophysics Data System (ADS)
Prasad, Shikha
Scintillation detectors have emerged as a viable He-3 replacement technology in the field of nuclear nonproliferation and safeguards. The scintillation light produced in the detectors is dependent on the energy deposited and the nucleus with which the interaction occurs. For neutrons interacting with hydrogen in organic liquid scintillation detectors, the energy-to-light conversion process is nonlinear. MCNPX-PoliMi is a Monte Carlo Code that has been used for simulating this detailed scintillation physics; however, until now, simulations have only been done in analog mode. Analog Monte Carlo simulations can take long times to run, especially in the presence of shielding and large source-detector distances, as in the case of typical nonproliferation problems. In this thesis, two nonanalog approaches to speed up MCNPX-PoliMi simulations of neutron scintillation detector response have been studied. In the first approach, a response matrix method (RMM) is used to efficiently calculate neutron pulse height distributions (PHDs). This method combines the neutron current incident on the detector face with an MCNPX-PoliMi-calculated response matrix to generate PHDs. The PHD calculations and their associated uncertainty are compared for a polyethylene-shielded and lead-shielded Cf-252 source for three different techniques: fully analog MCNPX-PoliMi, the RMM, and the RMM with source biasing. The RMM with source biasing reduces computation time or increases the figure-of-merit on an average by a factor of 600 for polyethylene and 300 for lead shielding (when compared to the fully analog calculation). The simulated neutron PHDs show good agreement with the laboratory measurements, thereby validating the RMM. In the second approach, MCNPX-PoliMi simulations are performed with the aid of variance reduction techniques. This is done by separating the analog and nonanalog components of the simulations. Inside the detector region, where scintillation light is produced, no variance
Merchant, Kusai A.; Noid, W. G.; Akiyama, Ryo; Finkelstein, Ilya J.; Goun, Alexei; McClain, Brian L.; Loring, Roger F.; Fayer, M. D.
2008-01-01
Spectrally resolved infrared stimulated vibrational echo data were obtained for sperm whale carbonmonoxymyoglobin (MbCO) at 300 K. The measured dephasing dynamics of the CO ligand are in agreement with dephasing dynamics calculated with molecular dynamics (MD) simulations for MbCO with the residue histidine-64 (His64) having its imidazole ε nitrogen protonated (Nε–H). The two conformational substate structures Bε and Rε observed in the MD simulations are assigned to the spectroscopic A1 and A3 conformational substates of MbCO, respectively, based on the agreement between the experimentally measured and calculated dephasing dynamics for these substates. In the A1 substate, the Nε–H proton and Nδ of His64 are approximately equidistant from the CO ligand, while in the A3 substate, the Nε–H of His64 is oriented toward the CO, and the Nδ is on the surface of the protein. The MD simulations show that dynamics of His64 represent the major source of vibrational dephasing of the CO ligand in the A3 state on both femtosecond and picosecond time scales. Dephasing in the A1 state is controlled by His64 on femtosecond time scales, and by the rest of the protein and the water solvent on longer time scales. PMID:14599220
Preliminary analysis of the dynamic heliosphere by MHD simulations
Washimi, H.; Zank, G. P.; Tanaka, T.
2006-09-26
A preliminary analysis of the dynamic heliosphere to estimate the termination shock (TS) distance from the sun around the time when Voyager 1 passed the termination shock at December 16, 2004 is performed by using MHD simulations. For input to this simulation, we use the Voyager 2 solar-wind data. We first find a stationary solution of the 3-D outer heliosphere by assigning a set of LISM parameters as our outer boundary conditions and then the dynamical analysis is performed. The model TS crossing is within 6 months of the observed date. The TS is pushed outward every time a high ram-pressure solar wind pulse arrives. After the end of the high ram-pressure wind, the TS shock shrinks inward. When the last Halloween event passed through the TS at DOY 250, 2004, the TS began to shrink inward very quickly and the TS crossed V1. The highest inward speed of the TS is over 400 km/s. The high ram-pressure solar wind transmitted through the TS becomes a high thermal-pressure plasma in the heliosheath, acting to push the TS inward. This suggests that the position of the TS is determined not only by the steady-state pressure balance condition between the solar wind ram-pressure and the LISM pressure, but by the dynamical ram pressure too. The period when the high ram-pressure solar wind arrives at the TS shock seems to correspond to the period of the TS particle event (Stone et al, 2005, Decker et al., 2005). The TS crossing date will be revised in future simulations using a more appropriate set of parameters for the LISM. This will enable us to undertake a detailed comparison of the simulation results with the TS particle events.
Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
Paquet, Eric; Viktor, Herna L.
2015-01-01
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262
Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review.
Paquet, Eric; Viktor, Herna L
2015-01-01
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262
Validation of Bubble Dynamics Equation for a Nano-scale Bubble via Molecular Dynamics Simulation
NASA Astrophysics Data System (ADS)
Tsuda, S.; Hyodo, H.; Watanabe, S.
2015-12-01
For a validation of the application of conventional bubble dynamics to a nano-scale bubble behaviour, we simulated a nano-scale bubble collapsing or vibration by Molecular Dynamics (MD) method and compared the result with the solution of Rayleigh-Plesset (RP) equation and that of Confined RP (CRP) equation, whose boundary condition was corrected to be consistent with that of MD simulation. As a result, a good coincidence was obtained between MD, RP, and CRP in the case of one-component fluid. In addition, also a good correspondence was obtained particularly in the comparison between MD and CRP in the case of two-component fluid containing non-condensable gas. The present results indicate that conventional bubble dynamics equation can be applied even to a nano-scale tiny bubble.
Shimamura, K; Shibuta, Y; Ohmura, S; Arifin, R; Shimojo, F
2016-04-13
The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed. PMID:26953616
NASA Astrophysics Data System (ADS)
Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.
2016-04-01
The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.
On the railway track dynamics with rail vibration absorber for noise reduction
NASA Astrophysics Data System (ADS)
Wu, T. X.
2008-01-01
A promising means to increase the decay rate of vibration along the rail is using a rail absorber for noise reduction. Compound track models with the tuned rail absorber are developed for investigation of the performance of the absorber on vibration reduction. Through analysis of the track dynamics with the rail absorber some guidelines are given on selection of the types and parameters for the rail absorber. It is found that a large active mass used in the absorber is beneficial to increase the decay rate of rail vibration. The effectiveness of the piecewise continuous absorber is moderate compared with the discrete absorber installed in the middle of sleeper span or at a sleeper. The most effective installation position for the discrete absorber is in the middle of sleeper span. Over high or over low loss factor of the damping material used in the absorber may degrade the performance on vibration reduction.