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Sample records for dynamic response simulations

  1. Dynamic Simulation of the Tank Gun Recoil Response

    Institute of Scientific and Technical Information of China (English)

    XING Jun-wen; WANG Liang-xi; SHI Yan; CHEN Chun-liang

    2005-01-01

    By using the ATV module of MSC. ADAMS, the dynamic simulation of recoil response of tank gun is analyzed.How the recoil force affects the bodywork and the suspension during gun firing, as well as the changing status of the gun muzzle's velocity are gained. All results and analyzing methods are offered for the designing basis of optimizing tank vehicle-gun match. The constructive exploration is beneficial to improving the general capability of tank.

  2. Shock responses of nanoporous aluminum by molecular dynamics simulations

    CERN Document Server

    Xiang, Meizhen; Yang, Yantao; Liao, Yi; Wang, Kun; Chen, Yun; Chen, Jun

    2016-01-01

    We present systematic investigations on the shock responses of nanoporous aluminum (np-Al) by nonequilibrium molecular dynamics simulations. The dislocation nucleation sites are found to concentrate in low latitude region near the equator of the spherical void surfaces. We propose a continuum wave reflection theory and a resolved shear stress model to explain the distribution of dislocation nucleation sites. The simulations reveals two mechanisms of void collapse: the plasticity mechanism and the internal jetting mechanism. The plasticity mechanism, which leads to transverse collapse of voids, prevails under relatively weaker shocks; while the internal jetting mechanism, which leads to longitudinal filling of the void vacuum, plays more significant role as the shock intensity increases. In addition, an abnormal thermodynamic phenomenon (i.e., arising of temperature with pressure dropping) in shocked np-Al is discovered. This phenomenon is incompatible with the conventional Rankine-Hugoniot theory, and is expl...

  3. Dynamic Response of Linear Mechanical Systems Modeling, Analysis and Simulation

    CERN Document Server

    Angeles, Jorge

    2012-01-01

    Dynamic Response of Linear Mechanical Systems: Modeling, Analysis and Simulation can be utilized for a variety of courses, including junior and senior-level vibration and linear mechanical analysis courses. The author connects, by means of a rigorous, yet intuitive approach, the theory of vibration with the more general theory of systems. The book features: A seven-step modeling technique that helps structure the rather unstructured process of mechanical-system modeling A system-theoretic approach to deriving the time response of the linear mathematical models of mechanical systems The modal analysis and the time response of two-degree-of-freedom systems—the first step on the long way to the more elaborate study of multi-degree-of-freedom systems—using the Mohr circle Simple, yet powerful simulation algorithms that exploit the linearity of the system for both single- and multi-degree-of-freedom systems Examples and exercises that rely on modern computational toolboxes for both numerical and symbolic compu...

  4. Simulation of the dynamic response of radioactive material shipping package-railcar systems during coupling operations

    Energy Technology Data Exchange (ETDEWEB)

    Fields, S.R.

    1983-10-01

    The basic equations of the computer model CARDS (Cask-Railcar Dynamic Simulator), developed for the US Nuclear Regulatory Commission to simulate the dynamic behavior of radioactive material shipping package - railcar systems, are presented. A companion model, CARRS (Cask Railcar Response Spectrum Generator), that generates system response as frequency response spectra is also presented in terms of its basic equations. 1 reference, 18 figures.

  5. Simulation of the dynamic response of radioactive material shipping package - railcar systems during coupling operations

    Energy Technology Data Exchange (ETDEWEB)

    Fields, S.R.

    1981-12-01

    The basic equations of the computer model CARDS (Cask-Railcar Dynamic Simulator), developed for the U.S. Nuclear Regulatory Commission to simulate the dynamic behavior of radioactive material shipping package - railcar systems, are presented. A companion model, CARRS (Casks Railcar Response Spectrum Generator), that generates system response as frequency response spectra is also presented in terms of its basic equations.

  6. Numerical Simulation of Dynamic Response of Supple Nets

    Institute of Scientific and Technical Information of China (English)

    ZHU Li-xin; LIANG Zhen-lin; HUANG Liu-yi; ZHAO Fen-fang

    2006-01-01

    A simulation method based on the lumped mass model is proposed for determining the dynamic behavior of nets exposed to a uniform current. Every mesh bar is modeled by a linear bar element. The lumped mass point is set at the ends of each element. The net can be simulated by a discretized model consisting of many point masses and elements without mass. 3D shapes and the distribution of tensions of the net at different moments can be found from time integration of a set of motion equations with a computer program. Two nets are simulated according to reference experiments. Calculated results are in accordance with experimental results. The method is applicable and can be applied to improving design of, and research into other flexible structures, such as net cages.

