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.
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.
A neural-network-based method of model reduction for the dynamic simulation of MEMS
NASA Astrophysics Data System (ADS)
Liang, Y. C.; Lin, W. Z.; Lee, H. P.; Lim, S. P.; Lee, K. H.; Feng, D. P.
2001-05-01
This paper proposes a neuro-network-based method for model reduction that combines the generalized Hebbian algorithm (GHA) with the Galerkin procedure to perform the dynamic simulation and analysis of nonlinear microelectromechanical systems (MEMS). An unsupervised neural network is adopted to find the principal eigenvectors of a correlation matrix of snapshots. It has been shown that the extensive computer results of the principal component analysis using the neural network of GHA can extract an empirical basis from numerical or experimental data, which can be used to convert the original system into a lumped low-order macromodel. The macromodel can be employed to carry out the dynamic simulation of the original system resulting in a dramatic reduction of computation time while not losing flexibility and accuracy. Compared with other existing model reduction methods for the dynamic simulation of MEMS, the present method does not need to compute the input correlation matrix in advance. It needs only to find very few required basis functions, which can be learned directly from the input data, and this means that the method possesses potential advantages when the measured data are large. The method is evaluated to simulate the pull-in dynamics of a doubly-clamped microbeam subjected to different input voltage spectra of electrostatic actuation. The efficiency and the flexibility of the proposed method are examined by comparing the results with those of the fully meshed finite-difference method.
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. Copyright © 2016 Elsevier Ltd. All rights reserved.
Influence of model order reduction methods on dynamical-optical simulations
NASA Astrophysics Data System (ADS)
Störkle, Johannes; Eberhard, Peter
2017-04-01
In this work, the influence of model order reduction (MOR) methods on optical aberrations is analyzed within a dynamical-optical simulation of a high precision optomechanical system. Therefore, an integrated modeling process and new methods have to be introduced for the computation and investigation of the overall dynamical-optical behavior. For instance, this optical system can be a telescope optic or a lithographic objective. In order to derive a simplified mechanical model for transient time simulations with low computational cost, the method of elastic multibody systems in combination with MOR methods can be used. For this, software tools and interfaces are defined and created. Furthermore, mechanical and optical simulation models are derived and implemented. With these, on the one hand, the mechanical sensitivity can be investigated for arbitrary external excitations and on the other hand, the related optical behavior can be predicted. In order to clarify these methods, academic examples are chosen and the influences of the MOR methods and simulation strategies are analyzed. Finally, the systems are investigated with respect to the mechanical-optical frequency responses, and in conclusion, some recommendations for the application of reduction methods are given.
NASA Astrophysics Data System (ADS)
Fan, De-Qiu; Sohn, H. Y.; Mohassab, Yousef; Elzohiery, Mohamed
2016-12-01
A three-dimensional computational fluid dynamics (CFD) model was developed to study the hydrogen reduction of magnetite concentrate particles in a laboratory flash reactor representing a novel flash ironmaking process. The model was used to simulate the fluid flow, heat transfer, and chemical reactions involved. The governing equations for the gas phase were solved in the Eulerian frame of reference while the particles were tracked in the Lagrangian framework. The change in the particle mass was related to the chemical reaction and the particle temperature was calculated by taking into consideration the heat of reaction, convection, and radiation. The stochastic trajectory model was used to describe particle dispersion due to turbulence. Partial combustion of H2 by O2 injected through a non-premixed burner was also simulated in this study. The partial combustion mechanism used in this model consisted of seven chemical reactions involving six species. The temperature profiles and reduction degrees obtained from the simulations satisfactorily agreed with the experimental measurements.
Jin, Haiyun; Goyal, Puja; Das, Akshaya Kumar; Gaus, Michael; Meuwly, Markus; Cui, Qiang
2016-03-03
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.
NASA Astrophysics Data System (ADS)
Starc, Blaž; Čepon, Gregor; Boltežar, Miha
2017-04-01
A new numerical procedure for efficient dynamics simulations of linear-elastic systems with unilateral contacts is proposed. The method is based on the event-driven integration of a contact problem with a combination of single- and set-valued force laws together with classical model-reduction techniques. According to the contact state, the developed event-driven integration enables the formulation of reduced system matrices. Moreover, to enable the transition among different reduced spaces the formulation of the initial conditions is also presented. The method has been developed separately for each of the four most popular model-reduction techniques (Craig-Bampton, MacNeal, Rubin and dual Craig-Bampton). The applicability of the newly presented method is demonstrated on a simple clamped-beam structure with a unilateral contact, which is excited with a harmonic force at the free end.
Zhang, Liqun
2017-04-01
Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5 (HD5) and human β defensin type 3 (hBD-3) have 6 cysteine residues which form 3 pairs of disulfide bonds in oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order have been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD-3 wildtype and analogs which have all 3 disulfide bonds released in reducing condition. The structure of hBD-3 was found to be more dynamic and flexible than HD5, based on RMSD, RMSF, and radius of gyration calculations. The disulfide bridge breaking order of HD5 and hBD-3 in reducing condition was predicted by two kinds of methods, which gave consistent results. It was found that the disulfide bonds breaking pathways for HD5 and hBD-3 are very different. The breaking of disulfide bonds can influence the dimer interface by making the dimer structure less stable for both kinds of defensin. In order to understand the difference in dynamics and disulfide bond breaking pathway, hydrophilic and hydrophobic accessible surface areas (ASA), buried surface area between cysteine pairs, entropy of cysteine pairs, and internal energy were calculated. Comparing to the wildtype, hBD-3 analog is more hydrophobic, while HD5 is more hydrophilic. For hBD-3, the disulfide breaking is mainly entropy driven, while other factors such as the solvation effects may take the major role in controlling HD5 disulfide breaking pathway. Proteins 2017; 85:665-681. © 2016 Wiley Periodicals, Inc.
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.
Kovalenko, Ilya B; Knyazeva, Olga S; Antal, Taras K; Ponomarev, Vladimir Y; Riznichenko, Galina Yu; Rubin, Andrei B
2017-09-01
A model of electron transport from cytochrome f to photosystem I mediated by plastocyanin was designed on the basis of the multiparticle Brownian dynamics method. The model combines events which occur over a wide time range, including protein diffusion along the thylakoid membrane, long-distance interactions between proteins, formation of a multiprotein complex, electron transfer within a complex and complex dissociation. Results of the modeling were compared with the experimental kinetics measured in chloroplast thylakoids. Computer simulation demonstrated that the complex interior of the photosynthetic membrane, electrostatic interactions and Brownian diffusion provide physical conditions for the directed electron flow along the photosynthetic electron transport chain. © 2017 Scandinavian Plant Physiology Society.
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.
Structural dynamics system model reduction
NASA Technical Reports Server (NTRS)
Chen, J. C.; Rose, T. L.; Wada, B. K.
1987-01-01
Loads analysis for structural dynamic systems is usually performed by finite element models. Because of the complexity of the structural system, the model contains large number of degree-of-freedom. The large model is necessary since details of the stress, loads and responses due to mission environments are computed. However, a simplified model is needed for other tasks such as pre-test analysis for modal testing, and control-structural interaction studies. A systematic method of model reduction for modal test analysis is presented. Perhaps it will be of some help in developing a simplified model for the control studies.
Molecular dynamics simulations.
Lindahl, Erik
2015-01-01
Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.
NASA Technical Reports Server (NTRS)
1987-01-01
The proceedings of the conference are presented. The objective was to provide a forum for the discussion of the structure and status of existing computer programs which are used to simulate the dynamics of a variety of tether applications in space. A major topic was different simulation models and the process of validating them. Guidance on future work in these areas was obtained from a panel discussion; the panel was composed of resource and technical managers and dynamic analysts in the tether field. The conclusions of this panel are also presented.
Dynamical Simulation of Probabilities
NASA Technical Reports Server (NTRS)
Zak, Michail
1996-01-01
It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-Lipschitz dynamics, without utilization of any man-made devices(such as random number generators). Self-orgainizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed. Special attention was focused upon coupled stochastic processes, defined in terms of conditional probabilities, for which joint probability does not exist. Simulations of quantum probabilities are also discussed.
Dynamical Simulation of Probabilities
NASA Technical Reports Server (NTRS)
Zak, Michail
1996-01-01
It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-Lipschitz dynamics, without utilization of any man-made devices(such as random number generators). Self-orgainizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed. Special attention was focused upon coupled stochastic processes, defined in terms of conditional probabilities, for which joint probability does not exist. Simulations of quantum probabilities are also discussed.
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
Molecular dynamics simulations.
Lindahl, Erik R
2008-01-01
Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.
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.
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.
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.
An interactive teaching device simulating intussusception reduction
Sanchez, Thomas; Roper, Glade E.; Wexler, Anthony S.; Arieli, Robert P.; Ho, Clark; Li, Joseph C.; Ozpinar, Alp; Soosman, Steffan K.
2010-01-01
Intussusception is relatively uncommon, occurring in 0.5 to 2.3 cases per 1,000 live births in the USA. Radiology residents, therefore, have few opportunities to participate in intussusception reduction during training, and practicing radiologists encounter it infrequently. Training is essential, as successful reduction avoids surgery. The judgment involved in reducing an intussusception is best gained with experience. We developed a training device that simulates fluoroscopic intussusception reduction with air. The device consists of a doll that contains a cylinder with similar stress and strain characteristics to the human colon. The trainee pumps air into the cylinder through a rectal tube using a standard hand-held air reduction pump. A sensor measures the pressure within the chamber and transmits readings to a computer, which displays images from actual intussusception reductions based on the pressure maintained within the device. A random component in the software gives the user a new experience each time and models uncertainties in the actual reduction process, including perforation. This intussusception reduction simulator can enhance resident education, giving residents the opportunity to practice this technique before employing it on a real patient. The simulator can also help practicing radiologists become more comfortable with intussusception air reduction. Electronic supplementary material The online version of this article (doi:10.1007/s00247-010-1764-x) contains supplementary material, which is available to authorized users. PMID:20652235
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
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.
Two-Stage Reduction Of Dynamical Models
NASA Technical Reports Server (NTRS)
Lee, Allan Y.; Tsuha, Walter S.
1993-01-01
No longer necessary to solve eigenvalue problems of high order. Component-mode projection-and-assembly model-reduction (COMPARE) method provides approximation of dynamics of vibrations of complicated, multiple flexible bodies by use of mathematical models of reduced order. Incorporates component-mode synthesis (CMS) method and enhanced projection-and-assembly (EP&A) method, described in "Enhanced Method of Reduction of Dynamical Models" (NPO-18402), providing for somewhat simplified two-stage process in which order of applicable mathematical models reduced. Reduced-order models used to design algorithms of control systems to suppress vibrations or otherwise control structure.
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
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, which is
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
Top, Philip; Woodward, Carol; Smith, Steve; Banks, Lawrence; Kelley, Brian
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.
Robot arm dynamic model reduction for control
NASA Technical Reports Server (NTRS)
Bejczy, A. K.; Lee, S.
1983-01-01
General methods are described by which the mathematical complexities of explicit and exact state equations of robot arms can be reduced to a simplified and compact state equation representation without introducing significant errors into the robot arm dynamic model. The model reduction methods are based on homogeneous coordinates and on the Langrangian algorithm for robot arm dynamics, and utilize matrix, vector and numeric analysis techniques. The derivation of differential vector representation of centripetal and Coriolis forces which has not yet been established in the literature is presented.
Breen, Kristin J; DeBlase, Andrew F; Guasco, Timothy L; Voora, Vamsee K; Jordan, Kenneth D; Nagata, Takashi; Johnson, Mark A
2012-01-26
The transition states of a chemical reaction in solution are generally accessed through exchange of thermal energy between the solvent and the reactants. As such, an ensemble of reacting systems approaches the transition state configuration of reactant and surrounding solvent in an incoherent manner that does not lend itself to direct experimental observation. Here we describe how gas-phase cluster chemistry can provide a detailed picture of the microscopic mechanics at play when a network of six water molecules mediates the trapping of a highly reactive "hydrated electron" onto a neutral CO(2) molecule to form a radical anion. The exothermic reaction is triggered from a metastable intermediate by selective excitation of either the reactant CO(2) or the water network, which is evidenced by the evaporative decomposition of the product cluster. Ab initio molecular dynamics simulations of energized CO(2)·(H(2)O)(6)(-) clusters are used to elucidate the nature of the network deformations that mediate intracluster electron capture, thus revealing the detailed solvent fluctuations implicit in the Marcus theory for electron-transfer kinetics in solution.
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.
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).
Modeling Molecular Dynamics from Simulations
Hinrichs, Nina Singhal
2009-01-28
Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.
Dynamic dimensionality reduction for hyperspectral imagery
NASA Astrophysics Data System (ADS)
Safavi, Haleh; Liu, Keng-Hao; Chang, Chein-I.
2011-06-01
Data dimensionality (DR) is generally performed by first fixing size of DR at a certain number, say p and then finding a technique to reduce an original data space to a low dimensional data space with dimensionality specified by p. This paper introduces a new concept of dynamic dimensionality reduction (DDR) which considers the parameter p as a variable by varying the value of p to make p adaptive compared to the commonly used DR, referred to as static dimensionality reduction (SDR) with the parameter p fixed at a constant value. In order to materialize the DDR another new concept, referred to as progressive DR (PDR) is also developed so that the DR can be performed progressively to adapt the variable size of data dimensionality determined by varying the value of p. The advantages of the DDR over SDR are demonstrated through experiments conducted for hyperspectral image classification.
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
2014-02-01
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. 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. 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 attenuator was relatively
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
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...
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...
Dynamical simulation of gravothermal catastrophe.
Klinko, Peter; Miller, Bruce N
2004-01-16
We investigate the dynamical evolution of gravothermal catastrophe in a model of a spherical cluster where, besides the energy and angular momentum, an additional integral of motion is also taken into account. Using dynamical simulation, we study a system of concentric, rotating, spherical shells employing a precise, event-driven, algorithm that permits the controlled exchange of internal angular momentum. Initially the system starts to relax to a locally stable state that is in good agreement with mean field predictions. This is followed by core collapse with the development of a core-halo structure and gravothermal oscillation.
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.
Molecular dynamics simulation of pyridine
NASA Astrophysics Data System (ADS)
Trumpakaj, Zygmunt; Linde, Bogumił
2015-04-01
Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.
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.
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 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 Multiscale Simulation of Polyelectrolyte Nanoassemblies
2008-08-21
REPORT Dynamic Multiscale Simulation of Polyelectrolyte Nanoassemblies 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The goal of this project is to...Std. Z39.18 - 31-May-2008 Dynamic Multiscale Simulation of Polyelectrolyte Nanoassemblies Report Title ABSTRACT The goal of this project is to...Total Number: Sub Contractors (DD882) Inventions (DD882) Final Progress Report Dynamic Multiscale Simulation of Polyelectrolyte Nanoassemblies
Dynamic adaptive chemistry for turbulent flame simulations
NASA Astrophysics Data System (ADS)
Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.
2013-02-01
The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.
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)
An Integrated Crustal Dynamics Simulator
NASA Astrophysics Data System (ADS)
Xing, H. L.; Mora, P.
2007-12-01
Numerical modelling offers an outstanding opportunity to gain an understanding of the crustal dynamics and complex crustal system behaviour. This presentation provides our long-term and ongoing effort on finite element based computational model and software development to simulate the interacting fault system for earthquake forecasting. A R-minimum strategy based finite-element computational model and software tool, PANDAS, for modelling 3-dimensional nonlinear frictional contact behaviour between multiple deformable bodies with the arbitrarily-shaped contact element strategy has been developed by the authors, which builds up a virtual laboratory to simulate interacting fault systems including crustal boundary conditions and various nonlinearities (e.g. from frictional contact, materials, geometry and thermal coupling). It has been successfully applied to large scale computing of the complex nonlinear phenomena in the non-continuum media involving the nonlinear frictional instability, multiple material properties and complex geometries on supercomputers, such as the South Australia (SA) interacting fault system, South California fault model and Sumatra subduction model. It has been also extended and to simulate the hot fractured rock (HFR) geothermal reservoir system in collaboration of Geodynamics Ltd which is constructing the first geothermal reservoir system in Australia and to model the tsunami generation induced by earthquakes. Both are supported by Australian Research Council.
Simulations of Dynamic Relativistic Magnetospheres
NASA Astrophysics Data System (ADS)
Parfrey, Kyle Patrick
Neutron stars and black holes are generally surrounded by magnetospheres of highly conducting plasma in which the magnetic flux density is so high that hydrodynamic forces are irrelevant. In this vanishing-inertia—or ultra-relativistic—limit, magnetohydrodynamics becomes force-free electrodynamics, a system of equations comprising only the magnetic and electric fields, and in which the plasma response is effected by a nonlinear current density term. In this dissertation I describe a new pseudospectral simulation code, designed for studying the dynamic magnetospheres of compact objects. A detailed description of the code and several numerical test problems are given. I first apply the code to the aligned rotator problem, in which a star with a dipole magnetic field is set rotating about its magnetic axis. The solution evolves to a steady state, which is nearly ideal and dissipationless everywhere except in a current sheet, or magnetic field discontinuity, at the equator, into which electromagnetic energy flows and is dissipated. Magnetars are believed to have twisted magnetospheres, due to internal magnetic evolution which deforms the crust, dragging the footpoints of external magnetic field lines. This twisting may be able to explain both magnetars' persistent hard X-ray emission and their energetic bursts and flares. Using the new code, I simulate the evolution of relativistic magnetospheres subjected to slow twisting through large angles. The field lines expand outward, forming a strong current layer; eventually the configuration loses equilibrium and a dynamic rearrangement occurs, involving large-scale rapid magnetic reconnection and dissipation of the free energy of the twisted magnetic field. When the star is rotating, the magnetospheric twisting leads to a large increase in the stellar spin-down rate, which may take place on the long twisting timescale or in brief explosive events, depending on where the twisting is applied and the history of the system
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.
Reduction and reconstruction methods for simulation and control of fluids
NASA Astrophysics Data System (ADS)
Ma, Zhanhua
In this thesis we develop model reduction/reconstruction methods that are applied to simulation and control of fluids. In the first part of the thesis, we focus on development of dimension reduction methods that compute reduced-order models (at the order of 101˜2) of systems with high-dimensional states (at the order of 105˜8) that are typical in computational fluid dynamics. The reduced-order models are then used for feedback control design for the full systems, as the control design tools are usually applicable only to systems of order up to 10 4. First, we show that a widely-used model reduction method for stable linear timeinvariant (LTI) systems, the approximate balanced truncation method (also called balanced POD), yields identical reduced-order models as Eigensystem Realization Algorithm (ERA), a well-known method in system identification. Unlike ERA, Balanced POD generates sets of modes that are useful in controller/observer design and systems analysis. On the other hand, ERA is more computationally efficient and does not need data from adjoint systems, which cannot be constructed in experiments and are often costly to construct and simulate numerically. The equivalence of ERA and balanced POD leads us to further design a version of ERA that works for unstable (linear) systems with one-dimensional unstable eigenspace and is equivalent to a recently developed version of balanced POD for unstable systems. We consider further generalization of balanced POD/ERA methods for linearized time-periodic systems around an unstable orbit. Four algorithms are presented: the lifted balanced POD/lifted ERA and the periodic balanced POD/periodic ERA. The lifting approach generates a LTI reduced-order model that updates the system once every period, and the periodic approach generates a periodic reduced-order model. By construction the lifted ERA is the most computationally efficient algorithm and it does not need adjoint data. By removing periodicity in periodic balanced
Dynamical simulations of sedimenting spheres
Ladd, A.J.C. )
1993-02-01
The sedimentation of monodisperse suspensions of rigid spheres has been studied by dynamical simulation; computational techniques are described and numerical results are reported. It has been found that there is a slow relaxation of the suspension microstructure during sedimentation, so that compared with the initial equilibrium distribution, there is an increased number of pairs of particles near contact; this leads to a 5%--10% increase in the average sedimentation velocity. Individual particle velocities fluctuate about the mean fall speed; these fluctuations are large and persist for long times. The resulting hydrodynamically induced dispersion of the particles can be characterized by strongly anisotropic diffusion coefficients; however, the dispersion process is non-Fickian at high solids concentrations.
Reduction of Tunnel Dynamics at the National Transonic Facility (Invited)
NASA Technical Reports Server (NTRS)
Kilgore, W. A.; Balakrishna, S.; Butler, D. H.
2001-01-01
This paper describes the results of recent efforts to reduce the tunnel dynamics at the National Transonic Facility. The results presented describe the findings of an extensive data analysis, the proposed solutions to reduce dynamics and the results of implementing these solutions. These results show a 90% reduction in the dynamics around the model support structure and a small impact on reducing model dynamics. Also presented are several continuing efforts to further reduce dynamics.
Enabling Strain Hardening Simulations with Dislocation Dynamics
Arsenlis, A; Cai, W
2006-12-20
Numerical algorithms for discrete dislocation dynamics simulations are investigated for the purpose of enabling strain hardening simulations of single crystals on massively parallel computers. The algorithms investigated include the /(N) calculation of forces, the equations of motion, time integration, adaptive mesh refinement, the treatment of dislocation core reactions, and the dynamic distribution of work on parallel computers. A simulation integrating all of these algorithmic elements using the Parallel Dislocation Simulator (ParaDiS) code is performed to understand their behavior in concert, and evaluate the overall numerical performance of dislocation dynamics simulations and their ability to accumulate percents of plastic strain.
Brownian dynamics simulation of DNA condensation.
Sottas, P E; Larquet, E; Stasiak, A; Dubochet, J
1999-01-01
DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA. PMID:10512808
Users guide for FRCS: fuel reduction cost simulator software.
Roger D. Fight; Bruce R. Hartsough; Peter. Noordijk
2006-01-01
The Fuel Reduction Cost Simulator (FRCS) spreadsheet application is public domain software used to estimate costs for fuel reduction treatments involving removal of trees of mixed sizes in the form of whole trees, logs, or chips from a forest. Equipment production rates were developed from existing studies. Equipment operating cost rates are from December 2002 prices...
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
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.
Molecular dynamics simulations of nanostructures
NASA Astrophysics Data System (ADS)
Yuan, Zaoshi
This dissertation is focused on multimillion-atom molecular dynamics (MD) simulations of nanoscale materials. In the past decade, nanoscale materials have made significant commercial impacts, which will potentially lead to the next industrial revolution. The interest lies in the novel and promising features nanoscale materials exhibit due to their confined sizes. However, not all novel behaviors are understood or controllable. Many uncontrollable parameters, e.g. defects and dangling bonds, are known to hinder the performance of nanodevices. Solutions to these problems rely on our understanding of fundamental elements in nanoscience: isolated individual nanostructures and their assemblies. In this dissertation, we will address atomistic foundations of several problems of technological importance in nanoscience. Specifically, three basic problems are discussed: (1) embrittlement of nanocrystalline metal; (2) novel thermo-mechanical behaviors of nanowires (NWs); and (3) planar defect generation in NWs. With a scalable algorithm implemented on massively parallel computing platforms and various data mining methods, MD simulations can provide valuable insights into these problems. An essential role of sulfur segregation-induced amorphization of crystalline nickel was recently discovered experimentally, but the atomistic mechanism of the amorphization remains unexplained. Our MD simulations reveal that the large steric size of sulfur impurity causes strong sulfur-sulfur interaction mediated by lattice distortion, which leads to amorphization near the percolation threshold at the sulfur-sulfur network in nickel crystal. The generality of the mechanism due to the percolation of an impurity network is further confirmed by a model binary system. In our study of novel behaviors of semiconductor NWs, MD simulations construct a rich size-temperature `phase diagram' for the mechanical response of a zinc-oxide NW under tension. For smaller diameters and higher temperatures, novel
Modeling Nanocomposites for Molecular Dynamics (MD) Simulations
2015-01-01
Maximum 200 Words) The minimum energy configuration for Molecular Dynamics (MD) simulations is found for a carbon nanotube (CNT)/polymer... Carbon Nanotubes (CNTs), Molecular Dynamics Simulations 15. NUMBER OF PAGES 18 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT... Carbon Nanotubes ,” Macromolecules, Volume 39, Number 16, pp. 5194-5205, July 2006. 6. “VMD-Visual Molecular Dynamics ,” March 2014, http
Molecular Dynamics Simulation of Supercritical Spray Phenomena
2008-09-26
Dynamics of the Rheological and Structural Properties of Linear and Branched Molecules. Simple Shear and Poiseuille Flows ; Instabilities and Slip...Michael Barrucco Publications: "Comparison of Wall Models for the Molecular Dynamics Simulation of Micro flows ," R. D. Branam and M. M...Performance 3. DATES COVERED (From - To) 1 Dec. 2003 - 31 May 2008 4. TITLE AND SUBTITLE Molecular Dynamics Simulation of Supercritical
Novel methods for molecular dynamics simulations.
Elber, R
1996-04-01
In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced.
Metrics for comparing dynamic earthquake rupture simulations
Barall, Michael; Harris, Ruth A.