  7. Continuum simulation of dislocation dynamics: Predictions for internal friction response

    Energy Technology Data Exchange (ETDEWEB)

    Greaney, P. Alex; Friedman, Lawrence H.; Chrzan, D.C.

    2002-02-19

    The amplitude dependent mechanical loss due to bosing of an idealized Frank-Read Source is studied using both simulation and analytical techniques. Dislocations are modeled within isotropic elasticity theory, and are assumed to be in the over-damped limit.

  8. An investigation into computer simulation of the dynamic response of a gas turbine engine

    OpenAIRE

    Hendricks, Todd B

    1997-01-01

    Transient performance of gas turbines has a strong bearing on output and component life. For this reason, several articles have been written on the dynamic simulation of gas turbine systems in electrical generation, cogeneration, and marine applications. These models provide a basis for this present work. This paper describes a mathematical and computer model that was developed to investigate the dynamic response of a simple (no reheat, regeneration, or other auxiliary equipment) single-shaft...

  9. Concurrent material point method and molecular dynamics approach for simulating transient responses

    Science.gov (United States)

    Chen, Zhen; Su, Yu-Chen; Zhang, Hetao; Jiang, Shan; Sewell, Thomas D.

    2017-01-01

    To effectively simulate multiscale transient responses such as impact and penetration without the need to invoke a master/slave treatment, the multiscale material point method (Multi-MPM) is being developed wherein molecular dynamics (MD) at the nanoscale or dissipative particle dynamics (DPD) at the mesoscale are handled concurrently within the framework of the original MPM (continuum scale). The proposed numerical scheme for concurrently linking different scales is described here along with a preliminary error analysis. Representative examples for concurrent MPM and DPD and concurrent MPM and MD simulations were presented at SCCM-2015. Because the original MPM is an extension from computational fluid dynamics to solid dynamics, the proposed Multi-MPM might also become robust for dealing with multiphase interactions involving failure evolution.

  10. Computational Simulation of Dynamic Response of Vehicle Tatra T815 and the Ground

    Science.gov (United States)

    Vlček, Jozef; Valašková, Veronika

    2016-10-01

    The effect of a moving load represents the actual problem which is analysed in engineering practice. The response of the vehicle and its dynamic effect on the pavement can be analysed by experimental or computational ways. The aim of this paper was to perform computer simulations of a vehicle-ground interaction. For this purpose, a half-part model of heavy lorry Tatra 815 and ground was modelled in computational programmes ADINA and PLAXIS based on FEM methods, utilizing analytical approaches. Two procedures were then selected for further calculations. The first one is based on the simplification of the stiffer pavement layers to the beam element supported by the springs simulating the subgrade layers using Winkler-Pasternak theory of elastic half-space. Modulus of subgrade reaction was determined in the standard programme trough the simulation of a plate load test. Second approach considers a multi-layered ground system with layers of different thicknesses and material properties. For comparison of outputs of both approaches, the same input values were used for every calculation procedure. Crucial parameter for the simulations was the velocity of the passing vehicle with regard to the ground response to the impulse of the pass. Lower velocities result in almost static response of the pavement, but higher velocities induce response that can be better described by the dynamic theory. For small deformations, an elastic material model seems to be sufficient to define the ground response to the moving load, but for larger deformations advanced material models for the ground environment would be more reliable.

  11. Oscillatory shear response of dilute ferrofluids: predictions from rotational Brownian dynamics simulations and ferrohydrodynamics modeling.

    Science.gov (United States)