2014-01-01
Earthquakes are complex events that involve a myriad of interactions among multiple geologic features and processes. One of the tools that is available to assist with their study is computer simulation, particularly dynamic rupture simulation. A dynamic rupture simulation is a numerical model of the physical processes that occur during an earthquake. Starting with the fault geometry, friction constitutive law, initial stress conditions, and assumptions about the condition and response of the near‐fault rocks, a dynamic earthquake rupture simulation calculates the evolution of fault slip and stress over time as part of the elastodynamic numerical solution (Ⓔ see the simulation description in the electronic supplement to this article). The complexity of the computations in a dynamic rupture simulation make it challenging to verify that the computer code is operating as intended, because there are no exact analytic solutions against which these codes’ results can be directly compared. One approach for checking if dynamic rupture computer codes are working satisfactorily is to compare each code’s results with the results of other dynamic rupture codes running the same earthquake simulation benchmark. To perform such a comparison consistently, it is necessary to have quantitative metrics. In this paper, we present a new method for quantitatively comparing the results of dynamic earthquake rupture computer simulation codes.
Three-dimensional dynamic range reduction techniques
NASA Astrophysics Data System (ADS)
Harding, Kevin G.; Qian, Xiaoping
2004-02-01
A significant limitation of the application of 3D structured light systems has been the large dynamic range of reflectivity of typical parts such as machined parts. The advent of digital cameras have helped this problem to some extent by providing a larger dynamic range of detection, but often parts must still be coated with white paint or powder to get a good enough return for 3D measurement techniques such as structured light. This paper will present an overview of methods that have been used to minimize the range of light reflections from many parts including polarization, multiple exposure, multiple viewing and masking techniques. Also presented will be methods of analysis such as phase analysis techniques which can provide improved robustness. Finally, we will discuss the pros and cons of these options as applied to the application of 3D structured light techniques to machined metal parts.
Mapping conformational dynamics of proteins using torsional dynamics simulations.
Gangupomu, Vamshi K; Wagner, Jeffrey R; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan
2013-05-07
All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein's experimentally established conformational substates. Conformational transition of calmodulin from the Ca(2+)-bound to the Ca(2+)-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in
Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations
Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan
2013-01-01
All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in
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.
Noise reduction by recycling dynamically coupled time series.
Mera, M Eugenia; Morán, Manuel
2011-12-01
We say that several scalar time series are dynamically coupled if they record the values of measurements of the state variables of the same smooth dynamical system. We show that much of the information lost due to measurement noise in a target time series can be recovered with a noise reduction algorithm by crossing the time series with another time series with which it is dynamically coupled. The method is particularly useful for reduction of measurement noise in short length time series with high uncertainties.
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.
Noise reduction by dynamic signal preemphasis.
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 (13)C 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. Copyright © 2010 Elsevier Inc. All rights reserved.
Simulation Exercises in Population Dynamics.
ERIC Educational Resources Information Center
Falk, Laurence L.; Falk, Carol J.
1986-01-01
Describes a computer simulation providing population change profiles at 5-year intervals for 100 years, projecting natural rate of increase and total population, per capita gross national product, energy consumption, age-specific fertility rates, and survival ratios. Data sources for the simulation, sample printed output, and learning activities…
Simulating protein dynamics: Novel methods and applications
NASA Astrophysics Data System (ADS)
Vishal, V.
This Ph.D dissertation describes several methodological advances in molecular dynamics (MD) simulations. Methods like Markov State Models can be used effectively in combination with distributed computing to obtain long time scale behavior from an ensemble of short simulations. Advanced computing architectures like Graphics Processors can be used to greatly extend the scope of MD. Applications of MD techniques to problems like Alzheimer's Disease and fundamental questions in protein dynamics are described.
Discrete Molecular Dynamics Simulation of Biomolecules
NASA Astrophysics Data System (ADS)
Ding, Feng
2011-10-01
Discrete molecular dynamics (DMD) simulation of hard spheres was the first implementation of molecular dynamics (MD) in history. DMD simulations are computationally more efficient than continuous MD simulations due to simplified interaction potentials. However, also due to these simplified potentials, DMD has often been associated with coarse-grained modeling, and hence continuous MD has become the dominant approach used to study the internal dynamics of biomolecules. With the recent advances in DMD methodology, including the development of high-resolution models for biomolecules and approaches to increase DMD efficiency, DMD simulations are emerging as an important tool in the field of molecular modeling, including the study of protein folding, protein misfolding and aggregation, and protein engineering. Recently, DMD methodology has been applied to modeling RNA folding and protein-ligand recognition. With these improvements to DMD methodology and the continuous increase in available computational power, we expect a growing role of DMD simulations in our understanding of biology.
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)
Visualizing Structure and Dynamics of Disaccharide Simulations
Matthews, J. F.; Beckham, G. T.; Himmel, M. E.; Crowley, M. F.
2012-01-01
We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.
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.
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.
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.
Simulation and model reduction for the AFW program
NASA Technical Reports Server (NTRS)
Buttrill, Carey; Bacon, Barton; Heeg, Jennifer; Houck, Jacob; Wood, David
1992-01-01
The simulation methodology used in the Active Flexible Wing wind-tunnel test program is described. An overview of the aeroservoelastic modeling used in building the required batch and hot-bench simulations is presented. Successful hot-bench implementation required that the full mathematical model be significantly reduced while assuring that accuracy be maintained for all combinations of 10 inputs and 56 outputs. The reduction was accomplished by using a method based on internally balanced realizations and focussing on the linear, aeroelastic portion of the full mathematical model. The error-bound properties of the internally balanced realization significantly contribute to its utility in the model reduction process. The reduction method and the results achieved are described.
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.
Model Order Reduction for Fluid Dynamics with Moving Solid Boundary
NASA Astrophysics Data System (ADS)
Gao, Haotian; Wei, Mingjun
2016-11-01
We extended the application of POD-Galerkin projection for model order reduction from usual fixed-domain problems to more general fluid-solid systems when moving boundary/interface is involved. The idea is similar to numerical simulation approaches using embedded forcing terms to represent boundary motion and domain change. However, such a modified approach will not get away with the unsteadiness of boundary terms which appear as time-dependent coefficients in the new Galerkin model. These coefficients need to be pre-computed for prescribed motion, or worse, to be computed at each time step for non-prescribed motion. The extra computational cost gets expensive in some cases and eventually undermines the value of using reduced-order models. One solution is to decompose the moving boundary/domain to orthogonal modes and derive another low-order model with fixed coefficients for boundary motion. Further study shows that the most expensive integrations resulted from the unsteady motion (in both original and domain-decomposition approaches) have almost negligible impact on the overall dynamics. Dropping these expensive terms reduces the computation cost by at least one order while no obvious effect on model accuracy is noticed. Supported by ARL.
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. PMID:26604800
Speckle reduction in laser projection using a dynamic deformable mirror.
Tran, Thi-Kim-Trinh; Chen, Xuyuan; Svensen, Øyvind; Akram, Muhammad Nadeem
2014-05-05
Despite of much effort and significant progress in recent years, speckle removal is still a challenge for laser projection technology. In this paper, speckle reduction by dynamic deformable mirror was investigated. Time varying independent speckle patterns were generated due to the angle diversity introduced by the dynamic mirror, and these speckle patterns were averaged out by the camera or human eyes, thus reducing speckle contrast in the final image. The speckle reduction by the wavelength diversity of the lasers was also studied. Both broadband lasers and narrowband laser were used for experiment. It is experimentally shown that speckle suppression can be attained by the widening of the spectrum of the lasers. Lower speckle contrast reduction was attained by the wavelength diversity for narrowband laser compared to the broadband lasers. This method of speckle reduction is suitable in laser projectors for wide screen applications where high power laser illumination is needed.
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.
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.
Computational plasticity algorithm for particle dynamics simulations
NASA Astrophysics Data System (ADS)
Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.
2017-03-01
The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.
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
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.
Dynamic simulation of particle sedimentation
NASA Astrophysics Data System (ADS)
Zhang, Zhongzhen; Prosperetti, Andrea
2004-11-01
The sedimentation of 1024 spheres has been simulated via a recently developed method:Physalis Method. Particles are initially randomly distributed and periodic boundary conditions are assumed. The time evolution of the particle spatial distribution is studied by meassuering the structure factor. Properties of particles velocity distribution, e.g. variance, time autocorrelation, have been studied. The effects of particle rotation and collision are discussed.
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
The data system dynamic simulation /DSDS/
NASA Technical Reports Server (NTRS)
Hooper, J. W.; Piner, J. R.
1978-01-01
The paper describes the development by NASA of the data system dynamic simulation (DSDS) which provides a data system simulation capability for a broad range of programs, with the capability to model and simulate all or any portion of an end-to-end data system to multiple levels of fidelity. Versatility is achieved by specifying parameters which define the performance characteristics of data system components, and by specifying control and data paths in a data system. DSDS helps reduce overall simulation cost and the time required for obtaining a data systems analysis, and helps provide both early realistic representations of data systems and the flexibility to study design changes and operating strategies.
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
Perspective: chemical dynamics simulations of non-statistical reaction dynamics.
Ma, Xinyou; Hase, William L
2017-04-28
Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Author(s).
Molecular dynamics simulation of dipalmitoylphosphatidylserine bilayer with Na+ counterions.
Pandit, Sagar A; Berkowitz, Max L
2002-01-01
We performed a molecular dynamics simulation of dipalmitoylphosphatidylserine (DPPS) bilayer with Na+ counterions. We found that hydrogen bonding between the NH group and the phosphate group leads to a reduction in the area per headgroup when compared to the area in dipalmitoylphosphatidylcholine bilayer. The Na+ ions bind to the oxygen in the carboxyl group of serine, thus giving rise to a dipolar bilayer similar to dipalmitoylphosphatidylethanolamine bilayer. The results of the simulation show that counterions play a crucial role in determining the structural and electrostatic properties of DPPS bilayer. PMID:11916841
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.
Dynamic centrifugal compressor model for system simulation
NASA Astrophysics Data System (ADS)
Jiang, Wei; Khan, Jamil; Dougal, Roger A.
A dynamic model of a centrifugal compressor capable of system simulation in the virtual test bed (VTB) computational environment is presented. The model is based on first principles, i.e. the dynamic performance including the losses is determined from the compressor geometry and not from the experimentally determined characteristic performance curves. In this study, the compressor losses, such as incidence and friction losses, etc., are mathematically modeled for developing compressor characteristics. For easy implementation in the VTB platform, the non-linear governing equations are discretized in resistive companion (RC) form. The developed simulation model can be applied to virtually any centrifugal compressor. By interfacing with a composite system, such as a Brayton cycle gas turbine, or a fuel cell, the compressor dynamic performance can be evaluated. The surge line for the compressor can also be determined from the simulation results. Furthermore, the model presented here provides a valuable tool for evaluating the system performance as a function of various operating parameters.
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.
Molecular dynamics simulations of substitutional diffusion
Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob
2016-12-18
In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less
Molecular dynamics simulations of substitutional diffusion
Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob
2016-12-18
In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example, we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.
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.
Dynamic modeling and simulation of planetary rovers
NASA Technical Reports Server (NTRS)
Lindemann, Randel A.
1992-01-01
This paper documents a preliminary study into the dynamic modeling and computer simulation of wheeled surface vehicles. The research centered on the feasibility of using commercially available multibody dynamics codes running on engineering workstations to perform the analysis. The results indicated that physically representative vehicle mechanics can be modeled and simulated in state-of-the-art Computer Aided Engineering environments, but at excessive cost in modeling and computation time. The results lead to the recommendation for the development of an efficient rover mobility-specific software system. This system would be used for vehicle design and simulation in planetary environments; controls prototyping, design, and testing; as well as local navigation simulation and expectation planning.
Choice of timestep in molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Fincham, David
1986-06-01
In molecular dynamics computer simulation of liquids it is important to use as large a timestep as possible in order to sample phase space rapidly and save on computer expense. The effect of the resulting algorithm errors in the trajectories of the molecules is not well understood. An empirical investigation into this question is reported. Several simulations differing only in the timestep used are compared. It is found that much larger timesteps than usual can be employed without producing significant errors in observed thermodynamic, structural or dynamic properties.
Massively-Parallel Dislocation Dynamics Simulations
Cai, W; Bulatov, V V; Pierce, T G; Hiratani, M; Rhee, M; Bartelt, M; Tang, M
2003-06-18
Prediction of the plastic strength of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of the existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, in order to be statistically representative and to reproduce experimentally observed microstructures. A new massively-parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We discuss the general aspects of this code that make such large scale simulations possible, as well as a few initial simulation results.
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.
Dynamics modeling and simulation of flexible airships
NASA Astrophysics Data System (ADS)
Li, Yuwen
The resurgence of airships has created a need for dynamics models and simulation capabilities of these lighter-than-air vehicles. The focus of this thesis is a theoretical framework that integrates the flight dynamics, structural dynamics, aerostatics and aerodynamics of flexible airships. The study begins with a dynamics model based on a rigid-body assumption. A comprehensive computation of aerodynamic effects is presented, where the aerodynamic forces and moments are categorized into various terms based on different physical effects. A series of prediction approaches for different aerodynamic effects are unified and applied to airships. The numerical results of aerodynamic derivatives and the simulated responses to control surface deflection inputs are verified by comparing to existing wind-tunnel and flight test data. With the validated aerodynamics and rigid-body modeling, the equations of motion of an elastic airship are derived by the Lagrangian formulation. The airship is modeled as a free-free Euler-Bernoulli beam and the bending deformations are represented by shape functions chosen as the free-free normal modes. In order to capture the coupling between the aerodynamic forces and the structural elasticity, local velocity on the deformed vehicle is used in the computation of aerodynamic forces. Finally, with the inertial, gravity, aerostatic and control forces incorporated, the dynamics model of a flexible airship is represented by a single set of nonlinear ordinary differential equations. The proposed model is implemented as a dynamics simulation program to analyze the dynamics characteristics of the Skyship-500 airship. Simulation results are presented to demonstrate the influence of structural deformation on the aerodynamic forces and the dynamics behavior of the airship. The nonlinear equations of motion are linearized numerically for the purpose of frequency domain analysis and for aeroelastic stability analysis. The results from the latter for the
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.
Numerical simulation of interplanetary dynamics
NASA Astrophysics Data System (ADS)
Wu, Chin-Chun
This dissertation discusses investigations into the physics of the propagation of solar generated disturbances in the interplanetary medium. The motivation to initiate this study was two-fold: (1) understanding the fundamental physics of the nonlinear interactions of solar generated MHD shocks and non-homogeneous interplanetary medium, and (2) understanding the physics of solar generated disturbance effects on the Earth's environment, (i.e. the solar connection to the geomagnetic storm). In order to achieve these goals, the authors employed two numerical models to encompass these studies. In the first part, a one-dimensional MHD code with adaptive grids is used to study the evolution of interplanetary slow shocks (ISS), the interaction of a forward slow shock with a reverse slow shock, and the interaction of a fast shock with a slow shock. Results show that the slow shocks can be generated by a decreasing density, velocity or temperature perturbation or by a pressure pulse by following a forward fast shock and that slow shocks can propagate over 1 AU; results also show that the ISS never evolves into fast shocks. Interestingly, it is also found that an ISS could be 'eaten up' by an interplanetary fast shock (IFS) catching up from behind. This could be a reason that the slow shock has been difficult to observe near 1 AU. In addition, a forward slow shock could be dissipated by following a strong forward fast shock (Mach number greater than 1.7). In the second part, a fully three-dimensional (3D), time-dependent, MHD interplanetary global model (3D IGM) is used to study the relationship between different forms of solar activity and transient variations of the north-south component, Bx, of the interplanetary magnetic field, IMF, at 1 AU. One form of solar activity, the flare, is simulated by using a pressure pulse at different locations near the solar surface and observing the simulated IMF evolution of Btheta (= -Bx) at 1 AU. Results show that, for a given pressure
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.
Quantum Simulation for Open-System Dynamics
NASA Astrophysics Data System (ADS)
Wang, Dong-Sheng; de Oliveira, Marcos Cesar; Berry, Dominic; Sanders, Barry
2013-03-01
Simulations are essential for predicting and explaining properties of physical and mathematical systems yet so far have been restricted to classical and closed quantum systems. Although forays have been made into open-system quantum simulation, the strict algorithmic aspect has not been explored yet is necessary to account fully for resource consumption to deliver bounded-error answers to computational questions. An open-system quantum simulator would encompass classical and closed-system simulation and also solve outstanding problems concerning, e.g. dynamical phase transitions in non-equilibrium systems, establishing long-range order via dissipation, verifying the simulatability of open-system dynamics on a quantum Turing machine. We construct an efficient autonomous algorithm for designing an efficient quantum circuit to simulate many-body open-system dynamics described by a local Hamiltonian plus decoherence due to separate baths for each particle. The execution time and number of gates for the quantum simulator both scale polynomially with the system size. DSW funded by USARO. MCO funded by AITF and Brazilian agencies CNPq and FAPESP through Instituto Nacional de Ciencia e Tecnologia-Informacao Quantica (INCT-IQ). DWB funded by ARC Future Fellowship (FT100100761). BCS funded by AITF, CIFAR, NSERC and USARO.
Gearbox bearing fault simulation using a finite element model reduction technique
NASA Astrophysics Data System (ADS)
Deshpande, L.; Sawalhi, N.; Randall, R. B.
2012-05-01
The dynamics of a mechanical system such as a gearbox assembly comprising shafts, gears and bearings can be simulated using Lumped Parameter Models (LPMs). Finite Element Method (FEM) reduction techniques based on the Craig-Bampton method of Component Mode Synthesis (CMS) are useful in creating more accurate dynamic models. These models, despite having more degrees-of-freedom for the individual components than the LPM, make very much larger FE models computationally tractable. In this paper both these approaches, namely LPM and reduced FEM, are compared to create a dynamic model of a gearbox. Earlier simulation models (both LPM and combined LPM and reduced FEM) are further improved to better match the geometry of the bearing faults used in the experimental measurements, and the experimental results from a gearbox test rig. The dynamic model is used to simulate the vibration signals in the presence of localised inner and outer race faults. The new results show better correspondence with the measured signals, in particular with respect to the detailed response to entry and exit from the fault, which can be used to determine fault size. The paper highlights the plausibility of fault simulation in Machine Condition Monitoring (MCM) where a large amount of data can be gathered without experiencing large numbers of actual failures or carrying out costly and time consuming experiments until failure with seeded faults. The simulation data can be used to train neural networks to automate the diagnostic and prognostic processes.
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.
Multiscale model approach for magnetization dynamics simulations
NASA Astrophysics Data System (ADS)
De Lucia, Andrea; Krüger, Benjamin; Tretiakov, Oleg A.; Kläui, Mathias
2016-11-01
Simulations of magnetization dynamics in a multiscale environment enable the rapid evaluation of the Landau-Lifshitz-Gilbert equation in a mesoscopic sample with nanoscopic accuracy in areas where such accuracy is required. We have developed a multiscale magnetization dynamics simulation approach that can be applied to large systems with spin structures that vary locally on small length scales. To implement this, the conventional micromagnetic simulation framework has been expanded to include a multiscale solving routine. The software selectively simulates different regions of a ferromagnetic sample according to the spin structures located within in order to employ a suitable discretization and use either a micromagnetic or an atomistic model. To demonstrate the validity of the multiscale approach, we simulate the spin wave transmission across the regions simulated with the two different models and different discretizations. We find that the interface between the regions is fully transparent for spin waves with frequency lower than a certain threshold set by the coarse scale micromagnetic model with no noticeable attenuation due to the interface between the models. As a comparison to exact analytical theory, we show that in a system with a Dzyaloshinskii-Moriya interaction leading to spin spirals, the simulated multiscale result is in good quantitative agreement with the analytical calculation.
Simulating Dynamic Equilibria: A Class Experiment
NASA Astrophysics Data System (ADS)
Harrison, John A.; Buckley, Paul D.
2000-08-01
A first-order reversible reaction is simulated on an overhead projector using small coins or discs. A simulation is carried out in which initially there are 24 discs representing reactant A and none representing reactant B. At the end of each minute half of the reactant A discs get converted to reactant B, and one quarter of the reactant B discs get converted to reactant A discs. Equilibrium is established with 8 A discs and 16 B discs, and no further net change is observed as the simulation continues. Another simulation beginning with 48 A discs and 0 B discs leads at equilibrium to 16 A discs and 32 B discs. These results illustrate how dynamic equilibria are established and allow the introduction of the concept of an equilibrium constant. Le Châtelier's principle is illustrated by further simulations.
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.
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.
Dynamics Simulation of Langmuir-Blodgett Films
1990-04-01
of water. During the dynamics simulation, theposition of the water molecules are frozen. A 1515 edge effect as shown in Fig. 4: the tilts for...temperature, I.e. 300K, by gradually assigning random understand. The strong edge effect makes it necessary to iintroduce periodic boundaries In future
Molecular dynamics simulations of magnetized dusty plasmas
NASA Astrophysics Data System (ADS)
Piel, Alexander; Reichstein, Torben; Wilms, Jochen
2012-10-01
The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)
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.
GROSS- GAMMA RAY OBSERVATORY ATTITUDE DYNAMICS SIMULATOR
NASA Technical Reports Server (NTRS)
Garrick, J.
1994-01-01
The Gamma Ray Observatory (GRO) spacecraft will constitute a major advance in gamma ray astronomy by offering the first opportunity for comprehensive observations in the range of 0.1 to 30,000 megaelectronvolts (MeV). The Gamma Ray Observatory Attitude Dynamics Simulator, GROSS, is designed to simulate this mission. The GRO Dynamics Simulator consists of three separate programs: the Standalone Profile Program; the Simulator Program, which contains the Simulation Control Input/Output (SCIO) Subsystem, the Truth Model (TM) Subsystem, and the Onboard Computer (OBC) Subsystem; and the Postprocessor Program. The Standalone Profile Program models the environment of the spacecraft and generates a profile data set for use by the simulator. This data set contains items such as individual external torques; GRO spacecraft, Tracking and Data Relay Satellite (TDRS), and solar and lunar ephemerides; and star data. The Standalone Profile Program is run before a simulation. The SCIO subsystem is the executive driver for the simulator. It accepts user input, initializes parameters, controls simulation, and generates output data files and simulation status display. The TM subsystem models the spacecraft dynamics, sensors, and actuators. It accepts ephemerides, star data, and environmental torques from the Standalone Profile Program. With these and actuator commands from the OBC subsystem, the TM subsystem propagates the current state of the spacecraft and generates sensor data for use by the OBC and SCIO subsystems. The OBC subsystem uses sensor data from the TM subsystem, a Kalman filter (for attitude determination), and control laws to compute actuator commands to the TM subsystem. The OBC subsystem also provides output data to the SCIO subsystem for output to the analysts. The Postprocessor Program is run after simulation is completed. It generates printer and CRT plots and tabular reports of the simulated data at the direction of the user. GROSS is written in FORTRAN 77 and
GROSS- GAMMA RAY OBSERVATORY ATTITUDE DYNAMICS SIMULATOR
NASA Technical Reports Server (NTRS)
Garrick, J.
1994-01-01
The Gamma Ray Observatory (GRO) spacecraft will constitute a major advance in gamma ray astronomy by offering the first opportunity for comprehensive observations in the range of 0.1 to 30,000 megaelectronvolts (MeV). The Gamma Ray Observatory Attitude Dynamics Simulator, GROSS, is designed to simulate this mission. The GRO Dynamics Simulator consists of three separate programs: the Standalone Profile Program; the Simulator Program, which contains the Simulation Control Input/Output (SCIO) Subsystem, the Truth Model (TM) Subsystem, and the Onboard Computer (OBC) Subsystem; and the Postprocessor Program. The Standalone Profile Program models the environment of the spacecraft and generates a profile data set for use by the simulator. This data set contains items such as individual external torques; GRO spacecraft, Tracking and Data Relay Satellite (TDRS), and solar and lunar ephemerides; and star data. The Standalone Profile Program is run before a simulation. The SCIO subsystem is the executive driver for the simulator. It accepts user input, initializes parameters, controls simulation, and generates output data files and simulation status display. The TM subsystem models the spacecraft dynamics, sensors, and actuators. It accepts ephemerides, star data, and environmental torques from the Standalone Profile Program. With these and actuator commands from the OBC subsystem, the TM subsystem propagates the current state of the spacecraft and generates sensor data for use by the OBC and SCIO subsystems. The OBC subsystem uses sensor data from the TM subsystem, a Kalman filter (for attitude determination), and control laws to compute actuator commands to the TM subsystem. The OBC subsystem also provides output data to the SCIO subsystem for output to the analysts. The Postprocessor Program is run after simulation is completed. It generates printer and CRT plots and tabular reports of the simulated data at the direction of the user. GROSS is written in FORTRAN 77 and
Accelerated molecular dynamics simulations of protein folding.
Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew
2015-07-30
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.
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.
Microsecond Molecular Dynamics Simulations of Lipid Mixing
2015-01-01
Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na+ ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes. PMID:25237736
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.
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
2016-01-06
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.
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
Identifying patients who may benefit from inferior turbinate reduction using computer simulations
Hariri, Benjamin M.; Rhee, John S.; Garcia, Guilherme J. M.