    Soto-Aquino, D; Rosso, D; Rinaldi, C

    2011-11-01

    Ferrofluids are colloidal suspensions of magnetic nanoparticles that exhibit normal liquid behavior in the absence of magnetic fields but respond to imposed magnetic fields by changing their viscosity without loss of fluidity. The response of ferrofluids to constant shear and magnetic fields has received a lot of attention, but the response of ferrofluids to oscillatory shear remains largely unexplored. In the present work we used rotational Brownian dynamics to study the dynamic properties of ferrofluids with thermally blocked nanoparticles under oscillatory shear and constant magnetic fields. Comparisons between simulations and modeling using the ferrohydrodynamics equations were also made. Simulation results show that, for small rotational Péclet number, the in-phase and out-of-phase components of the complex viscosity depend on the magnitude of the magnetic field and frequency of the shear, following a Maxwell-like model with field-dependent viscosity and characteristic time equal to the field-dependent transverse magnetic relaxation time of the nanoparticles. Comparison between simulations and the numerical solution of the ferrohydrodynamic equations shows that the oscillatory rotational magnetoviscosity for an oscillating shear field obtained using the kinetic magnetization relaxation equation quantitatively agrees with simulations for a wide range of Péclet number and Langevin parameter but has quantitative deviations from the simulations at high values of the Langevin parameter. These predictions indicate an apparent elastic character to the rheology of these suspensions, even though we are considering the infinitely dilute limit in which there are negligible particle-particle interactions and, as such, chains do not form. Additionally, an asymptotic analytical solution of the ferrohydrodynamics equations, valid for Pe<2, was used to demonstrate that the Cox-Merz rule applies for dilute ferrofluids under conditions of small shear rates. At higher shear

  12. A study on dynamic response of slopes under wave action using simulation tests

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    After the erection of the Three Gorges Dam, the water level of Yangtze River will reach 175 m, and the average wave crest will be up to 1 m. Therefore the wave action cannot be neglected for the slope stability. Through simulation tests, the waveinduced dynamic response of the slope is analyzed. The soil body is taken as linear elastic body when it has a small deformation under the small wave action. Based on tests, the excess pore pressure and slope displacement under the loading in different wave period are analyzed. The ratio of dynamic strength and static strength to the breaking process of the slope is discussed. It is demonstrated that smaller wave period gives rise to a larger strain of the slope under the same stress. At different depth of water, different weakness effect on the stability of the soil slope is observed and the slope has an adaptability to the wave action to some extent.

  13. Numerical Simulation of Dynamic Response and Collapse for Steel Frame Structures Subjected to Blast Load

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiuhua; DUAN Zhongdong; ZHANG Chunwei

    2008-01-01

    The progressive collapse of steel frame structures under the blast load was investigated using LS-DYNA.The multi-material Eulerian and Lagrangian coupling algorithm was adopted.A fluid-structure coupling finite element model was established which consists of Lagrange element for simulating steel frame structures and concrete ground,multiple ALE element for simulating air and TNT explosive material.Numerical simulations of the blast pressure wave propagation,structural dynamic responses and deformation,and progressive collapse of a five-story steel frame structure in the event of an explosion near above ground were performed.The numerical analysis showed that the Lagrangian and Eulerian coupling algorithm gave good simulations of the shock wave propagation in the mediums and blast load effects on the structure.The columns subjected to blast load may collapse by shear yielding rather than by flexural deformation.The columns and joints of steel beam to column in the front steel frame structure generated enormous plastic deformation subjected to intensive blast waves,and columns lost carrying capacity,subsequently leading to the collapse of the whole structure.The approach coupling influence between structural deformation and fluid load well simulated the progressive collapse process of structures,and provided an effective tool for analyzing the collapse mechanism of the steel frame structure under blast load.

  14. Numerical Simulation of the Spreading Dynamic Responses of the Multibody System with a Floating Base

    Institute of Scientific and Technical Information of China (English)

    Zhaobing Jiang; Luzhong Shao; Fei Shao

    2015-01-01

    To simulate the dynamic responses of the multibody system with a floating base when the upper parts spread with a certain sequence and relative speed, the homogeneous matrix method is employed to model and simulate a four-body system with a floating base and the motions are analyzed when the upper parts are spread sequentially or synchronously. The rolling, swaying and heaving temporal variations are obtained when the multibody system is under the conditions of the static water along with the wave loads and the mean wind loads or the single pulse wind loads, respectively. The moment variations of each joint under the single pulse wind load are also gained. The numerical results showed that the swaying of the floating base is almost not influenced by the spreading time or form when the upper parts spread sequentially or synchronously, while the rolling and the heaving mainly depend on the spreading time and forms. The swaying and heaving motions are influenced significantly by the mean wind loads. The single pulse wind load also has influences on the dynamic responses. The torque of joint 3 and joint 4 in the single pulse wind environment may be twice that in the windless environment when the system spreads with 60 s duration.

  15. Ice Storage Air-Conditioning System Simulation with Dynamic Electricity Pricing: A Demand Response Study

    Directory of Open Access Journals (Sweden)

    Chi-Chun Lo

    2016-02-01

    Full Text Available This paper presents an optimal dispatch model of an ice storage air-conditioning system for participants to quickly and accurately perform energy saving and demand response, and to avoid the over contact with electricity price peak. The schedule planning for an ice storage air-conditioning system of demand response is mainly to transfer energy consumption from the peak load to the partial-peak or off-peak load. Least Squares Regression (LSR is used to obtain the polynomial function for the cooling capacity and the cost of power consumption with a real ice storage air-conditioning system. Based on the dynamic electricity pricing, the requirements of cooling loads, and all technical constraints, the dispatch model of the ice-storage air-conditioning system is formulated to minimize the operation cost. The Improved Ripple Bee Swarm Optimization (IRBSO algorithm is proposed to solve the dispatch model of the ice storage air-conditioning system in a daily schedule on summer. Simulation results indicate that reasonable solutions provide a practical and flexible framework allowing the demand response of ice storage air-conditioning systems to demonstrate the optimization of its energy savings and operational efficiency and offering greater energy efficiency.

  16. Numerical Simulation of Dynamic Response of Fiber Reinforced Ceramic Matrix Composite Beam with Matrix Cracks Using Multiscale Modeling

    Institute of Scientific and Technical Information of China (English)

    Gao Xiguang; Song Yingdong; Sun Zhigang; Hu Xuteng

    2010-01-01

    A multiscale method for simulating the dynamic response of ceramic matrix composite (CMC) with matrix cracks is developed.At the global level,the finite element method is employed to simulate the dynamic response ofa CMC beam.While at the local level,the multiscale mechanical method is used to estimate the stress/strain response of the material.A distributed computing system is developed to speed up the simulation.The simulation of dynamic response of a Nicalon/CAS-Ⅱ beam being subjected to harmonic loading is performed as a numerical example.The results show that both the stress/strain responses under tension and compressive loading are nonlinear.These conditions result in a different response compared with that of elastic beam,such as:1) the displacement response is not symmetric about the axis of time;2) in the condition of small external load,the response at first order natural frequency is limited within a finite range;3) decreasing the matrix crack space will increase the displacement response of the beam.

  17. Shock initiated thermal and chemical responses of HMX crystal from ReaxFF molecular dynamics simulation.

    Science.gov (United States)

    Zhou, Tingting; Song, Huajie; Liu, Yi; Huang, Fenglei

    2014-07-21

    To gain an atomistic-level understanding of the thermal and chemical responses of condensed energetic materials under thermal shock, we developed a thermal shock reactive dynamics (TS-RD) computational protocol using molecular dynamics simulation coupled with ReaxFF force field. β-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) was selected as a a target explosive due to its wide usage in the military and industry. The results show that a thermal shock initiated by a large temperature gradient between the "hot" region and the "cold" region results in thermal expansion of the particles and induces a thermal-mechanical wave propagating back and forth in the system with an averaged velocity of 3.32 km s(-1). Heat propagating along the direction of thermal shock leads to a temperature increment of the system and thus chemical reaction initiation. Applying a continuum reactive heat conduction model combined with the temperature distribution obtained from the RD simulation, a heat conduction coefficient is derived as 0.80 W m(-1) K(-1). The chemical reaction mechanisms during thermal shock were analyzed, showing that the reaction is triggered by N-NO2 bond breaking followed by HONO elimination and ring fission. The propagation rates of the reaction front and reaction center are obtained to be 0.069 and 0.038 km s(-1), based on the time and spatial distribution of NO2. The pressure effect on the thermal shock was also investigated by employing uniaxial compression before the thermal shock. We find that compression significantly accelerates thermal-mechanical wave propagation and heat conduction, resulting in higher temperature and more excited molecules and thus earlier initiation and faster propagation of chemical reactions.

  18. Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response.

    Directory of Open Access Journals (Sweden)

    Elio A Cino

    Full Text Available Intrinsically disordered proteins (IDPs are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP Prothymosin alpha (ProTα and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2, with a common binding partner, Kelch-like ECH-associated protein 1(Keap1, are essential for regulating cellular response to oxidative stress. Misregulation of this pathway can lead to neurodegenerative diseases, premature aging and cancer. In order to understand the mechanisms these two disordered proteins employ to bind to Keap1, we performed extensive 0.5-1.0 microsecond atomistic molecular dynamics (MD simulations and isothermal titration calorimetry experiments to investigate the structure/dynamics of free-state ProTα and Neh2 and their thermodynamics of bindings. The results show that in their free states, both ProTα and Neh2 have propensities to form bound-state-like β-turn structures but to different extents. We also found that, for both proteins, residues outside the Keap1-binding motifs may play important roles in stabilizing the bound-state-like structures. Based on our findings, we propose that the binding of disordered ProTα and Neh2 to Keap1 occurs synergistically via preformed structural elements (PSEs and coupled folding and binding, with a heavy bias towards PSEs, particularly for Neh2. Our results provide insights into the molecular mechanisms Neh2 and ProTα bind to Keap1, information that is useful for developing therapeutics to enhance the oxidative stress response.