2015-01-01
Objectives (1) To determine objective criteria to predict which patients may benefit most from inferior turbinate reduction surgery. (2) To test whether the site of turbinate reduction, either along the nasal floor (bottom resection) or along the septal side (medial resection), impacts the extent to which nasal resistance is reduced. Study Design Case series. Methods Three-dimensional reconstructions of the nasal anatomy of five nasal airway obstruction patients were created based on pre-surgical computed tomography scans. Inferior turbinate reduction models were created for each patient using virtual surgery. Airflow, heat transfer, and humidity transport during inspiration were simulated using computational fluid dynamics (CFD). Results Nasal resistance curves revealed little to no difference between bottom resection and medial resection models. In two patients, little change was observed in nasal resistance after virtual inferior turbinate reduction, which was attributed to the narrowest cross-sections being restricted to the anterior nose (i.e., anterior to the inferior turbinate). The three patients whose nasal resistances decreased substantially after virtual inferior turbinate reduction had a narrower airspace in the turbinate region and higher nasal resistance pre-surgery. Nasal air conditioning capacity was more affected by medial resections. Conclusion CFD simulations predicted no significant difference in the decrease in nasal resistance between virtual inferior turbinate reductions performed by bottom vs. medial resection of the turbinate. However, bottom resections better preserved the calculated humidification efficiency. The simulations predicted that the greatest reduction in nasal resistance occurs in patients with highest pre-surgical resistance in the turbinate region. PMID:25963247
Identifying patients who may benefit from inferior turbinate reduction using computer simulations.
Hariri, Benjamin M; Rhee, John S; Garcia, Guilherme J M
2015-12-01
(1) To determine objective criteria to predict which patients may benefit most from inferior turbinate reduction surgery. (2) To test whether the site of turbinate reduction, either along the nasal floor (bottom resection) or along the septal side (medial resection), impacts the extent to which nasal resistance is reduced. Case series. Three-dimensional reconstructions of the nasal anatomy of five nasal airway obstruction patients were created based on presurgical computed tomography scans. Inferior turbinate reduction models were created for each patient using virtual surgery. Airflow, heat transfer, and humidity transport during inspiration were simulated using computational fluid dynamics (CFD). Nasal resistance curves revealed little to no difference between bottom resection and medial resection models. In two patients, little change was observed in nasal resistance after virtual inferior turbinate reduction, which was attributed to the narrowest cross-sections being restricted to the anterior nose (i.e., anterior to the inferior turbinate). The three patients whose nasal resistances decreased substantially after virtual inferior turbinate reduction had a narrower airspace in the turbinate region and higher nasal resistance presurgery. Nasal air conditioning capacity was more affected by medial resections. CFD simulations predicted no significant difference in the decrease in nasal resistance between virtual inferior turbinate reductions performed by bottom versus medial resection of the turbinate. However, bottom resections better preserved the calculated humidification efficiency. The simulations predicted that the greatest reduction in nasal resistance occurs in patients with the highest presurgical resistance in the turbinate region. 4. © 2015 The American Laryngological, Rhinological and Otological Society, Inc.
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 Multicore Processing for Pandemic Influenza Simulation
Eriksson, Henrik; Timpka, Toomas; Spreco, Armin; Dahlström, Örjan; Strömgren, Magnus; Holm, Einar
2016-01-01
Pandemic simulation is a useful tool for analyzing outbreaks and exploring the impact of variations in disease, population, and intervention models. Unfortunately, this type of simulation can be quite time-consuming especially for large models and significant outbreaks, which makes it difficult to run the simulations interactively and to use simulation for decision support during ongoing outbreaks. Improved run-time performance enables new applications of pandemic simulations, and can potentially allow decision makers to explore different scenarios and intervention effects. Parallelization of infection-probability calculations and multicore architectures can take advantage of modern processors to achieve significant run-time performance improvements. However, because of the varying computational load during each simulation run, which originates from the changing number of infectious persons during the outbreak, it is not useful to us the same multicore setup during the simulation run. The best performance can be achieved by dynamically changing the use of the available processor cores to balance the overhead of multithreading with the performance gains of parallelization. PMID:28269849
Network Visualization of Conformational Sampling during Molecular Dynamics Simulation
Ahlstrom, Logan S.; Baker, Joseph Lee; Ehrlich, Kent; Campbell, Zachary T.; Patel, Sunita; Vorontsov, Ivan I.; Tama, Florence; Miyashita, Osamu
2013-01-01
Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions. PMID:24211466
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.
Kinetic dynamics simulation of the detached plasma
NASA Astrophysics Data System (ADS)
Pianpanit, Theerasarn; Ishiguro, Seiji; Hasegawa, Hiroki
2015-11-01
The detached plasma has been proposed to reduce the heat flux to the divertor. Fluid code has been widely used to investigate the detached plasma but the cooling of plasma, trapped particle effects, and other kinetic dynamics in the detached plasma has not been well understood. Particle-in-Cell (PIC) simulation with the Monte Carlo collisions and the cumulative scattering angle coulomb collision are carried out to study dynamical kinetic behavior of the plasma. The constant pressure and temperature of neutral gas box in front of the divertor target model has been used in the simulation. The results show the decrease in electron temperature in front of the divertor plate strongly relate to the Coulomb collision frequency.
Brownian dynamics simulations of amelogenin microribbons formation
NASA Astrophysics Data System (ADS)
Li, Wei; Perez Lopez, Anthony; Liu, Ya; Chakrabarti, Amit; Gunton, James
2011-03-01
Recent advances in chemical particle synthesis have emphasized the fundamental role of surface colloidal heterogeneities and their detailed chemical composition, which is particularly significant for an important subclass of colloidal systems, namely, proteins. Recently, the process of self-assembly of amelogenin monomers with a hydrophobic/hydrophilic bipolar nature into ordered ribbon structures has been studied experimentally. In this work, we study this dynamical process by means of a Brownian dynamic simulation of a simple model which represents the bipolar character of the globular amelogenin molecule and the hydrophilic C-terminal tail. We monitor the kinetics of self-assembly through a study of the structure factor. We also calculate the phase diagram of the model using Gibbs ensemble Monte Carlo simulation and thermodynamic perturbation theory. This work is supported by grants from the NSF and Mathers Foundation.
Hydration dynamics in water clusters via quantum molecular dynamics simulations
Turi, László
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of
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.
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.
IGCC Dynamic Simulator and Training Center
Zitney, S.E.; Erbes, M.R.
2006-10-01
Integrated Gasification Combined Cycle (IGCC) is emerging as the technology of choice for providing clean, low-cost electricity for the next generation of coal-fired power plants and will play a central role in the development of high-efficiency, zero-emissions power plants such as FutureGen. Several major utilities and developers recently announced plans to build IGCC plants and other major utilities are evaluating IGCC’s suitability for base-load capacity additions. This recent surge of attention to IGCC power generation is creating a growing demand for experience with the analysis, operation, and control of commercial-scale IGCC plants. To meet this need, the National Energy Technology Laboratory (NETL) has launched a project to develop a generic, full-scope, IGCC dynamic plant simulator for use in establishing a state-of-the-art simulator training center at West Virginia University’s (WVU) National Research Center for Coal and Energy (NRCCE). The IGCC Dynamic Simulator & Training (DS&T) Center will be established under the auspices of the Collaboratory for Process & Dynamic Systems Modeling (“Collaboratory”) organized between NETL, WVU, the University of Pittsburgh, and Carnegie Mellon University.
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.
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
Adaptive wavelet simulation of global ocean dynamics
NASA Astrophysics Data System (ADS)
Kevlahan, N. K.-R.; Dubos, T.; Aechtner, M.
2015-07-01
In order to easily enforce solid-wall boundary conditions in the presence of complex coastlines, we propose a new mass and energy conserving Brinkman penalization for the rotating shallow water equations. This penalization does not lead to higher wave speeds in the solid region. The error estimates for the penalization are derived analytically and verified numerically for linearized one dimensional equations. The penalization is implemented in a conservative dynamically adaptive wavelet method for the rotating shallow water equations on the sphere with bathymetry and coastline data from NOAA's ETOPO1 database. This code could form the dynamical core for a future global ocean model. The potential of the dynamically adaptive ocean model is illustrated by using it to simulate the 2004 Indonesian tsunami and wind-driven gyres.
Brownian dynamics simulation of electrostatically interacting proteins
NASA Astrophysics Data System (ADS)
Ermakova, E.; Krushelnitsky, A. G.; Fedotov, V. D.
Brownian dynamics simulation software has been developed to study the dynamics of proteins as a whole in solution. The proteins were modelled as spheres with point dipoles embedded in the centre of sphere. A set of Brownian dynamics simulations at different values of the dipole moments, protein concentration and translational diffusion coefficient was performed to investigate the influence of interprotein electrostatic interactions on dynamic protein behaviour in solution. It was shown that these interactions led to the slowing down of protein rotation and a complex non-exponential shape of the rotational correlation function. Analysis of the correlation functions was performed within the frame of the model of electrostatic interprotein interactions advanced earlier on the basis of NMR and dielectric spectroscopy data. This model assumes that, due to electrostatic interactions, protein Brownian rotation becomes anisotropic. The lifetime of this anisotropy is controlled mainly by translational diffusion of proteins. Thus, the correlation function can be decomposed into two components corresponding to anisotropic Brownian rotation and an isotropic motion of an external electric field vector produced by the surrounding proteins.
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.
Molecular Dynamics Simulations of Network Glasses
NASA Astrophysics Data System (ADS)
Drabold, David A.
The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References
SPIRou @ CFHT: data reduction software and simulation tools
NASA Astrophysics Data System (ADS)
Artigau, Étienne; Bouchy, François; Delfosse, Xavier; Bonfils, Xavier; Donati, Jean-François; Figueira, Pedro; Thanjavur, Karun; Lafrenière, David; Doyon, René; Surace, Christian; Moutou, Claire; Boisse, Isabelle; Saddlemyer, Leslie; Loop, David; Kouach, Driss; Pepe, Francesco; Lovis, Christophe; Hernandez, Olivier; Wang, Shiang-Yu
2012-09-01
SPIRou is a near-infrared, echelle spectropolarimeter/velocimeter under design for the 3.6m Canada-France- Hawaii Telescope (CFHT) on Mauna Kea, Hawaii. The unique scientific capabilities and technical design features are described in the accompanying papers at this conference. In this paper we focus on the data reduction software (DRS) and the data simulation tool. The SPIRou DRS builds upon the experience of the existing SOPHIE, HARPS and ESPADONS spectrographs; class-leaders instruments for high-precision RV measurements and spectropolarimetry. While SPIRou shares many characteristics with these instruments, moving to the near- infrared domain brings specific data-processing challenges: the presence of a large number of telluric absorption lines, strong emission sky lines, thermal background, science arrays with poorer cosmetics, etc. In order for the DRS to be fully functional for SPIRou's first light in 2015, we developed a data simulation tool that incorporates numerous instrumental and observational e_ects. We present an overview of the DRS and the simulation tool architectures.
MDLab: a molecular dynamics simulation prototyping environment.
Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R; Izaguirre, Jesús A
2010-05-01
Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net. Copyright 2009 Wiley Periodicals, Inc.
Molecular dynamics simulation in virus research
Ode, Hirotaka; Nakashima, Masaaki; Kitamura, Shingo; Sugiura, Wataru; Sato, Hironori
2012-01-01
Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique. PMID:22833741
Nanodrop contact angles from molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim
2016-11-01
The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.
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.
Classical Molecular Dynamics Simulation of Nuclear Fuel
Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie
2015-10-10
Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.
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.
Microwave reduction of graphene oxide rationalized by reactive molecular dynamics.
Chaban, Vitaly V; Prezhdo, Oleg V
2017-03-17
Obtaining graphene (GRA) in industrial quantities is among the most urgent goals in today's nanotechnology. Elegant methods involve the oxidation of graphite with its subsequent solvent-assisted exfoliation. The reduction of graphene oxide (GO) is challenging leading to a highly-disordered oxygen-rich material. A particularly successful microwave-induced reduction of GO was reported recently (Science, 2016, 353, 1413-1416). We mimic the experiment by reactive molecular dynamics and establish the molecular mechanisms of reduction and their time scales as functions of temperature. We show that the rapid removal of oxygen groups achieved by microwave heating leaves GRA sheets intact. The epoxy groups are most stable within GO. They can rearrange into the carbonyl groups upon quick heating. It is important to avoid creating holes upon graphite oxidation. They cannot be healed easily and undermine GRA thermal stability and electronic properties. The edge oxygen groups cannot be removed by irradiation, but their effect is marginal on the properties of μm GRA sheets. We demonstrate that different oxygen groups are removed from GO at drastically different temperatures. Therefore, it is possible to obtain separate fractions, e.g. carbonyl-, hydroxyl- and carboxyl-free partially reduced GO. Our results guide the improvement of the GO reduction methods and can be tested directly by experiment.
Dynamic simulation of regulatory networks using SQUAD
Di Cara, Alessandro; Garg, Abhishek; De Micheli, Giovanni; Xenarios, Ioannis; Mendoza, Luis
2007-01-01
Background The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. Results We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. Conclusion The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or
Robot-musculoskeletal dynamic biomechanical model in robot-assisted diaphyseal fracture reduction.
Li, Changsheng; Wang, Tianmiao; Hu, Lei; Zhang, Lihai; Zhao, Yanpeng; Du, Hailong; Wang, Lifeng; Tang, Peifu
2015-01-01
A number of issues that exist in common fracture reduction surgeries can be mitigated by robot-assisted fracture reduction. However, the safety of patients and the performance of the robot, which are closely related to the muscle forces, are important indexes that restrict the development of robots. Though researchers have done a great deal of work on the biomechanics of the musculoskeletal system, the dynamics of the musculoskeletal system, particularly the aspects related to the function of the robot, is not well understood. For this reason, we represent the complex biological system by establishing a dynamic biomechanical model based on the Hill muscle model and the Kane method for the robot that we have developed and the musculoskeletal system. We analyzed the relationship between the motion and force of the bone fragments and the robot during a simulation of a robot-assisted fracture reduction. The influence of the muscle force on the robot system was predicted and managed. The simulation results provide a basis for a fracture reduction path plan that ensures patient safety and a useful reference for the mechanical design of the robot.
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.
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
Simulations to demonstrate reduction of the Gordon-Haus effect.
Marcuse, D
1992-01-01
The superposition of spontaneous emission noise on a train of soliton pulses produces a random change of the center frequency of the soliton spectrum that causes a change of the group velocity of individual solitons, which in long-light-wave systems translates into a random jitter of the position of the pulses at the receiver. This phenomenon is known as the Gordon-Haus effect. If uncontrolled, the Gordon-Haus effect sets a definite limit on the permissible data rate or on the length of soliton-based light-wave systems. Recently Kodama and Hasegawa [Opt. Lett. 17, 31 (1992)] have shown that the Gordon-Haus effect can be suppressed by placing filters along the fiber that reduce the frequency jitter and the concomitant group-velocity changes. We demonstrate the reduction of the Gordon-Haus effect by computer simulations.
Irving, Daniel; Sorrentino, Francesco
2012-11-01
We present a general framework to study stability of the synchronous solution for a hypernetwork of coupled dynamical systems. We are able to reduce the dimensionality of the problem by using simultaneous block diagonalization of matrices. We obtain necessary and sufficient conditions for stability of the synchronous solution in terms of a set of lower-dimensional problems and test the predictions of our low-dimensional analysis through numerical simulations. Under certain conditions, this technique may yield a substantial reduction of the dimensionality of the problem. For example, for a class of dynamical hypernetworks analyzed in the paper, we discover that arbitrarily large networks can be reduced to a collection of subsystems of dimensionality no more than 2. We apply our reduction technique to a number of different examples, including the class of undirected unweighted hypermotifs with 3 nodes.
Molecular dynamics simulation of fractal aggregate diffusion
NASA Astrophysics Data System (ADS)
Pranami, Gaurav; Lamm, Monica H.; Vigil, R. Dennis
2010-11-01
The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)10.1088/0305-4470/27/9/012] comprised of Np spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D) , but these can be corrected by carrying out simulations using different simulation box sizes. Specifically, the diffusion coefficient is inversely proportional to the length of a cubic simulation box, and the constant of proportionality appears to be independent of the aggregate mass and fractal dimension. Using this result, it is possible to compute infinite dilution diffusion coefficients (Do) for aggregates of arbitrary size and fractal dimension, and it was found that Do∝Np-1/df , as is often assumed by investigators simulating Brownian aggregation of fractal aggregates. The ratio of hydrodynamic radius to radius of gyration is computed and shown to be independent of mass for aggregates of fixed fractal dimension, thus enabling an estimate of the diffusion coefficient for a fractal aggregate based on its radius of gyration.
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.
Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.
Luk, Hoi Ling; Feist, Johannes; Toppari, J Jussi; Groenhof, Gerrit
2017-09-12
When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model with which the effect of the light-matter coupling on the molecular dynamics can be predicted accurately. Here we present a multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons. Using this model we have performed simulations with up to 1600 Rhodamine molecules in a cavity. The results of these simulations reveal that the contributions of the molecules to the polariton are time-dependent due to thermal fluctuations that break symmetry. Furthermore, the simulations suggest that in addition to the cavity quality factor, also the Stokes shift and number of molecules control the lifetime of the polariton. Because large numbers of molecules interacting with confined light can now be simulated in atomic detail, we anticipate that our method will lead to a better understanding of the effects of strong coupling on chemical reactivity. Ultimately the method may even be used to systematically design cavities to control photochemistry.
Detecting Allosteric Networks Using Molecular Dynamics Simulation.
Bowerman, S; Wereszczynski, J
2016-01-01
Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. © 2016 Elsevier Inc. All rights reserved.
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
Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties
Mereghetti, Paolo; Gabdoulline, Razif R.; Wade, Rebecca C.
2010-01-01
The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments. PMID:21112303
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.
2016-10-01
SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
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.
Mobility Laws in Dislocation Dynamics Simulations
Cai, W; Bulatov, V V
2003-10-21
Prediction of the plastic deformation behavior of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, to establish a statistically representative model of crystal plasticity. A new massively-parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We discuss an important ingredient of this code--the mobility laws dictating the behavior of individual dislocations. They are materials input for DD simulations and are constructed based on the understanding of dislocation motion at the atomistic level.
Molecular dynamics simulation of aluminium melting
NASA Astrophysics Data System (ADS)
Novak, Jakob
2016-06-01
Solid-liquid phase transition has been simulated by the molecular dynamics method, using isobaric-isoenthalpic ensemble. For interatomic potential, glue potential has been selected. The original algorithm for bookkeeping of the information on neighbouring relationships of the atoms has been developed and used in this research. Time consumption for calculation of interatomic forces has been reduced from o(N2) to o(N) by the use of this algorithm. Calculations show that phase transition from solid to liquid occurs between 1,000 K and 1,300 K. The simulated temperature of phase transition is higher than the experimental value due to the absence of crystal defects. If constant heat flux is supplied, temperature decreases during melting because the superheated state becomes unstable. During the cooling process, no significant changes of the observed variables were detected due to the high cooling rate, which prevents crystallisation.
Molecular Dynamics Simulations of Hypervelocity Impacts
NASA Astrophysics Data System (ADS)
Owens, Eli T.; Bachlechner, Martina E.
2007-03-01
Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.
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}.
Molecular Dynamics Simulations of Interface Failure
NASA Astrophysics Data System (ADS)
Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.
2007-03-01
The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.
Parallel beam dynamics simulation of linear accelerators
Qiang, Ji; Ryne, Robert D.
2002-01-31
In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity beams and to the study of beam transport in a proposed accelerator for the development of accelerator-driven waste transmutation technologies.
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.
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.
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..
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 Shade and Irradiance Simulation of Aquatic ...
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 accumulates across landscapes and is the main energy driver for increasing aquatic and landscape temperatures at both local and holistic scales. Landscape disturbances such as landuse change, clear cutting, and fire can cause significant variations in the resulting irradiance reaching particular locations. Penumbra can simulate solar angles and irradiance at definable temporal grains as low as one minute while simulating landscape shadowing up to an entire year. Landscapes can be represented at sub-meter resolutions with appropriate spatial data inputs, such as field data or elevation and surface object heights derived from light detection and ranging (LiDAR) data. This work describes Penumbra’s framework and methodology, external model integration capability, and appropriate model application for a variety of watershed restoration project types. First, an overview of Penumbra’s framework reveals what this model adds to the existing ecological modeling domain. Second, Penumbra’s stand-alone and integration modes are explained and demonstrated. Stand-alone modeling results are showcased within the 3-D visualization tool VISTAS (VISualizing Terrestrial-Aquatic Systems), which fluently summariz
Dimensionality reduction and dynamical filtering: Stimulated Brillouin scattering in optical fibers.
Setra, Rafael G; Arroyo-Almanza, Diana A; Ni, Zetian; Murphy, Thomas E; Roy, Rajarshi
2015-08-01
Stimulated Brillouin scattering (SBS) is a noise-driven nonlinear interaction between acoustical and optical waves. In optical fibers, SBS can be observed at relatively low optical powers and can severely limit signal transmission. Although SBS is initiated by high dimensional noise, it also exhibits many of the hallmarks of a complex nonlinear dynamical system. We report here a comprehensive experimental and numerical study of the fluctuations in the reflected Stokes wave produced by SBS in optical fibers. Using time series analysis, we demonstrate a reduction of dimensionality and dynamical filtering of the Stokes wave. We begin with a careful comparison of the measured average transmitted and reflected intensities from below the SBS threshold to saturation of the transmitted power. Initially the power spectra and correlation functions of the time series of the reflected wave fluctuations at the SBS threshold and above are measured and simulated. Much greater dynamical insight is provided when we study the scaling behavior of the intensity fluctuations using Hurst exponents and detrended fluctuation analysis for time scales extending over six orders of magnitude. At the highest input powers, we notice the emergence of three distinct dynamical scaling regimes: persistent, Brownian, and antipersistent. Next, we explore the Hilbert phase fluctuations of the intensity time series and amplitude-phase coupling. Finally, time-delay embedding techniques reveal a gradual reduction in dimensionality of the spatiotemporal dynamics as the laser input is increased toward saturation of the transmitted power. Through all of these techniques, we find a transition from noisier to smoother dynamics with increasing input power. We find excellent agreement between our experimental measurements and simulations.
All-atom simulations of crowding effects on ubiquitin dynamics.
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.
Brownian dynamics simulation of restricted rotational diffusion.
Martínez, M C; García de la Torre, J
1987-01-01
The restricted rotational diffusion of an axially symmetric particle is simulated by the Brownian dynamics technique. In addition to the wobbling-in-a-cone model, several continuous potentials are considered. The particle studied is particularly simple: a sphere anchored to a point fixed in space. However, presenting the results in a convenient, reduced form, they are valid for any axially symmetric particle. From simulated rotational trajectories, we calculate (P2(cos alpha] as a function of t, where alpha is the angle between two orientations separated by time t and P2 is the second Legendre polynomial. This correlation function is closely related to time-resolved electro-optic and spectroscopic properties. Simulated results for the cone model are in excellent agreement with the quasiexact results of Lipari and Szabo (1981, J. Chem. Phys., 75:2971-2976). Thus we confirm the good performance of the simulation technique and the validity of our working conditions. Novel results are presented for continuous restricting potentials, V(theta). The (P2) results for V = 1/2K theta 2 and V = Q(1 - cos theta) are practically the same if K and Q are chosen so tht the long-time (P2) values coincide. Thus, the quadratic potential seems to be a good representation of any monotonically increasing potential. However, for an uniaxial potential such as V = Csin2 theta, the decay is appreciably faster. The (P2) decays simulated for the continuous potentials are analyzed by the monoexponential version of the cone model. We found that such an analysis produces an overestimation of the true rotational diffusion coefficient of approximately 15% only, although for uniaxial potentials the error may be larger. PMID:3663834
Hybrid molecular dynamics simulation for plasma induced damage analysis
NASA Astrophysics Data System (ADS)
Matsukuma, Masaaki
2016-09-01
In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam
The Dynamics of Miscible Interfaces: Simulations
NASA Technical Reports Server (NTRS)
Meiburg, Eckart
2005-01-01
This research project focuses on the dynamics of interfacial regions between miscible fluids. While much attention has focused on immiscible interfaces in the past, miscible interfaces have been explored to a much lesser degree, so that there are many open questions regarding their dynamics at this time. Among the more pressing issues is the role that nonconventional stresses can play in such interfacial regions. Such stresses are typically not accounted for in efforts to model the dynamics of miscible flows. Our research aims to clarify under which circumstances these stresses do have to be taken into account, and what quantitative approaches are most suitable in this regard. In order to address these issues, we have focused on conducting linear stability analyses and nonlinear simulations for capillary tube and Hele-Shaw flows, and to compare the results with corresponding experiments performed in the labs of our co-investigators Prof. Maxworthy at USC, and Dr. Balasubramaniam at NASA. Over the duration of the project we have, among other things, focused on the effects of variable diffusion coefficients in such flows, and specifically on their influence in the growth of instabilities. Furthermore, our three-dimensional spectral element simulations have made good progress, so that we have come to a point where we can conduct more detailed comparisons with experimental observations. We are currently focusing our efforts on reproducing the tip-splitting instability observed by Maxworthy. Finally, we have discovered a new core-annular flow instability in the Stokes flow regime during the last year. This represents a significant finding, as this instability does not have an immiscible counterpart.
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.
Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations
NASA Astrophysics Data System (ADS)
Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong
2016-08-01
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 1ππ∗, 1nπ∗, 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 1ππ∗ system. The first is the diabatic ESIPT process along the 1ππ∗ potential energy profile. The generated 1ππ∗ keto species then decays to the S0 state via the keto 1ππ∗/gs conical intersection. The second is internal conversion to the dark 1nπ∗ state near the 1ππ∗ /1nπ∗ crossing point in the course of the diabatic 1ππ∗ ESIPT process. Our following dynamics simulations have shown that the ESIPT and 1ππ∗ → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the 1ππ∗ → S0 internal conversion in the keto region, the 1ππ∗ → 1nπ∗ internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.
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.
NASA Astrophysics Data System (ADS)
Olazabal-Loumé, M.; Nicolaï, Ph; Riazuelo, G.; Grech, M.; Breil, J.; Fujioka, S.; Sunahara, A.; Borisenko, N.; Tikhonchuk, V. T.
2013-08-01
The mechanisms of laser imprint reduction on a surface of a planar foil performed using an underdense foam are presented. The consequences on the Rayleigh-Taylor instability growth at the ablation front when the foil is accelerated are studied. The analysis is based on numerical simulations using a chain of codes: the electromagnetic paraxial code Parax provides the modifications of the intensity perturbation spectrum while the laser beam is crossing the foam. Two-dimensional axially symmetric simulations with the radiation hydrodynamic code CHIC describe the foam expansion and the foil dynamics. Finally, the perturbed flow calculations and the instability growth are investigated with the two-dimensional CHIC version in the planar geometry by using the initial and smoothed perturbation spectra. The dominant role of temporal laser smoothing during the time of foam crossing by the laser beam is demonstrated. Applications to the direct drive targets for inertial confinement fusion are discussed.
Molecular dynamics simulations of xDNA.
Varghese, Mathew K; Thomas, Renjith; Unnikrishnan, N V; Sudarsanakumar, C
2009-05-01
xDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force-field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5' G xT A xC xG C xA xG T3').(xA5' C T xG C G xT A xC A3') was explored using a 22 ns molecular dynamics simulation in explicit solvent. During the simulation, the duplex retained its Watson-Crick base-pairing and double helical structure, with deviations from the starting B-form geometry towards A-form; the deviations are mainly in the backbone torsion angles and in the helical parameters. The sugar pucker of the residues were distributed among a variety of modes; C2' endo, C1' exo, O4' endo, C4' exo, C2' exo, and C3' endo. The enhanced stacking interactions on account of the modification in the bases could help to retain the duplex nature of the helix with minor deviations from the ideal geometry. In our simulation, the xDNA showed a reduced minor groove width and an enlarged major groove width in comparison with the NMR structure. Both the grooves are larger than that of standard B-DNA, but major groove width is larger than that of A-DNA with almost equal minor groove width. The enlarged groove widths and the possibility of additional hydration in the grooves makes xDNA a potential molecule for various applications. Copyright (c) 2009 Wiley Periodicals, Inc.
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.
Molecular Dynamics Simulation of a RNA Aptasensor.
Ruan, Min; Seydou, Mahamadou; Noel, Vincent; Piro, Benoit; Maurel, François; Barbault, Florent
2017-04-14
Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.
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.
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
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
Inventory Reduction Using Business Process Reengineering and Simulation Modeling.
1996-12-01
center is analyzed using simulation modeling and business process reengineering (BPR) concepts. The two simulation models were designed and evaluated by...reengineering and simulation modeling offer powerful tools to aid the manager in reducing cycle time and inventory levels.
On sequential dynamical systems and simulation
Barrett, C.L.; Mortveit, H.S.; Reidys, C.M.
1999-06-01
The generic structure of computer simulations motivates a new class of discrete dynamical systems that captures this structure in a mathematically precise way. This class of systems consists of (1) a loopfree graph {Upsilon} with vertex set {l_brace}1,2,{hor_ellipsis},n{r_brace} where each vertex has a binary state, (2) a vertex labeled set of functions (F{sub i,{Upsilon}}:F{sub 2}{sup n} {r_arrow} F{sub 2}{sup n}){sub i} and (3) a permutation {pi} {element_of} S{sub n}. The function F{sub i,{Upsilon}} updates the state of vertex i as a function of the states of vertex i and its {Upsilon}-neighbors and leaves the states of all other vertices fixed. The permutation {pi} represents the update ordering, i.e., the order in which the functions F{sub i,{Upsilon}} are applied. By composing the functions F{sub i,{Upsilon}} in the order given by {pi} one obtains the dynamical system (equation given in paper) which the authors refer to as a sequential dynamical system, or SDS for short. The authors will present bounds for the number of functionally different systems and for the number of nonisomorphic digraphs {Gamma}[F{sub {Upsilon}},{pi}] that can be obtained by varying the update order and applications of these to specific graphs and graph classes. This will be done using both combinatorial/algebraic techniques and probabilistic techniques. Finally the authors give results on dynamical system properties for some special systems.
Replicative Use of an External Model in Simulation Variance Reduction
1996-03-01
measures used are confidence interval width reduction, realized coverage, and estimated Mean Square Error. Results of this study indicate analytical...control variates achieve comparable confidence interval width reduction with internal and external control variates. However, the analytical control
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.
An Adaptive Multipopulation Differential Evolution With Dynamic Population Reduction.
Ali, Mostafa Z; Awad, Noor H; Suganthan, Ponnuthurai Nagaratnam; Reynolds, Robert G
2016-10-25
Developing efficient evolutionary algorithms attracts many researchers due to the existence of optimization problems in numerous real-world applications. A new differential evolution algorithm, sTDE-dR, is proposed to improve the search quality, avoid premature convergence, and stagnation. The population is clustered in multiple tribes and utilizes an ensemble of different mutation and crossover strategies. In this algorithm, a competitive success-based scheme is introduced to determine the life cycle of each tribe and its participation ratio for the next generation. In each tribe, a different adaptive scheme is used to control the scaling factor and crossover rate. The mean success of each subgroup is used to calculate the ratio of its participation for the next generation. This guarantees that successful tribes with the best adaptive schemes are only the ones that guide the search toward the optimal solution. The population size is dynamically reduced using a dynamic reduction method. Comprehensive comparison of the proposed heuristic over a challenging set of benchmarks from the CEC2014 real parameter single objective competition against several state-of-the-art algorithms is performed. The results affirm robustness of the proposed approach compared to other state-of-the-art algorithms.
Yuan, Hongping; Chini, Abdol R; Lu, Yujie; Shen, Liyin
2012-03-01
During the past few decades, construction and demolition (C&D) waste has received increasing attention from construction practitioners and researchers worldwide. A plethora of research regarding C&D waste management has been published in various academic journals. However, it has been determined that existing studies with respect to C&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&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&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&D waste reduction. In this paper, seven causal loop diagrams that can deepen understanding about the feedback relationships underlying C&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 illustrate the validation and application of the proposed model. Results of the case study not only built confidence in the model so that it can be used for quantitative analysis, but also assessed and compared the effect of three designed policy scenarios on C&D waste reduction. One major contribution of this study is the development of a dynamic model for evaluating C&D waste reduction strategies under various scenarios, so that best management strategies could be identified before being implemented
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.
Protein Dynamics from NMR and Computer Simulation
NASA Astrophysics Data System (ADS)
Wu, Qiong; Kravchenko, Olga; Kemple, Marvin; Likic, Vladimir; Klimtchuk, Elena; Prendergast, Franklyn
2002-03-01
Proteins exhibit internal motions from the millisecond to sub-nanosecond time scale. The challenge is to relate these internal motions to biological function. A strategy to address this aim is to apply a combination of several techniques including high-resolution NMR, computer simulation of molecular dynamics (MD), molecular graphics, and finally molecular biology, the latter to generate appropriate samples. Two difficulties that arise are: (1) the time scale which is most directly biologically relevant (ms to μs) is not readily accessible by these techniques and (2) the techniques focus on local and not collective motions. We will outline methods using ^13C-NMR to help alleviate the second problem, as applied to intestinal fatty acid binding protein, a relatively small intracellular protein believed to be involved in fatty acid transport and metabolism. This work is supported in part by PHS Grant GM34847 (FGP) and by a fellowship from the American Heart Association (QW).
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.
Simulating the dynamics of complex plasmas.
Schwabe, M; Graves, D B
2013-08-01
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively coupled plasma with a fluid code written for the commercial package comsol. The output of this model is used to calculate forces on microparticles. The microparticles are modeled using the molecular dynamics package lammps, which we extended to include the forces from the plasma. Using this method, we are able to reproduce void formation, the separation of particles of different sizes into layers, lane formation, vortex formation, and other effects.
Euclidean lattice simulation for dynamical supersymmetry breaking
Kanamori, Issaku; Suzuki, Hiroshi; Sugino, Fumihiko
2008-05-01
The global supersymmetry is spontaneously broken if and only if the ground-state energy is strictly positive. We propose to use this fact to observe the spontaneous supersymmetry breaking in Euclidean lattice simulations. For lattice formulations that possess a manifest fermionic symmetry, there exists a natural choice of a Hamiltonian operator that is consistent with a topological property of the Witten index. We confirm validity of our idea in models of the supersymmetric quantum mechanics. We then examine a possibility of a dynamical supersymmetry breaking in the two-dimensional N=(2,2) super Yang-Mills theory with the gauge group SU(2), for which the Witten index is unknown. Differently from a recent conjectural claim, our numerical result tempts us to conclude that supersymmetry is not spontaneously broken in this system.
Simulating dynamical features of escape panic
NASA Astrophysics Data System (ADS)
Helbing, Dirk; Farkas, Illés; Vicsek, Tamás
2000-09-01
One of the most disastrous forms of collective human behaviour is the kind of crowd stampede induced by panic, often leading to fatalities as people are crushed or trampled. Sometimes this behaviour is triggered in life-threatening situations such as fires in crowded buildings; at other times, stampedes can arise during the rush for seats or seemingly without cause. Although engineers are finding ways to alleviate the scale of such disasters, their frequency seems to be increasing with the number and size of mass events. But systematic studies of panic behaviour and quantitative theories capable of predicting such crowd dynamics are rare. Here we use a model of pedestrian behaviour to investigate the mechanisms of (and preconditions for) panic and jamming by uncoordinated motion in crowds. Our simulations suggest practical ways to prevent dangerous crowd pressures. Moreover, we find an optimal strategy for escape from a smoke-filled room, involving a mixture of individualistic behaviour and collective `herding' instinct.
Strategies for the dynamical-optical simulation of high-performance optics
NASA Astrophysics Data System (ADS)
Störkle, Johannes; Eberhard, Peter
2016-07-01
In order to simulate and investigate the dynamical-optical behavior of high precision optics, integrated modeling strategies and methods are proposed within this work. For instance, this optical systems can be a telescope optic or a lithographic objective. In order to derive a simplified mechanical model for time simulations with low computational cost, the method of elastic multibody systems in combination with model order reduction methods can be used. For this, software-tools and interfaces are developed. Furthermore, mechanical and optical simulation models are derived and implemented. In order to clarify these methods, an academic mirror example is chosen and the influence of the model order reduction methods is analysed.
Reduction of the Gibbs Oscillation in Spectral Model Simulations.
NASA Astrophysics Data System (ADS)
Navapra, A.; Stern, W. F.; Miyakoda, K.
1994-08-01
Spectral atmospheric general circulation models (GCMS) have been used for many years for the simulation and prediction of the atmospheric circulation, and their value has been widely recognized. Over the years, however, some deficiencies have been noticed. One of the major drawbacks is the inability of the spectral spherical harmonies transform to represent discontinuous features, resulting in Gibbs oscillations. In particular, precipitation and cloud fields present annoying ripple patterns, which may obscure true drought episodes in climate runs. Other fields, such as the surface winds along the Andes, are also plagued by the fictitious oscillations. On the other hand, it is not certain to what extent the large-scale flow may be affected. An attempt is made in this paper to alleviate this problem by changing the spectral representation of the fields in the GCM. The technique is to apply various filters to reduce the Gibbs oscillations. Lanczos and Cesaro filters are tested for both one and two dimensions. In addition, for two-dimensional applications an isotropic filter is tested. This filter is based on the Cesaro summation principle with a constraint on the total wavenumber. At the end, two-dimensional physical space filters are proposed that can retain high-mountain peak values. Two applications of these filters are presented.In the first application the method is applied to the orography field by filtering out sharp gradients or discontinuities. The numerical results with this method show some improvement in the cloud and precipitation fields, along with some improvement of the surface wind pattern, resulting in an overall better simulation.In the second application, a Gibbs reduction technique is applied to the condensation process. In this paper the moist-adiabatic adjustment scheme is used for the cumulus parameterization, in addition to large-scale condensation. Numerical results with this method to reduce Gibbs oscillations due to condensation show some
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
Chemical complexity in astrophysical simulations: optimization and reduction techniques
NASA Astrophysics Data System (ADS)
Grassi, T.; Bovino, S.; Schleicher, D.; Gianturco, F. A.
2013-05-01
Chemistry plays a key role in the evolution of the interstellar medium, so it is highly important to follow its evolution in numerical simulations. However, it could easily dominate the computational cost when applied to large systems. In this paper we discuss two approaches to reduce these costs: (i) based on computational strategies, and (ii) based on the properties and on the topology of the chemical network. The first methods are more robust, while the second are meant to be giving important information on the structure of large, complex networks. We first discuss the numerical solvers for integrating the system of ordinary differential equations (ODE) associated with the chemical network, and then we propose a buffer method that decreases the computational time spent in solving the ODE system. We further discuss a flux-based method that allows one to determine and then cut on the fly the less active reactions. In addition we also present a topological approach for selecting the most probable species that will be active during the chemical evolution, thus gaining information on the chemical network that otherwise would be difficult to retrieve. This topological technique can also be used as an a priori reduction method for any size network. We implemented these methods into a 1D Lagrangian hydrodynamical code to test their effects: both classes lead to large computational speed-ups, ranging from ×2 to ×5. We have also tested some hybrid approaches finding that coupling the flux method with a buffer strategy gives the best trade-off between robustness and speed-up of calculations.
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
Coarse-grained protein molecular dynamics simulations.
Derreumaux, Philippe; Mousseau, Normand
2007-01-14
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Coarse-grained protein molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Molecular Dynamics Simulations of Ferroelectric Phase Transitions
NASA Astrophysics Data System (ADS)
Yu, Rici; Krakauer, Henry
1997-03-01
Based on an analysis of the wavevector dependence of the lattice instabilities in KNbO_3, we proposed a real-space chain-like instability and a scenario of sequential freezing out or onset of coherence of these instabilities, which qualitatively explains the sequence of observed temperature-dependent ferroelectric phases.(R. Yu and H. Krakauer, Phys. Rev. Lett. 74), 4067 (1995). We suggested that this chain-like instability should also be found in BaTiO_3, and this has been subsequently confirmed by Ghosez et al.(P. Ghosez et al.), Proc. 4th Williamsburg Workshop on First-Principles Calculations for Ferroelectrics, to be published We will present molecular dynamics simulations on BaTiO_3, using effective Hamiltonians constructed from first-principles calculations,(W. Zhong, D. Vanderbilt, and K. M. Rabe, Phys. Rev. Lett. 73), 1861 (1994). that reproduce the essential features of diffuse x-ray scattering measurements in the cubic, tetragonal, orthorhombic, and rhombohedral phases. The good agreement supports the interpretation of real-space chain-formation. Simulations for KNbO3 may also be reported.
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.
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.
Dynamical simulation of tether in orbit deployment
NASA Astrophysics Data System (ADS)
Smirnov, N. N.; Demyanov, Yu. A.; Zvyaguin, A. V.; Malashin, A. A.; Luzhin, A. A.
2010-08-01
The paper is aimed at studying the peculiarities of dynamical behavior of tether in its deployment in low Earth orbit during YES2 experiment in Foton-M3 mission, and performing flight data analysis with account of these effects. The analysis in the first part of the paper uses as input a pre-provided tension profile for the mission (resulting from a simulation to be independently validated). With this input it then performs an open-loop simulation which explains the sensitivity to the initial parameters. For the actual flight design a feedback mechanism and algorithm was used in order to control the deployment speed along a nominal profile, minimizing sensitivity to conditions such as initial velocity and endmass value. The paper provides solutions accounting for final velocities of wave propagation in tether, which is especially important for such stages of the deployment as sharp changing of the velocity direction and intensive braking. Moreover the YES2 data is used to validate the theoretical derivations.
PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations.
Berti, Claudio; Furini, Simone; Gillespie, Dirk
2016-03-08
We present PACO, a computationally efficient method for concentration boundary conditions in nonequilibrium particle simulations. Because it requires only particle counting, its computational effort is significantly smaller than other methods. PACO enables Brownian dynamics simulations of micromolar electrolytes (3 orders of magnitude lower than previously simulated). PACO for Brownian dynamics is integrated in the BROWNIES package (www.phys.rush.edu/BROWNIES). We also introduce a molecular dynamics PACO implementation that allows for very accurate control of concentration gradients.
Frontiers in molecular dynamics simulations of DNA.
Pérez, Alberto; Luque, F Javier; Orozco, Modesto
2012-02-21
It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global
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
The Dynamics of Miscible Interfaces: Simulations
NASA Technical Reports Server (NTRS)
Meiburg, Eckart
2002-01-01
The goal of this experimental/computational investigation (joint with Prof Maxworthy at USC) has been to study the dynamics of miscible interfaces, both from a scientific and a practical point of view, and to prepare a related experiment to be flown on the International Space Station. In order to address these effects, we have focused experimental and computational investigations on miscible displacements in cylindrical capillary tubes, as well as in Hele-Shaw cells. Regarding the flow in a capillary tube, the question was addressed as to whether Korteweg stresses and/or divergence effects can potentially account for discrepancies observed between conventional Stokes flow simulations and experiments for miscible flows in capillary tubes. An estimate of the vorticity and streamfunction fields induced by the Kortewegs stresses was derived, which shows these stresses to result in the formation of a vortex ring structure near the tip of the concentration front. Through this mechanism the propagation velocity of the concentration front is reduced, in agreement with the experimental observations. Divergence effects, on the other hand, were seen to be very small, and they have a negligible influence on the tip velocity. As a result, it can be concluded that they are not responsible for the discrepancies between experiments and conventional Stokes simulations. A further part of our investigation focussed on the development of high-accuracy three-dimensional spectral element simulation techniques for miscible flows in capillary tubes, including the effects of variable density and viscosity. Towards this end, the conservation equations are treated in cylindrical coordinates.
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
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...
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...
Batôt, G; Dahirel, V; Mériguet, G; Louis, A A; Jardat, M
2013-10-01
The dynamics of particles in solution or suspension is influenced by thermal fluctuations and hydrodynamic interactions. Several mesoscale methods exist to account for these solvent-induced effects such as Brownian dynamics with hydrodynamic interactions and hybrid molecular dynamics-stochastic rotation dynamics methods. Here we compare two ways of coupling solutes to the solvent with stochastic rotation dynamics (SRD) to Brownian dynamics with and without explicit hydrodynamic interactions. In the first SRD scheme [SRD with collisional coupling (CC)] the solutes participate in the collisional step with the solvent and in the second scheme [SRD with central force coupling (CFC)] the solutes interact through direct forces with the solvent, generating slip boundary conditions. We compare the transport coefficients of neutral and charged solutes in a model system obtained by these simulation schemes. Brownian dynamics without hydrodynamic interactions is used as a reference to quantify the influence of hydrodynamics on the transport coefficients as modeled by the different methods. We show that, in the dilute range, the SRD CFC method provides results similar to those of Brownian dynamics with hydrodynamic interactions for the diffusion coefficients and for the electrical conductivity. The SRD CC scheme predicts diffusion coefficients close to those obtained by Brownian dynamic simulations without hydrodynamic interactions, but accounts for part of the influence of hydrodynamics on the electrical conductivity.
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
Estimating the health impacts of tobacco harm reduction policies: a simulation modeling approach.
Ahmad, Sajjad; Billimek, John
2005-08-01
With adult smoking prevalence rates declining too slowly to reach national objectives, opinion leaders are considering policies to improve tobacco-related outcomes by regulating the composition of cigarettes to be (1) less harmful and/or (2) less addictive. Because harm reduction efforts may actually encourage higher cigarette consumption by promoting a safer image, and addictiveness reduction may increase the harmfulness of cigarettes by encouraging compensatory smoking behaviors, policymakers must consider the tradeoffs between these two approaches when proposing legislation to control cigarette content. To estimate health impacts, we developed a dynamic computer model simulating changes in the age- and gender-specific smoking behaviors of the U.S. population over time. Secondary data for model parameters were obtained from publicly available sources. Population health impacts were measured as change in smoking prevalence and the change in cumulative quality-adjusted life-years (QALYs) in the U.S. population over 75 years. According to the risk-use threshold matrix generated by the simulation, modifying cigarettes to reduce their harmfulness and/or addictiveness could result in important gains to the nation's health. Addictiveness reduction efforts producing a 60% improvement in smoking behavior change probabilities would produce a net gain in population health at every plausible level of increase of smoking-related harm that was modeled. A 40% reduction in smoking-related harm would produce a net QALY gain at every level of behavior change considered. This research should prove useful to policymakers as they contemplate giving the FDA the authority to regulate the composition of cigarettes.
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.
Shen, Tongye; Wong, Chung F
2015-01-01
This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum relaxation time. On the other hand, it is faster than molecular dynamics by approximating the solvent by a continuum and by operating in the over-damped limit. This chapter introduces the use of the University of Houston Brownian Dynamics (UHBD) program [1, 2] to perform Brownian dynamics simulation on peptides.
An NMR database for simulations of membrane dynamics
Leftin, Avigdor; Brown, Michael F.
2011-01-01
Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental 13C–1H and 2H NMR segmental order parameters (SCH or SCD) and spin-lattice (Zeeman) relaxation times (T1Z) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T1Z studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations. PMID:21134351
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.
Rotational Brownian dynamics simulations of clathrin cage formation.
Ilie, Ioana M; den Otter, Wouter K; Briels, Wim J
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.
Resting state networks in empirical and simulated dynamic functional connectivity.
Glomb, Katharina; Ponce-Alvarez, Adrián; Gilson, Matthieu; Ritter, Petra; Deco, Gustavo
2017-08-03
It is well-established that patterns of functional connectivity (FC) - measures of correlated activity between pairs of voxels or regions observed in the human brain using neuroimaging - are robustly expressed in spontaneous activity during rest. These patterns are not static, but exhibit complex spatio-temporal dynamics. Over the last years, a multitude of methods have been proposed to reveal these dynamics on the level of the whole brain. One finding is that the brain transitions through different FC configurations over time, and substantial effort has been put into characterizing these configurations. However, the dynamics governing these transitions are more elusive, specifically, the contribution of stationary vs. non-stationary dynamics is an active field of inquiry. In this study, we use a whole-brain approach, considering FC dynamics between 66 ROIs covering the entire cortex. We combine an innovative dimensionality reduction technique, tensor decomposition, with a mean field model which possesses stationary dynamics. It has been shown to explain resting state FC averaged over time and multiple subjects, however, this average FC summarizes the spatial distribution of correlations while hiding their temporal dynamics. First, we apply tensor decomposition to resting state scans from 24 healthy controls in order to characterize spatio-temporal dynamics present in the data. We simultaneously utilize temporal and spatial information by creating tensors that are subsequently decomposed into sets of brain regions ("communities") that share similar temporal dynamics, and their associated time courses. The tensors contain pairwise FC computed inside of overlapping sliding windows. Communities are discovered by clustering features pooled from all subjects, thereby ensuring that they generalize. We find that, on the group level, the data give rise to four distinct communities that resemble known resting state networks (RSNs): default mode network, visual network
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
2011-07-08
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.
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.
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.
Dynamic Simulation of EAF on RTDS for Compensation Sizing
NASA Astrophysics Data System (ADS)
Meera, K. S.
2017-02-01
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.
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.
Large-eddy simulation of combustion dynamics in swirling flows
NASA Astrophysics Data System (ADS)
Stone, Christopher Pritchard
The impact of premixer swirl number, S, and overall fuel equivalence ratio, phi, on the stability of a model swirl-stabilized, lean-premixed gas turbine combustor has been numerically investigated using a massively-parallel Large-Eddy Simulations Combustion Dynamics model. Through the use of a premixed combustion model, unsteady vortex-flame and acoustic-flame interactions are captured. It is observed that for flows with swirl intensity high enough to form Vortex-Breakdown (i.e., a phenomena associated with a large region of reverse or recirculating flow along the axis of rotation), the measured rms pressure amplitude (p') are attenuated significantly (over 6.6 dB reduction) compared to flows without this phenomena. The reduced p' amplitudes are accompanied by reduced longitudinal flame-front oscillations and reduced coherence in the shed vortices. Similar p' reduction levels are achieved through changes in the operating equivalence ratio, phi. Compared to the leanest equivalence ratio simulated (phi = 0.52), p' at a stoichiometric mixture is reduced by 6.0 dB. Methodologies for active control based on modulation of the inlet Swirl number (S, a measure of the intensity of swirl) and phi are also investigated. Open-loop control through S variation is demonstrated for a lean mixture with a significant reduction in the fluctuating mass-flow-rate and p' after a convective time-delay. A partially-premixed combustion model, which allows for variations in the local phi, is used to model both temporal and spatial variations in phi. It is found that the response time to changes in phi are much faster than those for changes in S. Also, it is shown that spatial variations in phi (or unmixedness) actually lead to p' attenuation in the current combustor configuration.