  19. Recent Research and Applications of Numerical Simulation for Dynamic Response of Long-Span Bridges Subjected to Multiple Loads

    Directory of Open Access Journals (Sweden)

    Zhiwei Chen

    2014-01-01

    Full Text Available Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach is based on numerical simulation technologies. This paper provides a detailed review of key issues involved in dynamic response analysis of long-span multiload bridges based on numerical simulation technologies, including dynamic interactions between running trains and bridge, between running road vehicles and bridge, and between wind and bridge, and in the wind-vehicle-bridge coupled system. Then a comprehensive review is conducted for engineering applications of newly developed numerical simulation technologies to safety assessment of long-span bridges, such as assessment of fatigue damage and assessment under extreme events. Finally, the existing problems and promising research efforts for the numerical simulation technologies and their applications to assessment of long-span multiload bridges are explored.

  20. Recent research and applications of numerical simulation for dynamic response of long-span bridges subjected to multiple loads.

    Science.gov (United States)

    Chen, Zhiwei; Chen, Bo

    2014-01-01

    Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach is based on numerical simulation technologies. This paper provides a detailed review of key issues involved in dynamic response analysis of long-span multiload bridges based on numerical simulation technologies, including dynamic interactions between running trains and bridge, between running road vehicles and bridge, and between wind and bridge, and in the wind-vehicle-bridge coupled system. Then a comprehensive review is conducted for engineering applications of newly developed numerical simulation technologies to safety assessment of long-span bridges, such as assessment of fatigue damage and assessment under extreme events. Finally, the existing problems and promising research efforts for the numerical simulation technologies and their applications to assessment of long-span multiload bridges are explored.

  1. Molecular dynamics simulation of materials response to high strain-rate loading

    Energy Technology Data Exchange (ETDEWEB)

    Belak, J

    1999-07-22

    A molecular dynamics (MD) analysis of conservation of momentum through a shock front is presented. The MD model uses a non-traditional boundary condition that allows simulation in the reference frame of the shock front. Higher order terms proportional to gradients in the density are shown to be non-negligible at the shock front. The simulation is used to study the sequence of thermodynamic states during shock loading. Melting is observed in the simulations, though above the thermodynamic melt curve as is common in homogeneous simulations of melting. High strain-rate tensile loading is applied to the growth of nanoscale voids in copper. Void growth is found to occur by plasticity mechanisms with dislocations emerging from the void surface. [molecular dynamics, shock loading, conservation of momentum, shock melting, void growth

  2. Artificial Neural Networks for Nonlinear Dynamic Response Simulation in Mechanical Systems

    DEFF Research Database (Denmark)

    Christiansen, Niels Hørbye; Høgsberg, Jan Becker; Winther, Ole

    2011-01-01

    It is shown how artificial neural networks can be trained to predict dynamic response of a simple nonlinear structure. Data generated using a nonlinear finite element model of a simplified wind turbine is used to train a one layer artificial neural network. When trained properly the network is able...

  3. Computational Fluid Dynamics Simulation of Combustion Instability in Solid Rocket Motor : Implementation of Pressure Coupled Response Function

    Directory of Open Access Journals (Sweden)

    S. Saha

    2016-04-01

    Full Text Available Combustion instability in solid propellant rocket motor is numerically simulated by implementing propellant response function with quasi steady homogeneous one dimensional formulation. The convolution integral of propellant response with pressure history is implemented through a user defined function in commercial computational fluid dynamics software. The methodology is validated against literature reported motor test and other simulation results. Computed amplitude of pressure fluctuations compare closely with the literarture data. The growth rate of pressure oscillations of a cylindrical grain solid rocket motor is determined for different response functions at the fundamental longitudinal frequency. It is observed that for response function more than a critical value, the motor exhibits exponential growth rate of pressure oscillations.

  4. Modelling and Simulation of the Dynamics of the Antigen-Specific T Cell Response Using Variable Structure Control Theory.

    Science.gov (United States)

    Anelone, Anet J N; Spurgeon, Sarah K

    2016-01-01

    Experimental and mathematical studies in immunology have revealed that the dynamics of the programmed T cell response to vigorous infection can be conveniently modelled using a sigmoidal or a discontinuous immune response function. This paper hypothesizes strong synergies between this existing work and the dynamical behaviour of engineering systems with a variable structure control (VSC) law. These findings motivate the interpretation of the immune system as a variable structure control system. It is shown that dynamical properties as well as conditions to analytically assess the transition from health to disease can be developed for the specific T cell response from the theory of variable structure control. In particular, it is shown that the robustness properties of the specific T cell response as observed in experiments can be explained analytically using a VSC perspective. Further, the predictive capacity of the VSC framework to determine the T cell help required to overcome chronic Lymphocytic Choriomeningitis Virus (LCMV) infection is demonstrated. The findings demonstrate that studying the immune system using variable structure control theory provides a new framework for evaluating immunological dynamics and experimental observations. A modelling and simulation tool results with predictive capacity to determine how to modify the immune response to achieve healthy outcomes which may have application in drug development and vaccine design.

  5. Simulation of cell-substrate traction force dynamics in response to soluble factors.

    Science.gov (United States)

    Liu, Tao

    2017-08-01

    Finite element (FE) simulations of contractile responses of vascular muscular thin films (vMTFs) and endothelial cells resting on an array of microposts under stimulation of soluble factors were conducted in comparison with experimental measurements reported in the literature. Two types of constitutive models were employed in the simulations, i.e. smooth muscle cell type and non-smooth muscle cell type. The time histories of the effects of soluble factors were obtained via calibration against experimental measurements of contractile responses of tissues or cells. The numerical results for vMTFs with micropatterned tissues suggest that the radius of curvature of vMTFs under stimulation of soluble factors is sensitive to width of the micropatterned tissue, i.e. the radius of curvature increases as the tissue width decreases. However, as the tissue response is essentially isometric, the time history of the maximum principal stress of the micropatterned tissues is not sensitive to tissue width. Good agreement has been achieved for predictions of the vasoconstrictor endothelin-1-induced contraction stress between the FE numerical simulation and the experiment-based approach of Alford (Integr Biol 3:1063-1070, 2011) for the vMTFs with 40, 60, 80 and 100 [Formula: see text] width patterns. This may suggest the contraction stress is weakly sensitive to the tissue width for these patterns. However, for 20 [Formula: see text] width tissue patterning, the numerical simulation result for contraction stress is less than the average value of experimental measurements, which may suggest the thinner and more elongated spindle-like cells within the 20 [Formula: see text] width tissue patterning have higher contractile output. The constitutive model for non-smooth muscle cells was used to simulate the contractile response of the endothelial cells. The substrate was treated as an effective continuum. For agonists such as lysophosphatidic acid and vascular endothelial growth factor

  6. Response of a single grafted polyethylene chain to simple shear flow: A Brownian dynamics simulation study

    Science.gov (United States)

    Haliloglu, Turkan; Bahar, Ivet; Erman, Burak

    1996-08-01

    The behavior of a single polyethylene chain grafted to an impenetrable surface, under shear flow, is investigated using Brownian dynamics simulations. Both short-range conformational energies and excluded volume effects are included in the model. Simulations are performed in good and poor solvent conditions in order to explore the effect of solvent quality. The shear flow is represented by the superposition of a force profile increasing linearly with the distance from the surface. Distribution of rotational angles, chain dimensions, components of the radius of gyration, segment density distribution, average layer thickness, and average orientation of bond vectors with respect to flow direction are determined and compared with other studies. Above a certain value of the shear rate, a significant increase in chain dimensions is observed for both good and poor solvents, the transition from coiled to stretched state being sharper in poor solvent. In good solvent, chain dimensions along the two perpendicular directions to the flow direction diminish with increasing shear rate. On the other hand, in poor solvent, there is an overall expansion in chain dimensions in all directions at low shear rates, which is subsequently followed by the orientation and alignment of the chain along the direction of flow. The experimentally observed increase in chain dimensions normal to the flow field at low shear rates is evidenced for the first time by simulations.

  7. Dynamical amplification of the stratospheric solar response simulated with the Chemistry-Climate Model LMDz-Reprobus

    Science.gov (United States)

    Marchand, M.; Keckhut, P.; Lefebvre, S.; Claud, C.; Cugnet, D.; Hauchecorne, A.; Lefèvre, F.; Lefebvre, M.-P.; Jumelet, J.; Lott, F.; Hourdin, F.; Thuillier, G.; Poulain, V.; Bossay, S.; Lemennais, P.; David, C.; Bekki, S.