Dynamically reconfigurable router for NoC congestion reduction
NASA Astrophysics Data System (ADS)
Rosales, Juan E.; Tobajas, Félix; de Armas, Valentín; Mori, José A.; Sarmiento, Roberto
2011-05-01
Multiprocessor System-on-Chip (MPSoCs) are emerging as one of the technologies providing a way to support the growing design complexity of embedded systems including several types of cores. The interconnection among cores of a MPSoC is proposed to be provided by Networks-on-Chip (NoC). In real applications it is usual to find different interconnection needs amongst cores, so distinct bandwidth is needed in each node of a NoC. Since larger FIFOs in NoC routers provide larger throughputs and smaller latencies, depths are usually sized for the worst case, compromising not only the routing area, but power consumption. In this paper, a reconfigurable router with a dynamic sharing mechanism of buffers at the input channels is proposed to reduce congestion in the network. In this situation, a channel may dynamically lend or borrow some non-used buffer units to or from neighboring channels, in accordance to the connection rates. The proposed reconfigurable router architecture was embedded in the Hermes NoC. The main advantages of the Hermes are its small size and modular design. This, as well as the open source approach, have lead to the selection of this NoC. The basic element of Hermes is a router with five bi-directional ports employing an XY routing algorithm. FIFO buffering is present only at the input channel, with all channels having the same buffer depth defined at design time. The proposed reconfigurable router has been coded in VHDL at RTL level from the adaptation of the Hermes router to fit into the proposed scheme. Results obtained from the simulation of the router under scenarios with different traffic characteristics and percentage of shared buffer, show that mean latency can be reduced up to a 30% in comparison to the original router.
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
Nonlinear Resonance Artifacts in Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Schlick, Tamar; Mandziuk, Margaret; Skeel, Robert D.; Srinivas, K.
1998-02-01
The intriguing phenomenon of resonance, a pronounced integrator-induced corruption of a system's dynamics, is examined for simple molecular systems subject to the classical equations of motion. This source of timestep limitation is not well appreciated in general, and certainly analyses of resonance patterns have been few in connection to biomolecular dynamics. Yet resonances are present in the commonly used Verlet integrator, in symplectic implicit schemes, and also limit the scope of current multiple-timestep methods that are formulated as symplectic and reversible. The only general remedy to date has been to reduce the timestep. For this purpose, we derive method-dependent timestep thresholds (e.g., Tables 1 and 2) that serve as useful guidelines in practice for biomolecular simulations. We also devise closely related symplectic implicit schemes for which the limitation on the discretization stepsize is much less severe. Specifically, we design methods to remove third-order, or both the third- and fourth-order, resonances. These severe low-order resonances can lead to instability or very large energies. Our tests on two simple molecular problems (Morse and Lennard-Jones potentials), as well as a 22-atom molecule, N-acetylalanyl-N '-methylamide, confirm this prediction; our methods can delay resonances so that they occur only at larger timesteps (EW method) or are essentially removed (LIM2 method). Although stable for large timesteps by this approach, trajectories show large energy fluctuations, perhaps due to the coupling with other factors that induce instability in complex nonlinear systems. Thus, the methods developed here may be more useful for conformational sampling of biomolecular structures. The analysis presented here for the blocked alanine model emphasizes that one-dimensional analysis of resonances can be applied to a more complex, multimode system to analyze resonance behavior, but that resonance due to frequency coupling is more complex to pinpoint
Molecular dynamics simulations of glycoclusters and glycodendrimers.
von der Lieth, Claus W; Frank, Martin; Lindhorst, Thisbe K
2002-05-01
Protein-carbohydrate recognition plays a crucial role in a wide range of biological processes, required both for normal physiological functions and the onset of disease. Nature uses multivalency in carbohydrate-protein interactions as a strategy to overcome the low affinity found for singular binding of an individual saccharide epitope to a single carbohydrate recognition domain of a lectin. To mimic the complex multi-branched oligosaccharides found in glycoconjugates, which form the structural basis of multivalent carbohydrate-protein interactions, so-called glycoclusters and glycodendrimers have been designed to serve as high-affinity ligands of the respective receptor proteins. To allow a rational design of glycodendrimer-type molecules with regard to the receptor structures involved in carbohydrate recognition, a deeper knowledge of the dynamics of such molecules is desirable. Most glycodendrimers have to be considered highly flexible molecules with their conformational preferences most difficult to elucidate by experimental methods. Longtime molecular dynamics (MD) simulations with inclusion of explicit solvent molecules are suited to explore the conformational space accessible to glycodendrimers. Here, a detailed geometric and conformational analysis of 15 glycodendrimers and glycoclusters has been accomplished, which differ with regard to their core moieties, spacer characteristics and the type of terminal carbohydrate units. It is shown that the accessible conformational space depends strongly on the structural features of the core and spacer moieties and even on the type of terminating sugars. The obtained knowledge about possible spatial distributions of the sugar epitopes exposed on the investigated hyperbranched neoglycoconjugates is detailed for all examples and forms important information for the interpretation and prediction of affinity data, which can be deduced from biological testing of these multivalent neoglycoconjugates.
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.
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
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
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
2007-05-15
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 A. 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.
A novel coupling of noise reduction algorithms for particle flow simulations
Zimoń, M.J.; Reese, J.M.; Emerson, D.R.
2016-09-15
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.
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.
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.
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.
Dynamical simulation of an abrasive wear process
NASA Astrophysics Data System (ADS)
Elalem, Khaled; Li, D. Y.
1999-05-01
A dynamic computer model was developed to simulate wear behavior of materials on micro-scales. In this model, a material system is discretized and mapped onto a lattice or grid. Each lattice site represents a small volume of the material. During a wear process, a lattice site may move under the influence of external force and the interaction between the site and its adjacent sites. The site-site interaction is a function of mechanical properties of the material such as the elastic modulus, yield strength, work hardening and the fracture strain. Newton's law of motion is used to determine the movement of lattice sites during a wear process. The strain between a pair of sites is recoverable if it is within the elastic deformation range; otherwise plastic deformation takes place. A bond between two adjacent sites is broken when its strain exceeds a critical value. A site or a cluster of sites is worn away if all bonds connecting the site or the cluster to its nearest neighbors are broken. The model well describes the strain distribution in a contact region, in consistence with a finite element analysis. This model was applied to several metallic materials abraded under the ASTM G65 abrasion condition, and the results were compared to experimental observations. Good agreement between the modeling and the experiment was found.
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.
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.
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…
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.
Library-based numerical reduction of the Hodgkin-Huxley neuron for network simulation.
Sun, Yi; Zhou, Douglas; Rangan, Aaditya V; Cai, David
2009-12-01
We present an efficient library-based numerical method for simulating the Hodgkin-Huxley (HH) neuronal networks. The key components in our numerical method involve (i) a pre-computed high resolution data library which contains typical neuronal trajectories (i.e., the time-courses of membrane potential and gating variables) during the interval of an action potential (spike), thus allowing us to avoid resolving the spikes in detail and to use large numerical time steps for evolving the HH neuron equations; (ii) an algorithm of spike-spike corrections within the groups of strongly coupled neurons to account for spike-spike interactions in a single large time step. By using the library method, we can evolve the HH networks using time steps one order of magnitude larger than the typical time steps used for resolving the trajectories without the library, while achieving comparable resolution in statistical quantifications of the network activity, such as average firing rate, interspike interval distribution, power spectra of voltage traces. Moreover, our large time steps using the library method can break the stability requirement of standard methods (such as Runge-Kutta (RK) methods) for the original dynamics. We compare our library-based method with RK methods, and find that our method can capture very well phase-locked, synchronous, and chaotic dynamics of HH neuronal networks. It is important to point out that, in essence, our library-based HH neuron solver can be viewed as a numerical reduction of the HH neuron to an integrate-and-fire (I&F) neuronal representation that does not sacrifice the gating dynamics (as normally done in the analytical reduction to an I&F neuron).
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.
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…
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…
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.
Dynamics of Bacterial Sulfate Reduction in a Eutrophic Lake
Ingvorsen, K.; Zeikus, J. G.; Brock, T. D.
1981-01-01
Bacterial sulfate reduction in the surface sediment and the water column of Lake Mendota, Madison, Wis., was studied by using radioactive sulfate (35SO42−). High rates of sulfate reduction were observed at the sediment surface, where the sulfate pool (0.2 mM SO42−) had a turnover time of 10 to 24 h. Daily sulfate reduction rates in Lake Mendota sediment varied from 50 to 600 nmol of SO42− cm−3, depending on temperature and sampling date. Rates of sulfate reduction in the water column were 103 times lower than that for the surface sediment and, on an areal basis, accounted for less than 18% of the total sulfate reduction in the hypolimnion during summer stratification. Rates of bacterial sulfate reduction in the sediment were not sulfate limited at sulfate concentrations greater than 0.1 mM in short-term experiments. Although sulfate reduction seemed to be sulfate limited below 0.1 mM, Michaelis-Menten kinetics were not observed. The optimum temperature (36 to 37°C) for sulfate reduction in the sediment was considerably higher than in situ temperatures (1 to 13°C). The response of sulfate reduction to the addition of various electron donors metabolized by sulfate-reducing bacteria in pure culture was investigated. The degree of stimulation was in this order: H2 > n-butanol > n-propanol > ethanol > glucose. Acetate and lactate caused no stimulation. PMID:16345898
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.
NASA Astrophysics Data System (ADS)
Virshup, Aaron M.; Chen, Jiahao; Martínez, Todd J.
2012-12-01
Conical intersections play a critical role in the nonadiabatic relaxation of excited electronic states. However, there are an infinite number of these intersections and it is difficult to predict which are actually relevant. Furthermore, traditional descriptors such as intrinsic reaction coordinates and steepest descent paths often fail to adequately characterize excited state reactions due to their highly nonequilibrium nature. To address these deficiencies in the characterization of excited state mechanisms, we apply a nonlinear dimensionality reduction scheme (diffusion mapping) to generate reaction coordinates directly from ab initio multiple spawning dynamics calculations. As illustrated with various examples of photoisomerization dynamics, excited state reaction pathways can be derived directly from simulation data without any a priori specification of relevant coordinates. Furthermore, diffusion maps also reveal the influence of intersection topography on the efficiency of electronic population transfer, providing further evidence that peaked intersections promote nonadiabatic transitions more effectively than sloped intersections. Our results demonstrate the usefulness of nonlinear dimensionality reduction techniques as powerful tools for elucidating reaction mechanisms beyond the statistical description of processes on ground state potential energy surfaces.
Zhang, Lin; Lu, Diannan; Liu, Zheng
2009-03-20
Conformational transitions of a protein in hydrophobic interaction based chromatography, including hydrophobic interaction chromatography (HIC) and reversed-phase liquid chromatography (RPLC), and their impact on the separation process and performance were probed by molecular dynamics simulation of a 46-bead beta-barrel coarse-grained model protein in a confined pore, which represents the porous adsorbent. The transition of the adsorbed protein from the native conformation to an unfolded one occurred as a result of strong hydrophobic interactions with the pore surface, which reduced the formation of protein aggregates. The conformational transition was also displayed in the simulation once an elution buffer characterized by weaker hydrophobicity was introduced to strip protein from pore surface. The discharged proteins that underwent conformational transition were prone to aggregation; thus, an unsatisfactory yield of the native protein was obtained. An orthogonal experiment revealed that in addition to the strengths of the protein-protein and protein-adsorbent hydrophobic interactions, the elution time required to reduce the above-mentioned interactions also determined the yield of native protein by HIC and RPLC. Stepwise elution, characterized by sequential reduction of the hydrophobic interactions between the protein and adsorbent, was presented as a dynamic strategy for tuning conformational transitions to favor the native conformation and reduce the formation of protein aggregates during the elution process. The yield of the native protein obtained by this dynamic operation strategy was higher than that obtained by steady-state elution. The simulation study qualitatively reproduced the experimental observations and provided molecular insight that would be helpful for designing and optimizing HIC and RPLC separation of proteins.
Post-processing interstitialcy diffusion from molecular dynamics simulations
Bhardwaj, U.; Bukkuru, S.; Warrier, M.
2016-01-15
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. -- Graphical abstract:.
Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics simulations.
Ou, Zhaoyang; Muthukumar, M
2006-04-21
We report a systematic study by Langevin dynamics simulation on the energetics of complexation between two oppositely charged polyelectrolytes of same charge density in dilute solutions of a good solvent with counterions and salt ions explicitly included. The enthalpy of polyelectrolyte complexation is quantified by comparisons of the Coulomb energy before and after complexation. The entropy of polyelectrolyte complexation is determined directly from simulations and compared with that from a mean-field lattice model explicitly accounting for counterion adsorption. At weak Coulomb interaction strengths, e.g., in solvents of high dielectric constant or with weakly charged polyelectrolytes, complexation is driven by a negative enthalpy due to electrostatic attraction between two oppositely charged chains, with counterion release entropy playing only a subsidiary role. In the strong interaction regime, complexation is driven by a large counterion release entropy and opposed by a positive enthalpy change. The addition of salt reduces the enthalpy of polyelectrolyte complexation by screening electrostatic interaction at all Coulomb interaction strengths. The counterion release entropy also decreases in the presence of salt, but the reduction only becomes significant at higher Coulomb interaction strengths. More significantly, in the range of Coulomb interaction strengths appropriate for highly charged polymers in aqueous solutions, complexation enthalpy depends weakly on salt concentration and counterion release entropy exhibits a large variation as a function of salt concentration. Our study quantitatively establishes that polyelectrolyte complexation in highly charged Coulomb systems is of entropic origin.
Virtual-Wall Model for Molecular Dynamics Simulation.
Qian, Lijuan; Tu, Chengxu; Bao, Fubing; Zhang, Yonghao
2016-12-09
A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed.
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.
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.
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.
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...
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...
Johnson, Todd; Bartol, Tom; Sejnowski, Terrence; Mjolsness, Eric
2015-06-18
A stochastic reaction network model of Ca(2+) 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.
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.
Multimillion atom molecular dynamics simulations of glasses and ceramic materials
NASA Astrophysics Data System (ADS)
Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro
1999-11-01
Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed.
Protein dynamics and enzyme catalysis: insights from simulations.
McGeagh, John D; Ranaghan, Kara E; Mulholland, Adrian J
2011-08-01
The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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.
Monte Carlo simulations of surface reactions: NO reduction by CO or H2
NASA Astrophysics Data System (ADS)
Álvarez-Falcón, L.; Alas, S. J.; Vicente, L.
2014-01-01
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+H2 and NO+CO. The extremely narrow production peak of N2 and CO2 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 H2 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.
Semenov, Serguei; Kellam, James; Nair, Bindu; Williams, Thomas; Quinn, Michael; Sizov, Yuri; Nazarov, Alexei; Pavlovsky, Andrey
2011-04-07
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.
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.
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.
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.
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.
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.
1991-03-01
Adjusted Estimators for Variance 1Redutilol in Computer Simutlation by Riichiardl L. R’ r March, 1991 D~issertation Advisor: Peter A.W. Lewis Approved for...OF NONLINEAR CONTROLS AND REGRESSION-ADJUSTED ESTIMATORS FOR VARIANCE REDUCTION IN COMPUTER SIMULATION 12. Personal Author(s) Richard L. Ressler 13a...necessary and identify by block number) This dissertation develops new techniques for variance reduction in computer simulation. It demonstrates that
Jiménez-Delgado, Juan J; Paulano-Godino, Félix; PulidoRam-Ramírez, Rubén; Jiménez-Pérez, J Roberto
2016-05-01
The development of support systems for surgery significantly increases the likelihood of obtaining satisfactory results. In the case of fracture reduction interventions these systems enable surgery planning, training, monitoring and assessment. They allow improvement of fracture stabilization, a minimizing of health risks and a reduction of surgery time. Planning a bone fracture reduction by means of a computer assisted simulation involves several semiautomatic or automatic steps. The simulation deals with the correct position of osseous fragments and fixation devices for a fracture reduction. Currently, to the best of our knowledge there is no computer assisted methods to plan an entire fracture reduction process. This paper presents an overall scheme of the computer based process for planning a bone fracture reduction, as described above, and details its main steps, the most common proposed techniques and their main shortcomings. In addition, challenges and new trends of this research field are depicted and analyzed.
Model order reduction applied to a hot-bench simulation of an aeroelastic wind-tunnel model
NASA Technical Reports Server (NTRS)
Buttrill, Carey S.; Bacon, Barton J.
1991-01-01
Simulations of an aeroelastically scaled wind-tunnel model were developed for hot-bench testing of a digital controller. The digital controller provided active flutter-suppression, rolling-maneuver-load alleviation, and plant estimation. To achieve an acceptable time scale for the hot-bench application, the mathematical model of the wind-tunnel model was reduced from 220 states to approximately 130 states while assuring that the required accuracy was preserved for all combinations of 10 inputs and 56 outputs. The reduction was achieved by focussing on a linear, aeroelastic submodel of the full mathematical model and by applying a method based on the internally balanced realization of a dynamic system. The error-bound properties of the internally balanced realization significantly contribute to its utility in the model reduction process. The reduction method and the results achieved are described.
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.
Dynamic Rupture Simulations with Plastic Yielding in Fault Damage Zone
NASA Astrophysics Data System (ADS)
Day, S. M.; Roten, D.; Olsen, K. B.; Cui, Y.
2016-12-01
Observations of fault-zone trapped waves indicate that faults are surrounded by damage zones with reduced seismic velocities. We investigate how plastic effects around the fault, enhanced by the reduced strength of pre-fractured rocks inside the low-velocity zone (LVZ), affect ground motions at various distances from the fault. 3-D dynamic rupture simulations are performed with the AWP-ODC finite difference code, using a slip-weakening fault friction law, a Drucker-Prager (DP) yield criterion and depth-dependent stress. We simulate M 7.5 earthquakes with a LVZ embedded in a horizontally layered model, as well as M 7.7 earthquakes on the southern San Andreas fault with a LVZ added to the 3D heterogeneous mesh (SCEC CVM 3c). Within a 500 m wide and 4 km deep inner fault zone, we assume a 30% reduction in shear-wave velocity with respect to wallrock, and a reduced Geological Strength Index (GSI) of 30, 50 or 75, representative of a fractured rock mass of poor, moderate and good quality, respectively. The Hoek-Brown criterion is then used to derive equivalent friction angles and cohesions, consistent with these GSI values, for the DP criterion. In the linear case, the presence of a LVZ increases mean near-surface peak slip rates by 50%, from 2 to 3 m/s. These amplifications are compensated by fault zone plasticity in poor and moderate quality rock masses, where near-surface peak slip rates average to 0.5 m/s and 1.5 m/s, respectively; no significant reduction is obtained in good quality (almost unfractured) fault zones. Trapping of seismic waves inside the LVZ results in reduced peak ground velocities (PGVs) outside of the fault zone even in the linear case; these reductions are more pronounced if plasticity is taken into account. Plasticity acts by truncating frequency-distribution curves of PGVs obtained near the fault. In the horizontally layered medium, the highest PGVs are reduced from 2.6 m/s to 2.2 for moderate, and to 1.7 m/s for poor quality fault zones. In
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.
Mantha, Sriteja; Yethiraj, Arun
2016-02-28
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, D(T), and rotational relaxation time, τ(R). 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 D(T) and τ(R) 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.
Naghibi Beidokhti, Hamid; Janssen, Dennis; Khoshgoftar, Mehdi; Sprengers, Andre; Perdahcioglu, Emin Semih; Van den Boogaard, Ton; Verdonschot, Nico
2016-10-01
The finite element (FE) method has been widely used to investigate knee biomechanics. Time integration algorithms for dynamic problems in finite element analysis can be classified as either implicit or explicit. Although previously both static/dynamic implicit and dynamic explicit method have been used, a comparative study on the outcomes of both methods is of high interest for the knee modeling community. The aim of this study is to compare static, dynamic implicit and dynamic explicit solutions in analyses of the knee joint to assess the prediction of dynamic effects, potential convergence problems, the accuracy and stability of the calculations, the difference in computational time, and the influence of mass-scaling in the explicit formulation. The heel-strike phase of fast, normal and slow gait was simulated for two different body masses in a model of the native knee. Our results indicate that ignoring the dynamic effect can alter joint motion. Explicit analyses are suitable to simulate dynamic loading of the knee joint in high-speed simulations, as this method offers a substantial reduction of the computational time with a similar prediction of cartilage stresses and meniscus strains. Although mass-scaling can provide even more gain in computational time, it is not recommended for high-speed activities, in which inertial forces play a significant role.
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.
NASA Astrophysics Data System (ADS)
Zimoń, M. J.; Prosser, R.; Emerson, D. R.; Borg, M. K.; Bray, D. J.; Grinberg, L.; Reese, J. M.
2016-11-01
Filtering of particle-based simulation data can lead to reduced computational costs and enable more efficient information transfer in multi-scale modelling. This paper compares the effectiveness of various signal processing methods to reduce numerical noise and capture the structures of nano-flow systems. In addition, a novel combination of these algorithms is introduced, showing the potential of hybrid strategies to improve further the de-noising performance for time-dependent measurements. The methods were tested on velocity and density fields, obtained from simulations performed with molecular dynamics and dissipative particle dynamics. Comparisons between the algorithms are given in terms of performance, quality of the results and sensitivity to the choice of input parameters. The results provide useful insights on strategies for the analysis of particle-based data and the reduction of computational costs in obtaining ensemble solutions.
Large-Scale Hybrid Dynamic Simulation Employing Field Measurements
Huang, Zhenyu; Guttromson, Ross T.; Hauer, John F.
2004-06-30
Simulation and measurements are two primary ways for power engineers to gain understanding of system behaviors and thus accomplish tasks in system planning and operation. Many well-developed simulation tools are available in today's market. On the other hand, large amount of measured data can be obtained from traditional SCADA systems and currently fast growing phasor networks. However, simulation and measurement are still two separate worlds. There is a need to combine the advantages of simulation and measurements. In view of this, this paper proposes the concept of hybrid dynamic simulation which opens up traditional simulation by providing entries for measurements. A method is presented to implement hybrid simulation with PSLF/PSDS. Test studies show the validity of the proposed hybrid simulation method. Applications of such hybrid simulation include system event playback, model validation, and software validation.
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.
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
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.
A new simulation model building process for use in dynamic systems integration research
NASA Technical Reports Server (NTRS)
Arbuckle, P. Douglas; Buttrill, Carey S.; Zeiler, Thomas A.
1987-01-01
A framework to build simulation models for aircraft dynamic systems integration is described. The objective of the framework is increased simulation model fidelity and reduced time required to develop and modify these models. The equations of motion for an elastic aircraft and their impact on the framework are discussed in broad terms. A software tool which automatically generates FORTRAN routines for tabular data lookups, the language used to develop a simulation model, and the structures for passing information into a simulation are discussed. A simulation variable nomenclature is presented. The framework has been applied to build an open-loop F/A-18 simulation model. This example model is used to illustrate model reduction issues. Current deficiencies in the framework are identified as areas for future research.
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.
Climate dynamics experiments using a GCM simulations
NASA Technical Reports Server (NTRS)
Fitzjarrald, Dan; Robertson, Franklin R.; Christy, John R.; Lu, H.-I.; Sohn, B.; Srikishen, J.
1991-01-01
The study of surface-atmosphere interactions has begun with studies of the effect of altering the ocean and land boundaries. A ten year simulation of global climate using observed sea surface temperature anomalies has begun using the NCAR Community Climate Model (CCM1). The results for low resolution (R15) were computed for the first 8 years of the simulation and compared with the observed surface temperatures and the MSU (Microwave Sounding Unit) observations of tropospheric temperature. A simulation at higher resolution (T42) was done to ascertain the effect of interactive soil hydrology on the system response to an El Nino sea surface temperature perturbation. Initial analysis of this simulations was completed.
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
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.
A Molecular Dynamics Simulation of C60-C60 Collision
NASA Astrophysics Data System (ADS)
Liu, Lei; Chen, Kaitai; Li, Yufen
1993-12-01
The formation process of C120-complex in C60-C60 collision has been clearly demonstrated by a molecular dynamics simulation. The complex, with a peanut-shell-like structure, is in a quite stable dynamical state. The results are consistent with recent observations.
A pollution reduction methodology for chemical process simulators
Mallick, S.K.; Cabezas, H.; Bare, J.C.; Sikdar, S.K.
1996-11-01
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 been modified by weighing the mass flowrate of each pollutant by its potential environmental impact score. This converts the mass balance into an environmental impact balance. This balance defines an impact index with units of environmental impact per mass of products. The impact index measures the potential environmental effects of process wastes. Three different schemes for chemical ranking were considered: (1) no ranking, (2) simple ranking from 0 to 3, and (3) ranking by a scientifically derived measure of human health and environmental effects. Use of the methodology is illustrated with two examples from the production of (1) methyl ethyl ketone and (2) synthetic ammonia.
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.