    2012-02-01

    The impact of the 11-year solar cycle on the stratosphere and, in particular, on the polar regions is investigated using simulations from the Chemistry Climate Model (CCM) LMDz-Reprobus. The annual solar signal clearly shows a stratospheric response largely driven by radiative and photochemical processes, especially in the upper stratosphere. A month-by-months analysis suggests that dynamical feedbacks play an important role in driving the stratospheric response on short timescales. CCM outputs on a 10 days frequency indicate how, in the northern hemisphere, changes in solar heating in the winter polar stratosphere may influence the upward propagation of planetary waves and thus their deposition of momentum, ultimately modifying the strength of the mean stratospheric overtuning circulation at middle and high latitudes. The model results emphasize that the main temperature and wind responses in the northern hemisphere can be explained by a different timing in the occurrence of Sudden Stratospheric Warmings (SSWs) that are caused by small changes in planetary wave propagation depending on solar conditions. The differences between simulations forced by different solar conditions indicate successive positive and negative responses during the course of the winter. The solar minimum simulation generally indicates a slightly stronger polar vortex early in the winter while the solar maximum simulation experiences more early SSWs with a stronger wave-mean flow interaction and reduced zonal wind at mid-latitudes in the upper stratosphere. The opposite response is observed during mid-winter, in February, with more SSWs simulated for solar minimum conditions while solar maximum conditions are associated with a damped planetary wave activity and a reinforced vortex after the initial stratospheric warming period. In late winter, the response is again reversed, as noticed in the temperature differences, with major SSW mostly observed in the solar maximum simulation and less

  8. Molecular dynamics simulation of phosphorylation-induced conformational transitions in the mycobacterium tuberculosis response regulator PrrA

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Guo [Los Alamos National Laboratory; Mcmahon, Benjamin H [Los Alamos National Laboratory; Tung, Chang - Shung [Los Alamos National Laboratory

    2008-01-01

    Phosphorylation-activated modulation of response regulators (RR) is predominantly used by bacteria as a strategy in regulating their two-component signaling (TCS) systems, the underlying molecular mechanisms are however far from fully understood. In this work we have conducted a molecular dynamics (MD) simulation of the phosphorylation-induced conformational transitions of RRs with the Mycobacterium Tuberculosis PrrA as a particular example. Starting from the full-length inactive structure of PrrA we introduced a local disturbance by phosphorylating the conserved aspartic acid residue, Asp-58, in the regulatory domain. A Go-model-type algorithm packaged with AMBER force fields was then applied to simulate the dynamics upon phosphorylation. The MD simulation shows that the phosphorylation of Asp-58 facilitates PrrA, whose inactive state has a compact conformation with a closed interdomain interface, to open up with its interdomain separation being increased by an average of about 1.5 {angstrom} for a simulation of 20 ns. The trans-activation loop, which is completely buried within the interdomain interface in the inactive PrrA, is found to become more exposed with the phosphorylated structure as well. These results provide more structural details of how the phosphorylation of a local aspartate activates PrrA to undergo a global conformational rearrangement toward its extended active state. This work also indicates that MD simulations can serve as a fast tool to unravel the regulation mechanisms of all RRs, which is especially valuable when the structures of full-length active RRs are currently unavailable.

  9. Molecular dynamics simulations

    OpenAIRE

    Tarmyshov, Konstantin B.

    2007-01-01

    Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...

  10. Interactive Dynamic-System Simulation

    CERN Document Server

    Korn, Granino A

    2010-01-01

    Showing you how to use personal computers for modeling and simulation, Interactive Dynamic-System Simulation, Second Edition provides a practical tutorial on interactive dynamic-system modeling and simulation. It discusses how to effectively simulate dynamical systems, such as aerospace vehicles, power plants, chemical processes, control systems, and physiological systems. Written by a pioneer in simulation, the book introduces dynamic-system models and explains how software for solving differential equations works. After demonstrating real simulation programs with simple examples, the author

  11. Dynamical Simulation of Probabilities

    Science.gov (United States)

    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.