Molecular Dynamic Modeling and Simulation for Polymers
2003-09-01
Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Paperwork Reduction...SSFLAG: input of most material data % SSPARM: chnage of some parameters (RDEL, VMAX, VDEL) only if necessary
Student Diagnostic Strategies in a Dynamic Simulation Environment.
ERIC Educational Resources Information Center
Recker, Mimi M.; Govindaraj, T.; Vasandani, Vijay
1998-01-01
Demonstrates the use of simulation systems for studying diagnostic problem solving and presents results from two empirical studies in which undergraduates diagnosed faults that occurred in a computer-based, dynamic simulation. Discusses dual problem space search that includes generating and testing hypotheses; suggests implications for designing…
Simulation, modeling and dynamical analysis of multibody flows
NASA Astrophysics Data System (ADS)
Blackmore, Denis; Rosato, Anthony; Sen, Surajit; Wu, Hao
2017-04-01
Recent particulate flow research using a discrete element simulation-dynamical systems approach is described. The simulation code used is very efficient and the mathematical model is an integro-partial differential equation. Examples are presented to show the effectiveness of the approach.
Inorganic nitrogen reduction and stability under simulated hydrothermal conditions.
Brandes, Jay A; Hazen, Robert M; Yoder, Hatten S
2008-12-01
Availability of reduced nitrogen is considered a prerequisite for the genesis of life from prebiotic precursors. Most atmospheric and oceanic models for the Hadean Earth predict a mildly oxidizing environment that is conducive to the formation and stability of only oxidized forms of nitrogen. A possible environment where reduction of oxidized nitrogen to ammonium has been speculated to occur is aqueous hydrothermal systems. We examined a suite of transition metal oxides and sulfides for their ability to reduce nitrate and nitrite, as well as oxidize ammonia, under hot (300 degrees C) high-pressure (50-500 MPa) aqueous conditions. In general, iron sulfides exhibited the most rapid and complete conversion noted, followed by nickel and copper sulfides to a much lower degree. Of the oxides examined, only magnetite exhibited any ability to reduce NO(3)(-) or NO(2)(-). Ammonium was stable or exhibited small losses (<20%) in contact with all the mineral phases and conditions tested. The results support the idea that hydrothermal systems could have provided significant amounts of reduced nitrogen to their immediate environments. The enhanced availability of reduced nitrogen in hydrothermal systems also has important implications for prebiotic metabolic pathways where nitrogen availability is critical to the production of amino acids and other nitrogenous compounds.
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.
Yi, Zheng; Lindner, Benjamin; Prinz, Jan -Hendrik; Noe, Frank; Smith, Jeremy C.
2013-11-01
Here, neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.
Optimized reduction of uncertainty in bursty human dynamics.
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.
ROCKET THRUST STAND SIMULATION OF SPACE VEHICLE FLIGHT DYNAMICS
The concept of rocket thrust stand simulation of space vehicle flight dynamics is developed. An electro-mechanical system is described wherein the... space vehicle rocket motor attach point motion may be simulated. The physical dimensions of the system are small such that it may be used in conjunction...with current environmental test cells. The degree of space vehicle simulation is a consequence of the limitations on the excursions of the active
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.
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.
Gamma ray observatory dynamics simulator in Ada (GRODY)
Not Available
1990-09-01
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.
Movement Characteristics Analysis and Dynamic Simulation of Collaborative Measuring Robot
NASA Astrophysics Data System (ADS)
guoqing, MA; li, LIU; zhenglin, YU; guohua, CAO; yanbin, ZHENG
2017-03-01
Human-machine collaboration is becoming increasingly more necessary, and so collaborative robot applications are also in high demand. We selected a UR10 robot as our research subject for this study. First, we applied D-H coordinate transformation of the robot to establish a link system, and we then used inverse transformation to solve the robot’s inverse kinematics and find all the joints. Use Lagrange method to analysis UR robot dynamics; use ADAMS multibody dynamics simulation software to dynamic simulation; verifying the correctness of the derived kinetic models.
Semiconductor nanostructure properties. Molecular Dynamic Simulations
NASA Astrophysics Data System (ADS)
Podolska, N. I.; Zhmakin, A. I.
2013-08-01
The need for research is based on the fact that development of non-planar semiconductor nanosystems and nanomaterials with controlled properties is an important scientific and industrial problem. So, final scientific and technological problem is the creation of adequate modern methods and software for growth and properties simulation and optimization of various III-V (GaAs, InAs, InP, InGaAs etc.) nanostructures (e.g. nanowires) with controlled surface morphology, crystal structure, optical, transport properties etc. Accordingly, now we are developing a specialized computer code for atomistic simulation of structural (distribution of atoms and impurities, elastic and force constants, strain distribution etc.) and thermodynamic (mixing energy, interaction energy, surface energy etc.) properties of the nanostructures. Some simulation results are shown too.
Svalkvist, Angelica; Båth, Magnus
2010-01-01
Adding noise to clinical radiographs to simulate dose reduction can be used to investigate the relationship between dose level and clinical image quality without exposing patients to additional radiation. The purpose of the present paper was to examine the benefits of using a method that accounts for detective quantum efficiency (DQE) variations that may occur in different dose ranges in the simulated dose reduction process. A method initially intended for simulated dose reduction in tomosynthesis was applied to extremely low-dose posterioanterior radiographs of an anthropomorphic chest phantom, selected from a group of projection images included in a tomosynthesis examination and compared with a previous method that do not account for DQE variations. A comparison of images simulated to be collected at a lower dose level (73 % of the original dose level) and images actually collected at this lower dose level revealed that the error in the integrated normalised noise power spectrum was smaller than 4 % for the method that accounts for DQE variations in the simulated dose reduction, whereas the error was larger than 20 % for the previous method. This indicates that an increased validity in dose reduction simulation of digital radiographic systems is obtained with a method accounting for DQE variations.
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.
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.
Molecular Dynamics Simulations of Crystal Copper: Bulk Modulus and Shocks
NASA Astrophysics Data System (ADS)
Warrier, M.; Rawat, S.; Chaturvedi, S.
2011-07-01
Molecular dynamics is used to study the response of single crystal copper target to impacts by single crystal copper at velocities in the range 1 km/s to 3 km/s. The Embedded Atom Method (EAM) potential by Foiles et al. for Cu [1] was used in the simulation. The potential and its implementation in the open source, Large-scale Atomic Molecular Massively Parallel Simulator (LAMMPS) [2] was verified by reproducing the experimental values of bulk modulus of Cu. The shock velocity (us) as a function of particle velocity (up) matches published experimental and molecular dynamic simulations results.
Robust state preparation in quantum simulations of Dirac dynamics
NASA Astrophysics Data System (ADS)
Song, Xue-Ke; Deng, Fu-Guo; Lamata, Lucas; Muga, J. G.
2017-02-01
A nonrelativistic system such as an ultracold trapped ion may perform a quantum simulation of a Dirac equation dynamics under specific conditions. The resulting Hamiltonian and dynamics are highly controllable, but the coupling between momentum and internal levels poses some difficulties to manipulate the internal states accurately in wave packets. We use invariants of motion to inverse engineer robust population inversion processes with a homogeneous, time-dependent simulated electric field. This exemplifies the usefulness of inverse-engineering techniques to improve the performance of quantum simulation protocols.
AceCloud: Molecular Dynamics Simulations in the Cloud.
Harvey, M J; De Fabritiis, G
2015-05-26
We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.
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...
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...
Test and validation for robot arm control dynamics simulation
NASA Technical Reports Server (NTRS)
Yae, K. Harold; Kim, Sung-Soo; Haug, Edward J.; Seering, Warren; Sundaram, Kamala; Thompson, Bruce; Turner, James; Chun, Hon; Frisch, Harold P.; Schnurr, Richard
1989-01-01
The Flight Telerobotic Servicer (FTS) program will require an ability to develop, in a cost effective manner, many simulation models for design, analysis, performance evaluation, and crew training. Computational speed and the degree of modeling fidelity associated with each simulation must be commensurate with problem objectives. To demonstrate evolving state-of-the-art general purpose multibody modeling capabilities, to validate these by laboratory testing, and to expose their modeling shortcomings, two focus problems at the opposite ends of the simulation spectrum are defined: (1) Coarse Acquisition Control Dynamics. Create a real time man-in-the-control-loop simulator. Provide animated graphical display of robot arm dynamics and tactile feedback sufficient for cueing the operator. Interface simulator software with human operated tactile feedback controller; i.e., the Kraft mini-master. (2) Fine, Precision Mode Control Dynamics. Create a high speed, high fidelity simulation model for the design, analysis, and performance evaluation of autonomous 7 degree-of-freedom (DOF) trajectory control algorithms. This model must contain detail dynamic models for all significant dynamics elements within the robot arm, such as joint drive mechanisms.
The effects of gear reduction on robot dynamics
NASA Technical Reports Server (NTRS)
Chen, J.
1989-01-01
The effect of the joint drive system with gear reduction for a generic two-link system is studied. It is done by comparing the kinetic energy of such a system with that of a direct drive two-link system. The only difference are two terms involving the inertia of the motor rotor and gear ratio. Modifications of the equations of motion from a direct drive system are then developed and generalized to various cases encountered in robot manipulators.
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.
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.
Planning acetabular fracture reduction using patient-specific multibody simulation of the hip
NASA Astrophysics Data System (ADS)
Oliveri, Hadrien; Boudissa, Mehdi; Tonetti, Jerome; Chabanas, Matthieu
2017-03-01
Acetabular fractures are a challenge in orthopedic surgery. Computer-aided solutions were proposed to segment bone fragments, simulate the fracture reduction or design the osteosynthesis fixation plates. This paper addresses the simulation part, which is usually carried out by freely moving bone fragments with six degrees of freedom to reproduce the pre-fracture state. Instead we propose a different paradigm, closer to actual surgeon's requirements: to simulate the surgical procedure itself rather than the desired result. A simple, patient-specific, biomechanical multibody model is proposed, integrating the main ligaments and muscles of the hip joint while accounting for contacts between bone fragments. Main surgical tools and actions can be simulated, such as clamps, Schanz screws or traction of the femur. Simulations are computed interactively, which enables clinicians to evaluate different strategies for an optimal surgical planning. Six retrospective cases were studied, with simple and complex fracture patterns. After interactively building the models from preoperative CT, gestures from the surgical reports were reproduced. Results of the simulations could then be compared with postoperative CT data. A qualitative study shows the model behavior is excellent and the simulated reductions fit the observed data. A more quantitative analysis is currently being completed. Two cases are particularly significant, for which the surgical reduction actually failed. Simulations show it was indeed not possible to reduce these fractures with the chosen approach. Had our simulator being used, a better planning may have avoided a second surgery to these patients.
SIMULATIONS OF ENERGETIC PARTICLES INTERACTING WITH DYNAMICAL MAGNETIC TURBULENCE
Hussein, M.; Shalchi, A. E-mail: husseinm@myumanitoba.ca
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/B{sub 0} = 0.5.
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.
Computational models of protein kinematics and dynamics: beyond simulation.
Gipson, Bryant; Hsu, David; Kavraki, Lydia E; Latombe, Jean-Claude
2012-01-01
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.
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
Generalized dynamic engine simulation techniques for the digital computer
NASA Technical Reports Server (NTRS)
Sellers, J.; Teren, F.
1974-01-01
Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design-point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar all-digital programs on future engine simulation philosophy is also discussed.
Generalized dynamic engine simulation techniques for the digital computer
NASA Technical Reports Server (NTRS)
Sellers, J.; Teren, F.
1974-01-01
Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program, DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design-point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar all-digital programs on future engine simulation philosophy is also discussed.
Generalized dynamic engine simulation techniques for the digital computers
NASA Technical Reports Server (NTRS)
Sellers, J.; Teren, F.
1975-01-01
Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program, DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar digital programs on future engine simulation philosophy is also discussed.
Dynamics of nitrogen dissociation from direct molecular simulation
NASA Astrophysics Data System (ADS)
Valentini, Paolo; Schwartzentruber, Thomas E.; Bender, Jason D.; Candler, Graham V.
2016-08-01
We present a molecular-level investigation of nitrogen dissociation at high temperature. The computational technique, called direct molecular simulation (DMS), solely relies on an ab initio potential energy surface and both N2+N2 and N +N2 processes are simulated as they concurrently take place in an evolving nonequilibrium gas system. Quasiclassical trajectory calculations (QCT) reveal that dissociation rate coefficients calculated at thermal equilibrium, i.e., assuming Boltzmann energy distributions, are approximately equal (within less than 15%) for both N2+N2 and N +N2 collisions for the range of temperatures considered. The DMS (nonequilibrium) results indicate, however, that the presence of atomic nitrogen significantly affects the dissociation rate of molecular nitrogen, but indirectly. In fact, the presence of atomic nitrogen causes an important reduction of the vibrational relaxation time of N2, by almost one order of magnitude. This, in turn, speeds up the replenishment of high-v states that are otherwise significantly depleted if only N2+N2 collisions are considered. Because of the strong favoring of dissociation from high-v states, this results in dissociation rates that are 2-3 times higher when significant atomic nitrogen is present compared to systems composed of mainly diatomic nitrogen, such as during the initial onset of dissociation. Specifically, we find that exchange events occur frequently during N +N2 collisions and that such exchange collisions constitute an effective mechanism of scrambling the internal energy states, resulting in multiquantum jumps in vibrational energy levels that effectively promote energy transfers. The resulting vibrational relaxation time constant we calculate for N +N2 collisions is significantly lower than the widely used Millikan-White model. Significant discrepancies are found between predictions of the Park two-temperature model (using the Millikan-White vibrational relaxation model) and the DMS results for
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…
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.
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...
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...
Classical trajectory simulations of post-transition state dynamics
NASA Astrophysics Data System (ADS)
Lourderaj, Upakarasamy; Park, Kyoyeon; Hase, William L.
Classical chemical dynamics simulations of post-transition state dynamics are reviewed. Most of the simulations involve direct dynamics for which the potential energy and gradient are obtained directly from an electronic structure theory. The chemical reaction attributes and chemical systems presented are product energy partitioning for Cl- ··· CH3Br → ClCH3 + Br- and C2H5F → C2H4 + HF dissociation, non-RRKM dynamics for cyclopropane stereomutation and the Cl- ··· CH3Cl complexes mediating the Cl- + CH3Cl SN2 nucleophilic substitution reaction, and non-IRC dynamics for the OH- + CH3F and F- + CH3OOH chemical reactions. These studies illustrate the important role of chemical dynamics simulations in understanding atomic-level reaction dynamics and interpreting experiments. They also show that widely used paradigms and model theories for interpreting reaction kinetics and dynamics are often inaccurate and are not applicable.
šponer, Jiří; Cang, Xiaohui; Cheatham, Thomas E.
2013-01-01
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids. PMID:22525788
Multiple time scale based reduction scheme for nonlinear chemical dynamics
NASA Astrophysics Data System (ADS)
Das, D.; Ray, D. S.
2013-07-01
A chemical reaction is often characterized by multiple time scales governing the kinetics of reactants, products and intermediates. We eliminate the fast relaxing intermediates in autocatalytic reaction by transforming the original system into a new one in which the linearized part is diagonal. This allows us to reduce the dynamical system by identifying the associated time scales and subsequent adiabatic elimination of the fast modes. It has been shown that the reduced system sustains the robust qualitative signatures of the original system and at times the generic form of the return map for the chaotic system from which complex dynamics stems out in the original system can be identified. We illustrate the scheme for a three-variable cubic autocatalytic reaction and four-variable peroxidase-oxidase reaction.
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.
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
Hybrid Dynamics Simulation Engine for Metalloproteins
Sparta, Manuel; Shirvanyants, David; Ding, Feng; Dokholyan, Nikolay V.; Alexandrova, Anastassia N.
2012-01-01
Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins’ structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca2+ form of the enzyme catechol O-methyl transferase, which, unlike the native Mg2+ form, is catalytically inactive. The Mg2+ site is ochtahedral, but the Ca2+ is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight. PMID:22947938
Improvement of surgical simulation using dynamic volume rendering.
Radetzky, A; Schröcker, F; Auer, L M
2000-01-01
In the last years high efforts have been taken to develop surgical simulators for computer assisted training. However, most of these simulators use simple models of the human's anatomy, which are manually created using modeling software. Nevertheless, medical experts need to perform the training directly with the patient's complex anatomy, which can be received, for example, from digital imaging datasets (CT, MR). A common technique to display these datasets is volume rendering. However, even with high-end hardware only static models can be handled interactively. In surgical simulators a dynamic component is also needed because tissues must be deformed and partially removed. With the combination of springmass models, which are improved by neuro-fuzzy systems, and the recently developed OpenGL Volumizer, surgical simulation using real-time deformable (or dynamic) volume rendering became possible. As an application example the simulator ROBOSIM for minimally invasive neurosurgery is presented.
Strong Analog Classical Simulation of Coherent Quantum Dynamics
NASA Astrophysics Data System (ADS)
Wang, Dong-Sheng
2017-02-01
A strong analog classical simulation of general quantum evolution is proposed, which serves as a novel scheme in quantum computation and simulation. The scheme employs the approach of geometric quantum mechanics and quantum informational technique of quantum tomography, which applies broadly to cases of mixed states, nonunitary evolution, and infinite dimensional systems. The simulation provides an intriguing classical picture to probe quantum phenomena, namely, a coherent quantum dynamics can be viewed as a globally constrained classical Hamiltonian dynamics of a collection of coupled particles or strings. Efficiency analysis reveals a fundamental difference between the locality in real space and locality in Hilbert space, the latter enables efficient strong analog classical simulations. Examples are also studied to highlight the differences and gaps among various simulation methods. Funding support from NSERC of Canada and a research fellowship at Department of Physics and Astronomy, University of British Columbia are acknowledged
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.
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.
Fast simulation of Brownian dynamics in a crowded environment.
Smith, Stephen; Grima, Ramon
2017-01-14
Brownian dynamics simulations are an increasingly popular tool for understanding spatially extended biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics (BD) simulations; however these methods are extremely slow owing to the sheer number of possible collisions between particles. Here we propose a rigorous "crowder-free" method to dramatically increase the simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the cases where the reactive particles are point particles, and where they themselves occupy a volume. Using simulations of simple chemical reaction networks, we show that the "crowder-free" method is up to three orders of magnitude faster than conventional BD and yet leads to nearly indistinguishable results from the latter.
Mantha, Sriteja; Yethiraj, Arun
2016-02-24
The properties of water under confinement are of practical and fundamental interest. Here 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, D_{T} , and rotational relaxation time, τ_{R}. 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 decoupling 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 D_{T} and τ_{R} 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 and neutron spin echo measurements would be a valuable technique in addition to QENS.
Mantha, Sriteja; Yethiraj, Arun
2016-02-24
The properties of water under confinement are of practical and fundamental interest. Here 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 valuesmore » to those directly measured in the simulations. We find that the decoupling 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 and neutron spin echo measurements would be a valuable technique in addition to QENS.« less
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.
Benchmarking nitrogen removal suspended-carrier biofilm systems using dynamic simulation.
Vanhooren, H; Yuan, Z; Vanrolleghem, P A
2002-01-01
We are witnessing an enormous growth in biological nitrogen removal from wastewater. It presents specific challenges beyond traditional COD (carbon) removal. A possibility for optimised process design is the use of biomass-supporting media. In this paper, attached growth processes (AGP) are evaluated using dynamic simulations. The advantages of these systems that were qualitatively described elsewhere, are validated quantitatively based on a simulation benchmark for activated sludge treatment systems. This simulation benchmark is extended with a biofilm model that allows for fast and accurate simulation of the conversion of different substrates in a biofilm. The economic feasibility of this system is evaluated using the data generated with the benchmark simulations. Capital savings due to volume reduction and reduced sludge production are weighed out against increased aeration costs. In this evaluation, effluent quality is integrated as well.
Gas dynamics for accretion disk simulations
NASA Technical Reports Server (NTRS)
Whitehurst, R.
1994-01-01
The behavior of accretion disks can largely be understood in terms of the basic physical processes of mass, energy, and momentum conservation. Despite this, detailed modeling of these systems using modern computational techniques is challenging and controversial. Disturbing differences exist between methods used widely in astrophysics, namely Eulerian finite-difference techniques and particle codes such as SPH. Therefore neither technique is fully satisfactory for accretion disk simulations. This paper describes a new fully Lagrangian method designed to resolve these difficulties.
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.
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.
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
Insights from molecular dynamics simulations for computational protein design.
Childers, Matthew Carter; Daggett, Valerie
2017-02-01
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
Enhanced sampling techniques in molecular dynamics simulations of biological systems.
Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus
2015-05-01
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. 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. 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. 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. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.
Using integrated multi-body systems for dynamical-optical simulations
NASA Astrophysics Data System (ADS)
Störkle, Johannes; Eberhard, Peter
2016-08-01
In this work, the in uence of model order reduction methods on optical aberrations is analysed within an dynamical-optical simulation of a high precision optomechanical system. Therefore, an integrated modeling process and new methods have to be introduced for the computation and investigation of the dynamical-optical behaviour. For instance, this optical system can be a telescope optic or a lithographic objective. In order to derive a simplified mechanical model for transient time simulations with low computational cost, the method of elastic multibody systems in combination with model order reduction methods can be used. For this, software-tools and interfaces are utilized. Furthermore, mechanical and optical simulation models are derived and implemented. With these, on the one hand, the mechanical sensitivity can be investigated for arbitrary external excitations and on the other hand, the related optical behaviour can be predicted. In order to clarify these methods, academic examples are chosen and the influences of the model order reduction methods and simulation strategies are analysed. Finally, the systems are investigated with respect to the mechanical-optical frequency responses.
Dynamic computer simulations of electrophoresis: three decades of active research.
Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A
2009-06-01
Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.
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
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.
Multiscale simulation of microbe structure and dynamics.
Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V; Cheluvaraja, Srinath C; Ortoleva, Peter J
2011-10-01
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.
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
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.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver
2015-06-01
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.
Group theoretic reduction of Laplacian dynamical problems on fractal lattices
Schwalm, W.A.; Schwalm, M.K.; Giona, M.
1997-06-01
Discrete forms of the Schr{umlt o}dinger equation, the diffusion equation, the linearized Landau-Ginzburg equation, and discrete models for vibrations and spin dynamics belong to a class of Laplacian-based finite difference models. Real-space renormalization of such models on finitely ramified regular fractals is known to give exact recursion relations. It is shown that these recursions commute with Lie groups representing continuous symmetries of the discrete models. Each such symmetry reduces the order of the renormalization recursions by one, resulting in a system of recursions with one fewer variable. Group trajectories are obtained from inverse images of fixed and invariant sets of the recursions. A subset of the Laplacian finite difference models can be mapped by change of boundary conditions and time dependence to a diffusion problem with closed boundaries. In such cases conservation of mass simplifies the group flow and obtaining the groups becomes easier. To illustrate this, the renormalization recursions for Green functions on four standard examples are decoupled. The examples are (1) the linear chain, (2) an anisotropic version of Dhar{close_quote}s 3-simplex, similar to a model dealt with by Hood and Southern, (3) the fourfold coordinated Sierpi{acute n}ski lattice of Rammal and of Domany {ital et al.}, and (4) a form of the Vicsek lattice. Prospects for applying the group theoretic method to more general dynamical systems are discussed. {copyright} {ital 1997} {ital The American Physical Society}
Flicker reduction in tone mapped high dynamic range video
NASA Astrophysics Data System (ADS)
Guthier, Benjamin; Kopf, Stephan; Eble, Marc; Effelsberg, Wolfgang
2011-01-01
In order to display a high dynamic range (HDR) video on a regular low dynamic range (LDR) screen, it needs to be tone mapped. A great number of tone mapping (TM) operators exist - most of them designed to tone map one image at a time. Using them on each frame of an HDR video individually leads to flicker in the resulting sequence. In our work, we analyze three tone mapping operators with respect to flicker. We propose a criterion for the automatic detection of image flicker by analyzing the log average pixel brightness of the tone mapped frame. Flicker is detected if the difference between the averages of two consecutive frames is larger than a threshold derived from Stevens' power law. Fine-tuning of the threshold is done in a subjective study. Additionally, we propose a generic method to reduce flicker as a post processing step. It is applicable to all tone mapping operators. We begin by tone mapping a frame with the chosen operator. If the flicker detection reports a visible variation in the frame's brightness, its brightness is adjusted. As a result, the brightness variation is smoothed over several frames, becoming less disturbing.
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.
Numerical simulations of blobs with ion dynamics
NASA Astrophysics Data System (ADS)
Nielsen, A. H.; Rasmussen, J. Juul; Madsen, J.; Xu, G. S.; Naulin, V.; Olsen, J. M. B.; Løiten, M.; Hansen, S. K.; Yan, N.; Tophøj, L.; Wan, B. N.
2017-02-01
The transport of particles and energy into the scrape-off layer (SOL) region at the outboard midplane of medium-sized tokamaks, operating in low confinement mode, is investigated by applying the first-principle HESEL (hot edge-sol-electrostatic) model. HESEL is a four-field drift-fluid model including finite electron and ion temperature effects, drift wave dynamics on closed field lines, and sheath dynamics on open field lines. Particles and energy are mainly transported by intermittent blobs. Therefore, blobs have a significant influence on the corresponding profiles. The formation of a ‘shoulder’ in the SOL density profile can be obtained by increasing the collisionality or connection length, thus decreasing the efficiency of the SOL’s ability to remove plasma. As the ion pressure has a larger perpendicular but smaller parallel dissipation rate compared to the electron pressure, ion energy is transported far into the SOL. This implies that the ion temperature in the SOL exceeds the electron temperature by a factor of 2-4 and significantly broadens the power deposition profile.
A new battery-charging method suggested by molecular dynamics simulations.
Abou Hamad, Ibrahim; Novotny, M A; Wipf, D O; Rikvold, P A
2010-03-20
Based on large-scale molecular dynamics simulations, we propose a new charging method that should be capable of charging a lithium-ion battery in a fraction of the time needed when using traditional methods. This charging method uses an additional applied oscillatory electric field. Our simulation results show that this charging method offers a great reduction in the average intercalation time for Li(+) ions, which dominates the charging time. The oscillating field not only increases the diffusion rate of Li(+) ions in the electrolyte but, more importantly, also enhances intercalation by lowering the corresponding overall energy barrier.
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.
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.
New ways to boost molecular dynamics simulations.
Krieger, Elmar; Vriend, Gert
2015-05-15
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
A reduction for spiking integrate-and-fire network dynamics ranging from homogeneity to synchrony.
Zhang, J W; Rangan, A V
2015-04-01
In this paper we provide a general methodology for systematically reducing the dynamics of a class of integrate-and-fire networks down to an augmented 4-dimensional system of ordinary-differential-equations. The class of integrate-and-fire networks we focus on are homogeneously-structured, strongly coupled, and fluctuation-driven. Our reduction succeeds where most current firing-rate and population-dynamics models fail because we account for the emergence of 'multiple-firing-events' involving the semi-synchronous firing of many neurons. These multiple-firing-events are largely responsible for the fluctuations generated by the network and, as a result, our reduction faithfully describes many dynamic regimes ranging from homogeneous to synchronous. Our reduction is based on first principles, and provides an analyzable link between the integrate-and-fire network parameters and the relatively low-dimensional dynamics underlying the 4-dimensional augmented ODE.
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.
Multilevel model reduction for uncertainty quantification in computational structural dynamics
NASA Astrophysics Data System (ADS)
Ezvan, O.; Batou, A.; Soize, C.; Gagliardini, L.
2017-02-01
This work deals with an extension of the reducedorder models (ROMs) that are classically constructed by modal analysis in linear structural dynamics for which the computational models are assumed to be uncertain. It is based on a multilevel projection strategy consisting in introducing three reduced-order bases that are obtained by using a spatial filtering methodology of local displacements. This filtering involves global shape functions for the kinetic energy. The proposed multilevel stochastic ROM is constructed by using the nonparametric probabilistic approach of uncertainties. It allows for affecting a specific level of uncertainties to each type of displacements associated with the corresponding vibration regime. The proposed methodology is applied to the computational model of an automobile structure, for which the multilevel stochastic ROM is identified with respect to experimental measurements. This identification is performed by solving a statistical inverse problem.
Predicting protein interactions by Brownian dynamics simulations.
Meng, Xuan-Yu; Xu, Yu; Zhang, Hong-Xing; Mezei, Mihaly; Cui, Meng
2012-01-01
We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions.
Simulation of nanofractal dynamics with MBN Explorer
NASA Astrophysics Data System (ADS)
Solov'yov, Ilia A.; Solov'yov, Andrey V.
2013-06-01
One of the goals of nanotechnology is the development of controlled, reproducible, and industrially transposable nanostructured materials. In this context, controlling of the final architecture of such materials by tuneable parameters is one of the fundamental problems. Post-growth processes occurring in patterns grown on a surface were studied using a multi-purpose computer code MBN EXPLORER introduced in the present paper. The package allows to model molecular systems of varied level of complexity, and in the present paper was used, in particular, to study dynamics of silver nanofractal formation and fragmentation on graphite surface. We demonstrate that the detachment of particles from the fractal and their diffusion within the fractal and over the surface determines the shape of the islands remaining on a surface after the fractal fragmentation.
Passive Vibration Reduction with Silicone Springs and Dynamic Absorber
NASA Astrophysics Data System (ADS)
Lee, Ji-hoon; Dong, Yanlu; Lee, Moon G.
In the precision manufacturing field, the major structural components are often made of rigid and massive elements. Those mechanisms are so fluctuated by swaying of building and resonating of ground floor that the precision gets lower. As a result, quality of products is declined. So far, to minimize the influences of result from external irregular vibration, various technical methods of the absorbing vibration are used. For example, vibration isolation table which use air damper and heavy granite surface plate are used. But, these devices need high cost and low mobility. In this paper, our target is to analyze the external vibration and then to develop a mechanism which is able to reduce the effect. It is also able to be produced at a lower cost. Firstly, a silicone support is proposed as a simple vibration isolating mechanism. Swaying and resonating of a building have 2∼4 Hz vibrating frequency when a person is running on a treadmill, similar phenomena happen. Therefore, the supports are mounted under the running pad of a treadmill. This is a passive vibration isolator. The support is designed to have low stiffness and high deformation to isolate and absorb the vibration. As a result, it reduces the peak amplitude of vibration by about 80%. Secondly, a dynamic vibration absorber is developed to minimize the repetitive vibration. The absorber has a fundamental resonating frequency by its spring and mass. The resonating frequency is designed to have close value to the vibrating frequency of the treadmill. The length of beam can be adjusted to have variable resonance according to the external vibration. This absorber also reduces vibration by 84%. The passive vibration isolator and dynamic vibration absorber can be applied to precision equipments with repetitive motion or with disturbance of swaying of building.
Symplectic molecular dynamics simulations on specially designed parallel computers.
Borstnik, Urban; Janezic, Dusanka
2005-01-01
We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.
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.
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 simulation of thin-film growth
NASA Astrophysics Data System (ADS)
Schneider, M.; Schuller, I. K.; Rahman, A.
1987-01-01
The epitaxial growth of thin films has been studied by molecular-dynamics computer simulation. In these simulations atoms are projected towards a temperature-controlled substrate, and the equations of motion of all atoms are solved for a given interaction potential. The calculations give insight into the microscopic structure of thin films, the dynamics of the adsorption process, and they help answer the way in which substrate temperature, form of the substrate, flux of impinging atoms, and form of the interaction potential, affect epitaxial growth. Simulations were performed for monatomic and binary systems with spherically symmetric atomic interactions, and for systems in which the atoms are interacting via a three-body potential to simulate the epitaxial growth of silicon.
A dynamic skull model for simulation of cerebral cortex folding.
Chen, Hanbo; Guo, Lei; Nie, Jingxin; Zhang, Tuo; Hu, Xintao; Liu, Tianming
2010-01-01
The mechanisms of human cerebral cortex folding and their interactions during brain development are largely unknown, partly due to the difficulties in biological experiments and data acquisition for the developing fetus brain. Computational modeling and simulation provide a novel approach to the understanding of cortex folding processes in normal or aberrant neurodevelopment. Based on our recently developed computational model of the cerebral cortex folding using neuronal growth model and mechanical skull constraint, this paper presents a computational dynamic model of the brain skull that regulates the cortical folding simulation. Our simulation results show that the dynamic skull model is more biologically realistic and significantly improves our cortical folding simulation results. This work provides further computational support to the hypothesis that skull is an important regulator of cortical folding.
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.
Simulated dynamics and control of an extractive alcoholic fermentation.
Costa, A C; Dechechi, E C; Silva, F L; Maugeri, F; Maciel, R
2000-01-01
In this study, we investigated the dynamics of a computer simulation of a continuous alcoholic fermentation process combined with a flash column under vacuum. The alcohol was partially extracted in order to maintain its concentration at about 40 kg/m3 in the fermentor. The mathematical model of the fermentation was developed for industrial conditions and considers the effect of the temperature on the kinetic parameters. The performance of the dynamic matrix control algorithm, single input single output and multiple input multiple output, for the control of the extractive process was studied. The concepts of factorial design were used in a simulation study to determine the best control structures for the process.
Molecular Dynamics Simulations of Gas Transport in Polymer Films
NASA Astrophysics Data System (ADS)
Whitley, David; Butler, Simon; Adolf, David
2010-03-01
Parallel molecular dynamics simulations have been carried out to determine the permeability of O2 and N2 through polyethylene terephthalate, polypropylene and cis(1-4) polybutadiene. The permeability of both mixed and unmixed gas penetrants is studied within films of these well known gas barrier polymers. Results are obtained either through the solubility and diffusion (i.e. P=D*S) or via the permeability directly. Encouraging results are obtained. Additional analysis focuses on ``unmixed/mixed gas'' intracomparisons of the simulated permeability data in addition to corresponding penetrant and host polymer local dynamics.
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.
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.
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.
Simulation of Naval Guns' Breechblock System Dynamics Based on ADAMS
NASA Astrophysics Data System (ADS)
Tan, Bo; Liu, Hui-Min; Liu, Kai
In order to study the dynamical characteristics of the breechblock system during gun firing, a virtual prototype model was established based on ADAMS, in which motion and force transmission among mechanisms are realized by collision. By simulation, kinematics and dynamics properties of main components are obtained, and the relationships between the motion of breechblock and the position of breechblock opening plate are analyzed. According to the simulation results, the collision among the breechblock opening plate and the roller is discontinuous, which may make the breechblock system fail to hitch the breechblock reliably. And within allowable scope of the structure, the breechblock opening template should be installed near the upside as much as possible.
Lessons Learned From Dynamic Simulations of Advanced Fuel Cycles
Steven J. Piet; Brent W. Dixon; Jacob J. Jacobson; Gretchen E. Matthern; David E. Shropshire
2009-04-01
Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe “lessons learned” from dynamic simulations but attempt to answer the “so what” question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.
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
Hybrid simulations with dynamical quarks: Spectra, screening and thermodynamics
Sinclair, D.K.
1987-11-18
We summarize simulations made by the Argonne/University of Illinois group using the Hybrid algorithm to include dynamical staggered fermions. Recent work on the mass spectrum and screening effects due to the inclusion of four light flavors of dynamical quarks is presented. We also present a brief overview of what we have learned about the finite temperature chiral phase transition. 5 refs., 4 figs., 1 tab.
Computer simulation and image guidance for individualised dynamic spinal stabilization.
Kantelhardt, S R; Hausen, U; Kosterhon, M; Amr, A N; Gruber, K; Giese, A
2015-08-01
Dynamic implants for the human spine are used to re-establish regular segmental motion. However, the results have often been unsatisfactory and complications such as screw loosening are common. Individualisation of appliances and precision implantation are needed to improve the outcome of this procedure. Computer simulation, virtual implant optimisation and image guidance were used to improve the technique. A human lumbar spine computer model was developed using multi-body simulation software. The model simulates spinal motion under load and degenerative changes. After virtual degeneration of a L4/5 segment, virtual pedicle screw-based implants were introduced. The implants' positions and properties were iteratively optimised. The resulting implant positions were used as operative plan for image guidance and finally implemented in a physical spine model. In the simulation, the introduction and optimisation of virtually designed dynamic implants could partly compensate for the effects of virtual lumbar segment degeneration. The optimised operative plan was exported to two different image-guidance systems for transfer to a physical spine model. Three-dimensional computer graphic simulation is a feasible means to develop operative plans for dynamic spinal stabilization. These operative plans can be transferred to commercially available image-guidance systems for use in implantation of physical implants in a spine model. This concept has important potential in the design of operative plans and implants for individualised dynamic spine stabilization surgery.
Dynamical QCD+QED simulation with staggered quarks
Zhou, Ran; Gottlieb, Steven
2014-11-15
Electromagnetic effects play an important role in many phenomena such as isospin-symmetry breaking in the hadron spectrum and the hadronic contributions to g-2. We have generalized the MILC QCD code to include the electromagnetic field. In this work, we focus on simulations including charged sea quarks using the RHMC algorithm. We show details of the dynamical QCD+QED simulation algorithm with compact QED. We analyze the code performance and results for hadron-spectrum observables.
Molecular dynamics simulation of carbon disulphide with a Gaussian correction
NASA Astrophysics Data System (ADS)
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2017-02-01
Molecular Dynamics (MD) simulations of liquid carbon disulphide (CS2) in the temperature range 164-318 K under normal pressure and at experimental density were performed using an expa-6 potential with a Gaussian correction plus electrostatic interactions. This correction allowed to modify the curvature of the potential. The results of the MD simulation are compared with available experimental data. The agreement is good.
Molecular dynamics simulation of a nanoscopic nematic twist cell
NASA Astrophysics Data System (ADS)
Mirantsev, Leonid V.; Virga, Epifanio G.
2007-08-01
We present molecular dynamics simulations of a nanoscopic nematic twist cell confined within two bounding substrates with conflicting anchoring conditions. The results of our simulations show that the torque transmitted through the cell drops significantly below a certain critical cell’s thickness, thus confirming the predictions of the continuum Landau theory extrapolated down to the nanoscopic scale [F. Bisi, E. G. Virga, and G. E. Durand, Phys. Rev. E 70, 042701 (2004)].
Monte Carlo simulation of excitation and ionization collisions with complexity reduction
NASA Astrophysics Data System (ADS)
Le, Hai P.; Yan, Bokai; Caflisch, Russel E.; Cambier, Jean-Luc
2017-10-01
Kinetic simulation of plasmas with detailed excitation and ionization collisions presents a significant computational challenge due to the multiscale feature of the collisional rates. In the present work, we propose a complexity reduction method based on atomic level grouping for modeling excitation and ionization collisions. High order of accuracy of the reduction method is realized by allowing an internal distribution within each group. We apply the reduction method to the standard Monte Carlo collision algorithm to model an atomic Hydrogen plasma. Numerical results suggest that the stiffness of the collisional kinetics can be significantly reduced with minimal loss in accuracy.
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.
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.
Dissipative Particle Dynamics simulation of colloidal suspensions
NASA Astrophysics Data System (ADS)
Jamali, Safa; Boromand, Arman; Maia, Joao
2014-03-01
DPD as a mesoscale method was firstly proposed to study dynamics of suspensions under flow condition. However the proposed method failed to capture shear properties of suspensions because it lacked: first a potential to reproduce lubrication forces and second a clear definition for the colloid surface. Recently we reported a modified DPD method which defines colloidal particles as particles with hard core and a dissipative coat. An additional lubrication force was introduced to include the short-range hydrodynamics that are not captured in original DPD. The model was found to be able to reproduce shear properties of suspensions for a wide range of different systems, from monodisperse to bimodal with different volume fractions, compositions and size ratios. In present work our modified DPD method is employed to study both equilibrium and flow properties of colloidal suspension. Zero shear viscosity of suspension is measured using Green-Kubo expressions and the results are compared to theoretical predictions. Furthermore, structure formation in suspensions is studied in respect to energy landscape of the fluid both at rest and under flow.
Studies of thermal transport properties using molecular dynamics simulation techniques
NASA Astrophysics Data System (ADS)
Ratanapisit, Juraivan
The purpose of this research has been to investigate the transport properties of fluids using novel techniques in molecular dynamics simulations: symplectic integration algorithms for equations of motion, Baranyai's thermostatted fluid wall algorithm, and Rapaport's algorithm for hard chain fluids. In the symplectic integration study, an extensive series of equilibrium molecular dynamic simulations have been performed to investigate the accuracy, stability and efficiency of second order explicit symplectic integrators: position Verlet, velocity Verlet, and the McLauchlan-Atela algorithms. To our knowledge, previous studies of the symplectic integrators have only looked at the thermodynamic energy using a simple model fluid. Our work presents realistic but perhaps the simplest simulations possible to test the effect of the integrators on the three main transport properties. Our results suggest that if an algorithm fails to adequately conserve energy, it will also show significant uncertainties in transport property calculations. A large portion of the simulation study focused on a new algorithm for thermal conductivity based on Baranyai's fluid wall method. This algorithm is stable enough to perform simulations even using large time steps and provides reasonable values and uncertainties for the thermal conductivity. The investigation was conducted using two different thermostat algorithms: the Gaussian and Nosé-Hoover thermostats. The final part of this research focused on the viscosity of hard chain fluids. This study was initiated with an investigation of the equilibrium molecular dynamic simulations of pure hard-sphere molecules. The natural extension of that work was to hard chain fluids. (Abstract shortened by UMI.)
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
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
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.
NASA Astrophysics Data System (ADS)
Kawamura, Kohei; Ueno, Yosuke; Nakamura, Yoshiaki
In the present study we have developed a numerical method to simulate the flight dynamics of a small flying body with unsteady motion, where both aerodynamics and flight dynamics are fully considered. A key point of this numerical code is to use computational fluid dynamics and computational flight dynamics at the same time, which is referred to as CFD2, or double CFDs, where several new ideas are adopted in the governing equations, the method to make each quantity nondimensional, and the coupling method between aerodynamics and flight dynamics. This numerical code can be applied to simulate the unsteady motion of small vehicles such as micro air vehicles (MAV). As a sample calculation, we take up Taketombo, or a bamboo dragonfly, and its free flight in the air is demonstrated. The eventual aim of this research is to virtually fly an aircraft with arbitrary motion to obtain aerodynamic and flight dynamic data, which cannot be taken in the conventional wind tunnel.
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
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
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.
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.
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.
NASA Astrophysics Data System (ADS)
Salvetti, Maria Vittoria; Mariotti, Alessandro; Buresti, Guido
2016-11-01
The present work focuses on strategies for aerodynamic drag reduction of elongated axisymmetric bluff bodies, which can be viewed as simplified models of a road vehicles. We combine boat-tailing, i.e. a gradual reduction of the body cross-section before a sharp-edged base, with properly contoured transverse grooves. The effectiveness of this strategy was assessed through experiments and simulations. Experiments showed that the introduction of a single groove leads to a further delay of boundary-layer separation and to a reduction of drag compared with the boat-tail configuration without grooves. In this talk, we present Large-Eddy Simulations (LES). LES results agree with the experimental findings. The success of the proposed flow control strategy is due to the relaxation of the no-slip condition in the small recirculation region inside the groove, which reduces the momentum losses near the wall and thus delays boundary layer separation. The effects of the introduction of the groove on the mean topology and on the dynamics of the near wake are also highlighted. Finally, a sensitivity analysis of the proposed control strategy efficiency to the groove location and to the boat-tail geometry is shown.
Tethsim - A dynamics simulation software package for tethered system
NASA Astrophysics Data System (ADS)
Venditti, F.; Cibrario, B.; Origgi, G.
This paper presents the description of a dynamics simulation package, called Tethsim, devoted to the investigation of tethered systems behavior in space. The papers also analyzes specific problems related to tethered system simulation such as validation, varying-length tether growth model, and CPU time consumption and describes the approaches used to solve them. The system is modeled in Tethsim as composed by rigid bodies and point-masses connected by spring-dashpot, to form an open-line configuration. Strong emphasis has been placed on easing user interfaces with the program; in particular, the software can be flexibly adapted to the specific system to be simulated.
A Fault Evolution Model Including the Rupture Dynamic Simulation
NASA Astrophysics Data System (ADS)
Wu, Y.; Chen, X.
2011-12-01
We perform a preliminary numerical simulation of seismicity and stress evolution along a strike-slip fault in a 3D elastic half space. Following work of Ben-Zion (1996), the fault geometry is devised as a vertical plane which is about 70 km long and 17 km wide, comparable to the size of San Andreas Fault around Parkfield. The loading mechanism is described by "backslip" method. The fault failure is governed by a static/kinetic friction law, and induced stress transfer is calculated with Okada's static solution. In order to track the rupture propagation in detail, we allow induced stress to propagate through the medium at the shear wave velocity by introducing a distance-dependent time delay to responses to stress changes. Current simulation indicates small to moderate earthquakes following the Gutenberg-Richter law and quasi-periodical characteristic large earthquakes, which are consistent with previous work by others. Next we will consider introducing a more realistic friction law, namely, the laboratory-derived rate- and state- dependent law, which can simulate more realistic and complicated sliding behavior such as the stable and unstable slip, the aseismic sliding and the slip nucleation process. In addition, the long duration of aftershocks is expected to be reproduced due to this time-dependent friction law, which is not available in current seismicity simulation. The other difference from previous work is that we are trying to include the dynamic ruptures in this study. Most previous study on seismicity simulation is based on the static solution when dealing with failure induced stress changes. However, studies of numerical simulation of rupture dynamics have revealed lots of important details which are missing in the quasi-static/quasi- dynamic simulation. For example, dynamic simulations indicate that the slip on the ground surface becomes larger if the dynamic rupture process reaches the free surface. The concentration of stress on the propagating crack
Dynamic simulation and validation of a satellite docking system
NASA Astrophysics Data System (ADS)
Hays, Anthony B.; Tchoryk, Peter, Jr.; Pavlich, Jane C.; Wassick, Gregory
2003-08-01
In recent years, Michigan Aerospace has approached the problem of gentle autonomous spacecraft rendezvous and docking using a flexible soft-dock cable that is extended from the docking spacecraft to the target spacecraft. Because of the nature of a soft-dock cable, testing and validation of the technology is difficult in normal gravity. To properly emulate the behavior of this soft-dock cable, we have performed dynamic computer simulations so that the effects of micro-gravity could be simulated. The Autonomous Satellite Docking System (ASDS) was initially prototyped and tested at Marshall Space Flight Center"s air-bearing floor facility. The test data was compared to the simulations and used to validate the model. Once a good correlation between the simulation"s predicted results and the actual data was shown, the model was used to predict future performance of the ASDS mechanism on several potential spacecraft for the Orbital Express program. A new dynamic simulation model was created and compared to test data from a recent KC-135 flight test to further validate the modeling approach used. This paper will describe the methodology used in modeling and simulating the ASDS mechanism. Correlation between the models and the test data will be discussed.
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.
De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut
2011-07-15
With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.
Simulation Analysis of Helicopter Ground Resonance Nonlinear Dynamics
NASA Astrophysics Data System (ADS)
Zhu, Yan; Lu, Yu-hui; Ling, Ai-min
2017-07-01
In order to accurately predict the dynamic instability of helicopter ground resonance, a modeling and simulation method of helicopter ground resonance considering nonlinear dynamic characteristics of components (rotor lead-lag damper, landing gear wheel and absorber) is presented. The numerical integral method is used to calculate the transient responses of the body and rotor, simulating some disturbance. To obtain quantitative instabilities, Fast Fourier Transform (FFT) is conducted to estimate the modal frequencies, and the mobile rectangular window method is employed in the predictions of the modal damping in terms of the response time history. Simulation results show that ground resonance simulation test can exactly lead up the blade lead-lag regressing mode frequency, and the modal damping obtained according to attenuation curves are close to the test results. The simulation test results are in accordance with the actual accident situation, and prove the correctness of the simulation method. This analysis method used for ground resonance simulation test can give out the results according with real helicopter engineering tests.
Method for simulating dose reduction in digital mammography using the Anscombe transformation.
Borges, Lucas R; Oliveira, Helder C R de; Nunes, Polyana F; Bakic, Predrag R; Maidment, Andrew D A; Vieira, Marcelo A C
2016-06-01
This work proposes an accurate method for simulating dose reduction in digital mammography starting from a clinical image acquired with a standard dose. 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. 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%. 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 transformation. NNPS, PS, and local noise
Molecular dynamics simulation study of binary fullerene mixtures
NASA Astrophysics Data System (ADS)
Ruberto, R.; Abramo, M. C.; Caccamo, C.
2004-10-01
We report constant-pressure molecular dynamics (MD) simulations of binary C60/Cn fullerene-mixtures ( n=70 , 76, 84, 96) modeled in terms of a spherically symmetric two-body potential. By starting from a liquid configuration of the system, we cool mixtures down to freezing and beyond, until room temperature is reached, in order to verify the formation of solid solutions, namely, of configurations characterized by a unique crystalline lattice whose sites are randomly occupied by the two component fullerene species. We first explore the entire concentration range of the C60x/C70(1-x)(0
Dynamic testing and simulation of the Mars Exploration Rover
NASA Technical Reports Server (NTRS)
Lindemann, Randel
2005-01-01
In January of 2004, NASA landed two mobile robotic spacecraft on the surface of Mars as part of the Mars Exploration Rover (MER) project. The results and lessons learned of the test and dynamic simulation of the MER vehicles is provided in this paper.
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…
Brownian dynamics simulation of the interactions between DNA and histones
NASA Astrophysics Data System (ADS)
Wang, Peng-Ye; Li, Wei; Dou, Shuo-Xing; Tong, Pei-Qing
2003-03-01
In eukaryotic cells, the basic structural unit of chromatin is a nucleosome which consists of 146bp of DNA and histones. The interaction between DNA and histone is one of the essential factors influencing the formation of chromosome structure. We have studied the dynamic process of the interaction of DNA and histones in the formation of nucleosome by Brownian dynamics simulation. The aim of our work is to search for important features in the formation of nucleosome by observing the snapshots of the dynamic process of DNA wrapping around histones. In the simulation, we have used the stochastic Runge-Kutta numerical method. It is found that, with proper parameter values, DNA can correctly wrap around the histone octamer about two turns as in the actual situations. The simulation shows that the interaction potential between DNA and histone plays the main rule for the wrapping of DNA, and the temperature is also an important parameter in the process. The stretching dynamics of the chromatin by an externally applied force has also been simulated.
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…
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.
Protocols for Molecular Dynamics Simulations of RNA Nanostructures.
Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A
2017-01-01
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.
Molecular dynamics simulation of aqueous solutions of glycine betaine
NASA Astrophysics Data System (ADS)
Civera, Monica; Fornili, Arianna; Sironi, Maurizio; Fornili, Sandro L.
2003-01-01
Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine- N-oxide, a bioprotectant closely related to glycine betaine.
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.
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…
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…
Evaluating the Accuracy of Hessian Approximations for Direct Dynamics Simulations.
Zhuang, Yu; Siebert, Matthew R; Hase, William L; Kay, Kenneth G; Ceotto, Michele
2013-01-08
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.
Effects of Mg2+ on the bivalent mercury reduction behaviors in simulated wet FGD absorbents.
Wang, Yuejun; Liu, Yue; Mo, Jiansong; Wu, Zhongbiao
2012-10-30
This paper studied the bivalent mercury reduction behaviors after Mg(2+) addition in the simulated Ca-based and Dual-Alkali flue gas desulfurization (FGD) absorbents. Experimental results showed that the reduction of bivalent mercury was increased in the Ca-based FGD absorbent and inhibited in the Dual-Alkali FGD absorbent. It was proposed that the former was mainly attributed to the enhanced dissolution and recrystallization of CaSO(3) particles by Mg(2+) addition, which provided more active surface for mercury adsorption and reduction, whilst the latter was mainly due to the formation of neutral MgSO(3)(0) ion pair, which tended to lower the active sulfite concentration in the simulated solution.
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.
Molecular dynamics simulation: A tool for exploration and discovery
NASA Astrophysics Data System (ADS)
Rapaport, Dennis C.
2009-03-01
The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).
Ion Move Brownian Dynamics (IMBD)--simulations of ion transport.
Kurczynska, Monika; Kotulska, Malgorzata
2014-01-01
Comparison of the computed characteristics and physiological measurement of ion transport through transmembrane proteins could be a useful method to assess the quality of protein structures. Simulations of ion transport should be detailed but also timeefficient. The most accurate method could be Molecular Dynamics (MD), which is very time-consuming, hence is not used for this purpose. The model which includes ion-ion interactions and reduces the simulation time by excluding water, protein and lipid molecules is Brownian Dynamics (BD). In this paper a new computer program for BD simulation of the ion transport is presented. We evaluate two methods for calculating the pore accessibility (round and irregular shape) and two representations of ion sizes (van der Waals diameter and one voxel). Ion Move Brownian Dynamics (IMBD) was tested with two nanopores: alpha-hemolysin and potassium channel KcsA. In both cases during the simulation an ion passed through the pore in less than 32 ns. Although two types of ions were in solution (potassium and chloride), only ions which agreed with the selectivity properties of the channels passed through the pores. IMBD is a new tool for the ion transport modelling, which can be used in the simulations of wide and narrow pores.
Acoustic properties in glycerol glass-former: Molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Busselez, Remi; Pezeril, Thomas; Institut des Materiaux et Molecules du Mans Team
2013-03-01
Study of high-frequency collective dynamics around TeraHertz region in glass former has been a subject of intense investigations and debates over the past decade. In particular, the presence of the Boson peak characteristic of glassy material and its relation to other glass anomalies. Recently, experiments and simulations have underlined possible relation between Boson peak and transverse acoustic modes in glassy materials. In particular, simulations of simple Lennard Jones glass former have shown a relation between Ioffe-Regel criterion in transverse modes and Boson peak. We present here molecular dynamics simulation on high frequency dynamics of glycerol. In order to study mesoscopic order (0.5-5nm-1), we made use of large simulation box containing 80000 atoms. Analysis of collective longitudinal and transverse acoustic modes shows striking similarities in comparison with simulation of Lennard-Jones particles. In particular, it seems that a connection may exist between Ioffe-Regel criterion for transverse modes and Bose Peak frequency. However,in our case we show that this connection may be related with structural correlation arising from molecular clusters.
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.
Understanding Diabetes Population Dynamics Through Simulation Modeling and Experimentation
Jones, Andrew P.; Homer, Jack B.; Murphy, Dara L.; Essien, Joyce D. K.; Milstein, Bobby; Seville, Donald A.
2006-01-01
Health planners in the Division of Diabetes Translation and others from the National Center for Chronic Disease Prevention and Health Promotion of the Centers for Disease Control and Prevention used system dynamics simulation modeling to gain a better understanding of diabetes population dynamics and to explore implications for public health strategy. A model was developed to explain the growth of diabetes since 1980 and portray possible futures through 2050. The model simulations suggest characteristic dynamics of the diabetes population, including unintended increases in diabetes prevalence due to diabetes control, the inability of diabetes control efforts alone to reduce diabetes-related deaths in the long term, and significant delays between primary prevention efforts and downstream improvements in diabetes outcomes. PMID:16449587
Understanding diabetes population dynamics through simulation modeling and experimentation.
Jones, Andrew P; Homer, Jack B; Murphy, Dara L; Essien, Joyce D K; Milstein, Bobby; Seville, Donald A
2006-03-01
Health planners in the Division of Diabetes Translation and others from the National Center for Chronic Disease Prevention and Health Promotion of the Centers for Disease Control and Prevention used system dynamics simulation modeling to gain a better understanding of diabetes population dynamics and to explore implications for public health strategy. A model was developed to explain the growth of diabetes since 1980 and portray possible futures through 2050. The model simulations suggest characteristic dynamics of the diabetes population, including unintended increases in diabetes prevalence due to diabetes control, the inability of diabetes control efforts alone to reduce diabetes-related deaths in the long term, and significant delays between primary prevention efforts and downstream improvements in diabetes outcomes.
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).
Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.
Markegard, Cade B; Mazaheripour, Amir; Jocson, Jonah-Micah; Burke, Anthony M; Dickson, Mary N; Gorodetsky, Alon A; Nguyen, Hung D
2015-09-03
Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks.
The effect of simulator dynamics on pilot response
NASA Technical Reports Server (NTRS)
Weener, E. F.
1974-01-01
The effects of visual display dynamics on the altitude tracking performance of a subject in a fixed base flight simulator are considered. The subject, flying the linearized longitudinal equations of motion, attempts to maintain the same altitude as two airplanes positioned three hundred feet ahead, as in level formation flying. The horizon together with the two leading aircraft are represented symbolically on a CRT display. The subject's aircraft is disturbed by atmospheric turbulence. The data indicate a relationship between the bandwidth of the display dynamics and the short period characteristics of the simulated airplane. For an airplane with a relatively fast pitch response the presence of altitude display dynamics, with a bandwidth as high as five times the short period natural frequency, causes significant degradation of altitude tracking performance.
4D simulation of explosive eruption dynamics at Vesuvius
NASA Astrophysics Data System (ADS)
Neri, Augusto; Esposti Ongaro, Tomaso; Menconi, Gianluca; De'Michieli Vitturi, Mattia; Cavazzoni, Carlo; Erbacci, Giovanni; Baxter, Peter J.
2007-02-01
We applied a new simulation model, based on multiphase transport laws, to describe the 4D (3D spatial coordinates plus time) dynamics of explosive eruptions. Numerical experiments, carried out on a parallel supercomputer, describe the collapse of the volcanic eruption column and the propagation of pyroclastic density currents (PDCs), for selected medium scale (sub-Plinian) eruptive scenarios at Vesuvius, Italy. Simulations provide crucial insights into the effects of the generation mechanism of the flows - partial collapse vs boiling-over - on their evolution and hazard potential, the unstable dynamics of the fountain, and the influence of Mount Somma on the propagation of PDCs into the circum-Vesuvian area, one of the world's most hazardous volcanic settings. Results also show that it is possible to characterize the volcanic column behavior in terms of percentage of the mass of pyroclasts collapsed to the ground and how this parameter strongly influences the dynamics and hazard of the associated PDCs.
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.
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.
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.
Numerical simulations of complex fluid-fluid interface dynamics
NASA Astrophysics Data System (ADS)
Krüger, T.; Frijters, S.; Günther, F.; Kaoui, B.; Harting, J.
2013-05-01
Interfaces between two fluids are ubiquitous and of special importance for industrial applications, e.g., stabilisation of emulsions. The dynamics of fluid-fluid interfaces is difficult to study because these interfaces are usually deformable and their shapes are not known a priori. Since experiments do not provide access to all observables of interest, computer simulations pose attractive alternatives to gain insight into the physics of interfaces. In the present article, we restrict ourselves to systems with dimensions comparable to the lateral interface extensions. We provide a critical discussion of three numerical schemes coupled to the lattice Boltzmann method as a solver for the hydrodynamics of the problem: (a) the immersed boundary method for the simulation of vesicles and capsules, the Shan-Chen pseudopotential approach for multi-component fluids in combination with (b) an additional advection-diffusion component for surfactant modelling and (c) a molecular dynamics algorithm for the simulation of nanoparticles acting as emulsifiers.
Linear Optics Simulation of Quantum Non-Markovian Dynamics
Chiuri, Andrea; Greganti, Chiara; Mazzola, Laura; Paternostro, Mauro; Mataloni, Paolo
2012-01-01
The simulation of open quantum dynamics has recently allowed the direct investigation of the features of system-environment interaction and of their consequences on the evolution of a quantum system. Such interaction threatens the quantum properties of the system, spoiling them and causing the phenomenon of decoherence. Sometimes however a coherent exchange of information takes place between system and environment, memory effects arise and the dynamics of the system becomes non-Markovian. Here we report the experimental realisation of a non-Markovian process where system and environment are coupled through a simulated transverse Ising model. By engineering the evolution in a photonic quantum simulator, we demonstrate the role played by system-environment correlations in the emergence of memory effects. PMID:23236588
Linear Optics Simulation of Quantum Non-Markovian Dynamics
NASA Astrophysics Data System (ADS)
Chiuri, Andrea; Greganti, Chiara; Mazzola, Laura; Paternostro, Mauro; Mataloni, Paolo
2012-12-01
The simulation of open quantum dynamics has recently allowed the direct investigation of the features of system-environment interaction and of their consequences on the evolution of a quantum system. Such interaction threatens the quantum properties of the system, spoiling them and causing the phenomenon of decoherence. Sometimes however a coherent exchange of information takes place between system and environment, memory effects arise and the dynamics of the system becomes non-Markovian. Here we report the experimental realisation of a non-Markovian process where system and environment are coupled through a simulated transverse Ising model. By engineering the evolution in a photonic quantum simulator, we demonstrate the role played by system-environment correlations in the emergence of memory effects.
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.
Multiscale and multimodel simulation of Bloch-point dynamics
NASA Astrophysics Data System (ADS)
Andreas, Christian; Kákay, Attila; Hertel, Riccardo
2014-04-01
We present simulation results on the structure and dynamics of micromagnetic point singularities with atomistic resolution. This is achieved by embedding an atomistic computational region into a standard micromagnetic algorithm. Several length scales are bridged by means of an adaptive mesh refinement and a seamless coupling between the continuum theory and a Heisenberg formulation for the atomistic region. The code operates on graphical processing units and is able to detect and track the position of strongly inhomogeneous magnetic regions. This enables us to reliably simulate the dynamics of Bloch points, which means that a fundamental class of micromagnetic switching processes can be analyzed with unprecedented accuracy. We test the code by comparing it with established results and present its functionality with the example of a simulated field-driven Bloch-point motion in a soft-magnetic cylinder.
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 simulation of friction of hydrocarbon thin films
Tamura, Hiroyuki; Yoshida, Muneo; Kusakabe, Kenichi
1999-10-26
Molecular Dynamics (MD) simulations were performed to investigate the dynamic behavior of hydrocarbon molecules under shear conditions. Frictional properties of cyclohexane, n-hexane, and iso-hexane thin films confirmed between two solid surfaces were calculated. Because the affinity of the solid surfaces in these simulations is strong, slippages occurred at inner parts of the confined films, whereas no slippages were observed at the solid boundaries. The hexagonal closest packing structure was observed for the adsorbed cyclohexane molecular layers. The branched methyl groups in the iso-hexane molecules increase the shear stress between the molecular layers. For the n-hexane monolayer, molecules were observed to roll during the sliding simulations. Rolling of the n-hexane molecules decreased the shear stress.
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. © 2015 The Protein Society.
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%.
Information diversity in structure and dynamics of simulated neuronal networks.
Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena
2011-01-01
Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.
PISCES High Contrast Integral Field Spectrograph Simulations and Data Reduction Pipeline
NASA Technical Reports Server (NTRS)
Llop Sayson, Jorge Domingo; Memarsadeghi, Nargess; McElwain, Michael W.; Gong, Qian; Perrin, Marshall; Brandt, Timothy; Grammer, Bryan; Greeley, Bradford; Hilton, George; Marx, Catherine
2015-01-01
The PISCES (Prototype Imaging Spectrograph for Coronagraphic Exoplanet Studies) is a lenslet array based integral field spectrograph (IFS) designed to advance the technology readiness of the WFIRST (Wide Field Infrared Survey Telescope)-AFTA (Astrophysics Focused Telescope Assets) high contrast Coronagraph Instrument. We present the end to end optical simulator and plans for the data reduction pipeline (DRP). The optical simulator was created with a combination of the IDL (Interactive Data Language)-based PROPER (optical propagation) library and Zemax (a MatLab script), while the data reduction pipeline is a modified version of the Gemini Planet Imager's (GPI) IDL pipeline. The simulations of the propagation of light through the instrument are based on Fourier transform algorithms. The DRP enables transformation of the PISCES IFS data to calibrated spectral data cubes.
PISCES High Contrast Integral Field Spectrograph Simulations and Data Reduction Pipeline
NASA Technical Reports Server (NTRS)
Llop Sayson, Jorge Domingo; Memarsadeghi, Nargess; McElwain, Michael W.; Gong, Qian; Perrin, Marshall; Brandt, Timothy; Grammer, Bryan; Greeley, Bradford; Hilton, George; Marx, Catherine
2015-01-01
The PISCES (Prototype Imaging Spectrograph for Coronagraphic Exoplanet Studies) is a lenslet array based integral field spectrograph (IFS) designed to advance the technology readiness of the WFIRST (Wide Field Infrared Survey Telescope)-AFTA (Astrophysics Focused Telescope Assets) high contrast Coronagraph Instrument. We present the end to end optical simulator and plans for the data reduction pipeline (DRP). The optical simulator was created with a combination of the IDL (Interactive Data Language)-based PROPER (optical propagation) library and Zemax (a MatLab script), while the data reduction pipeline is a modified version of the Gemini Planet Imager's (GPI) IDL pipeline. The simulations of the propagation of light through the instrument are based on Fourier transform algorithms. The DRP enables transformation of the PISCES IFS data to calibrated spectral data cubes.
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.
Dynamic simulation for distortion image with turbulence atmospheric transmission effects
NASA Astrophysics Data System (ADS)
Du, Huijie; Fei, Jindong; Qing, Duzheng; Zhao, Hongming; Yu, Hong; Cheng, Chen
2013-09-01
The imaging through atmospheric turbulence is an inevitable problem encountered by infrared imaging sensors working in the turbulence atmospheric environment. Before light-rays enter the window of the imaging sensors, the atmospheric turbulence will randomly interfere with the transmission of the light waves came from the objects, causing the distribution of image intensity values on the focal plane to diffuse, the peak value to decrease, the image to get blurred, and the pixels to deviate, and making image identification very difficult. Owing to the fact of the long processing time and that the atmospheric turbulent flow field is unknown and hard to be described by mathematical models, dynamic simulation for distortion Image with turbulence atmospheric transmission effects is much more difficult and challenging in the world. This paper discusses the dynamic simulation for distortion Image of turbulence atmospheric transmission effect. First of all, with the data and the optical transmission model of the turbulence atmospheric, the ray-tracing method is applied to obtain the propagation path of optical ray which propagates through the high-speed turbulent flow field, and then to calculate the OPD from the reference wave to the reconverted wave front and obtain the point spread function (PSF). Secondly, infrared characteristics models of typical scene were established according to the theory of infrared physics and heat conduction, and then the dynamic infrared image was generated by OpenGL. The last step is to obtain the distortion Image with turbulence atmospheric transmission effects .With the data of atmospheric transmission computation, infrared simulation image of every frame was processed according to the theory of image processing and the real-time image simulation, and then the dynamic distortion simulation images with effects of blurring, jitter and shifting were obtained. Above-mentioned simulation method can provide the theoretical bases for recovering
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
The molecular dynamics simulation of ion-induced ripple growth
NASA Astrophysics Data System (ADS)
Süle, P.; Heinig, K.-H.
2009-11-01
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 (λ) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths (λ <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 λ >35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in λ long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for λ >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.
Human Sensibility Ergonomics Approach to Vehicle Simulator Based on Dynamics
NASA Astrophysics Data System (ADS)
Son, Kwon; Choi, Kyung-Hyun; Yoon, Ji-Sup
Simulators have been used to evaluate drivers' reactions to various transportation products. Most research, however, has concentrated on their technical performance. This paper considers driver's motion perception on a vehicle simulator through the analysis of human sensibility ergonomics. A sensibility ergonomic method is proposed in order to improve the reliability of vehicle simulators. A simulator in a passenger vehicle consists of three main modules such as vehicle dynamics, virtual environment, and motion representation modules. To evaluate drivers' feedback, human perceptions are categorized into a set verbal expressions collected and investigated to find the most appropriate ones for translation and angular accelerations of the simulator. The cut-off frequency of the washout filter in the representation module is selected as one sensibility factor. Sensibility experiments were carried out to find a correlation between the expressions and the cut-off frequency of the filter. This study suggests a methodology to obtain an ergonomic database that can be applied to the sensibility evaluation of dynamic simulators.
Molecular Dynamics of Dense Fluids: Simulation-Theory Symbiosis
NASA Astrophysics Data System (ADS)
Yip, Sidney
35 years ago Berni J. Alder showed the Boltzmann-Enskog kinetic theory failed to adequately account for the viscosity of fluids near solid density as determined by molecular dynamics simulation. This work, along with other notable simulation findings, provided great stimulus to the statistical mechanical studies of transport phenomena, particularly in dealing with collective effects in the time correlation functions of liquids. An extended theoretical challenge that remains partially resolved at best is the shear viscosity of supercooled liquids. How can one give a unified explanation of the so-called fragile and strong characteristic temperature behavior, with implications for the dynamics of glass transition? In this tribute on the occasion of his 90th birthday symposium, we recount a recent study where simulation, combined with heuristic (transition-state) and first principles (linear response) theories, identifies the molecular mechanisms governing glassy-state relaxation. Such an interplay between simulation and theory is progress from the early days; instead of simulation challenging theory, now simulation and theory complement each other.
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.
Research on hyperspectral dynamic scene and image sequence simulation
NASA Astrophysics Data System (ADS)
Sun, Dandan; Gao, Jiaobo; Sun, Kefeng; Hu, Yu; Li, Yu; Xie, Junhu; Zhang, Lei
2016-10-01
This paper presents a simulation method of hyper-spectral dynamic scene and image sequence for hyper-spectral equipment evaluation and target detection algorithm. Because of high spectral resolution, strong band continuity, anti-interference and other advantages, in recent years, hyper-spectral imaging technology has been rapidly developed and is widely used in many areas such as optoelectronic target detection, military defense and remote sensing systems. Digital imaging simulation, as a crucial part of hardware in loop simulation, can be applied to testing and evaluation hyper-spectral imaging equipment with lower development cost and shorter development period. Meanwhile, visual simulation can produce a lot of original image data under various conditions for hyper-spectral image feature extraction and classification algorithm. Based on radiation physic model and material characteristic parameters this paper proposes a generation method of digital scene. By building multiple sensor models under different bands and different bandwidths, hyper-spectral scenes in visible, MWIR, LWIR band, with spectral resolution 0.01μm, 0.05μm and 0.1μm have been simulated in this paper. The final dynamic scenes have high real-time and realistic, with frequency up to 100 HZ. By means of saving all the scene gray data in the same viewpoint image sequence is obtained. The analysis results show whether in the infrared band or the visible band, the grayscale variations of simulated hyper-spectral images are consistent with the theoretical analysis results.
Research on hyperspectral dynamic scene and image sequence simulation
NASA Astrophysics Data System (ADS)
Sun, Dandan; Liu, Fang; Gao, Jiaobo; Sun, Kefeng; Hu, Yu; Li, Yu; Xie, Junhu; Zhang, Lei
2016-10-01
This paper presents a simulation method of hyperspectral dynamic scene and image sequence for hyperspectral equipment evaluation and target detection algorithm. Because of high spectral resolution, strong band continuity, anti-interference and other advantages, in recent years, hyperspectral imaging technology has been rapidly developed and is widely used in many areas such as optoelectronic target detection, military defense and remote sensing systems. Digital imaging simulation, as a crucial part of hardware in loop simulation, can be applied to testing and evaluation hyperspectral imaging equipment with lower development cost and shorter development period. Meanwhile, visual simulation can produce a lot of original image data under various conditions for hyperspectral image feature extraction and classification algorithm. Based on radiation physic model and material characteristic parameters this paper proposes a generation method of digital scene. By building multiple sensor models under different bands and different bandwidths, hyperspectral scenes in visible, MWIR, LWIR band, with spectral resolution 0.01μm, 0.05μm and 0.1μm have been simulated in this paper. The final dynamic scenes have high real-time and realistic, with frequency up to 100 HZ. By means of saving all the scene gray data in the same viewpoint image sequence is obtained. The analysis results show whether in the infrared band or the visible band, the grayscale variations of simulated hyperspectral images are consistent with the theoretical analysis results.
Fast Simulation of Dynamic Ultrasound Images Using the GPU.
Storve, Sigurd; Torp, Hans
2017-10-01
Simulated ultrasound data is a valuable tool for development and validation of quantitative image analysis methods in echocardiography. Unfortunately, simulation time can become prohibitive for phantoms consisting of a large number of point scatterers. The COLE algorithm by Gao et al. is a fast convolution-based simulator that trades simulation accuracy for improved speed. We present highly efficient parallelized CPU and GPU implementations of the COLE algorithm with an emphasis on dynamic simulations involving moving point scatterers. We argue that it is crucial to minimize the amount of data transfers from the CPU to achieve good performance on the GPU. We achieve this by storing the complete trajectories of the dynamic point scatterers as spline curves in the GPU memory. This leads to good efficiency when simulating sequences consisting of a large number of frames, such as B-mode and tissue Doppler data for a full cardiac cycle. In addition, we propose a phase-based subsample delay technique that efficiently eliminates flickering artifacts seen in B-mode sequences when COLE is used without enough temporal oversampling. To assess the performance, we used a laptop computer and a desktop computer, each equipped with a multicore Intel CPU and an NVIDIA GPU. Running the simulator on a high-end TITAN X GPU, we observed two orders of magnitude speedup compared to the parallel CPU version, three orders of magnitude speedup compared to simulation times reported by Gao et al. in their paper on COLE, and a speedup of 27000 times compared to the multithreaded version of Field II, using numbers reported in a paper by Jensen. We hope that by releasing the simulator as an open-source project we will encourage its use and further development.
The Fermi-Pasta-Ulam problem: Simulation and modern dynamics
Weissert, T.P.
1992-01-01
In 1952, Enrico Fermi, John Pasta and Stanislaw Ulam (FPU) simulated the loaded string model, perturbed with small, nonlinear interaction terms. Because Poincare's theorem guarantees the non-existence of a complete set of integrals for three-body problem, they expected to see the diffusion of energy from its single-mode initial condition to all other modes of the string. But for every combination of initial conditions, the energy remained bounded within the lowest few modes. No theoretical explanation existed for this failure of the underlying hypothesis that erogidicity follows from the lack of a complete set of integrals of the motion in a Hamiltonian model. The author traces the history of this problem from the FPU simulation to the point that a consensus was reached concerning its solution twenty years later. During this period, the simulation of nonlinearly-perturbed integral models became the methodology for a new era in dynamics. Through the use of simulation, dynamicists discovered deterministic chaos, in which the exponential separation of pair orbits generate randomness in deterministic macroscopic systems, and a new kind of structure-related to the KAM theorem-that provides limited order in the absence of analytic integrals of the motions. The author maps the set of conceptually-related journal articles into a chronological inference topology that tracks the understanding of this problem of dynamics. Simulating non-integrable models on a digital computer requires the discretization of time and space. These approximations affect what the simulation can reveal about the model, and the model about reality. Simulations play the role of experiments on mathematical models. A discussion is presented of the issues that emerge with the use of simulation as a heuristic device and the groundwork is laid for an epistemology of simulation.
Ghatee, Mohammad Hadi; Zolghadr, Amin Reza; Moosavi, Fatemeh; Ansari, Younes
2012-03-28
Bulk and surface properties of the ionic liquids 1-alkyl-3-methyl-imidazolium iodides ([C(n)mim]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 [C(4)mim]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 [C(4)mim]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 [C(8)mim]I > [C(6)mim]I > [C(4)mim]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
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.
Erban, Radek
2016-02-01
Molecular dynamics (MD) simulations of ions (K(+), Na(+), Ca(2+) 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.
Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams
NASA Astrophysics Data System (ADS)
Ohya, Kaoru
2017-03-01
The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.