  12. Coarse-graining scheme for simulating uniaxial stress-strain response of glassy polymers through molecular dynamics.

    Science.gov (United States)

    Majumder, Manoj K; S, Ramkumar; Mahajan, Dhiraj K; Basu, Sumit

    2010-01-01

    Simulation of the deformation of polymers below their glass transition through molecular dynamics provides an useful route to correlate their molecular architecture to deformation behavior. However, present computational capabilities severely restrict the time and length scales that can be simulated when detailed models of these macromolecules are used. Coarse-graining techniques for macromolecular structures intend to make bigger and longer simulations possible by grouping atoms into superatoms and devising ways of determining reasonable force fields for the superatoms in a manner that retains essential macromolecular features relevant to the process under study but jettisons unnecessary details. In this work we systematically develop a coarse-graining scheme aimed at simulating uniaxial stress-strain behavior of polymers below their glass transition. The scheme involves a two step process of obtaining the coarse grained force field parameters above glass transition. This seems to be enough to obtain "faithful" stress-strain responses after quenching to below the glass transition temperature. We apply the scheme developed to a commercially important polymer polystyrene, derive its complete force field parameters and thus demonstrate the effectiveness of the technique.

  13. Computerized simulation of the dynamic response of a coal-fired power plant with pressurized fluidized bed

    Science.gov (United States)

    Plackmeyer, J.

    1982-07-01

    The simple way of desulfurizing, the efficient combustion of coal, and low carbon monoxide flue gas content of a fluidized bed combustion installation were studied. The dynamic response of a pressurized fluidized bed should also be studied before any construction is started. The physical-mathematical models of all single components were developed and combined in a total computer program. Starting point was the planned pilot plant with gas turbine engine. Various modifications of the purely air cooled plant as well as the extension to a combined cycle with additional steam turbine were considered. Operating cases were simulated: starting up, increasing from partial load to full load and vice versa, shut down and breakdowns. Results show that all operating cases could be brought under control as well as breakdowns. The constructive precautions and correct plant practice are described.

  14. IMF By effects on ground magnetometer response to increased solar wind dynamic pressure derived from global MHD simulations

    Science.gov (United States)

    Ozturk, Dogacan Su; Zou, Shasha; Slavin, James A.

    2017-05-01

    During sudden solar wind dynamic pressure enhancements, the magnetosphere undergoes rapid compression resulting in a reconfiguration of the global current systems, most notably the field-aligned currents (FACs). Ground-based magnetometers are traditionally used to study such compression events. However, factors affecting the polarity and magnitude of the ground-based magnetic perturbations are still not well understood. In particular, interplanetary magnetic field (IMF) By is known to create significant asymmetries in the FAC patterns. We use the University of Michigan Block Adaptive Tree Roe Upwind Scheme (BATS'R'US) magnetohydrodynamic code to investigate the effects of IMF By on the global variations of ground magnetic perturbations during solar wind dynamic pressure enhancements. Using virtual magnetometers in three idealized simulations with varying IMF By, we find asymmetries in the peak amplitude and magnetic local time of the ground magnetic perturbations during the preliminary impulse (PI) and the main impulse (MI) phases. These asymmetries are especially evident at high-latitude ground magnetometer responses where the peak amplitudes differ by 50 nT at different locations. We show that the FACs related with the PI are due to magnetopause deformation, and the FACs related with the MI are generated by vortical flows within the magnetosphere, consistent with other simulation results. The perturbation FACs due to pressure enhancements and their magnetospheric sources do not differ much under different IMF By polarities. However, the conductance profile affected by the superposition of the preexisting FACs and the perturbation FACs including their closure currents is responsible for the magnitude and location asymmetries in the ground magnetic perturbations.

  15. Recent Research and Applications of Numerical Simulation for Dynamic Response of Long-Span Bridges Subjected to Multiple Loads

    OpenAIRE

    Zhiwei Chen; Bo Chen

    2014-01-01

    Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach...

  16. COMPUTATIONAL TOOL FOR SIMULATION OF THE DYNAMIC RESPONSE OF VALVE TRAIN

    Directory of Open Access Journals (Sweden)

    Krešimir Osman

    2014-03-01

    Full Text Available This paper presents the development of the MOTORI 2004 computing tool that calculates the distance, speed and acceleration of a car engine valve train’s oscillating mass m, which is reduced to the valve axis. Distance diagrams, speed and accelerations are provided in dependence on the camshaft twist angle at a constant rotational speed in several consecutive revolutions. The computing tool implements a mathematical description and numerical solution for the motion of mass m of a valve gear dynamic model. Valve lift h is given numerically using a series of equidistant points in the period of one camshaft revolution. The variabilities of camshaft rotation and spring thread vibration as a result of cam lift harmonic excitation. The computing solutions were tested at valve opening points and in imaginary extreme operating conditions (soft/hard spring, low/high damping, low/high rotational speed and increased clearance.

  17. Data Systems Dynamic Simulator

    Science.gov (United States)

    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.

  18. Numerical Simulation of Dynamic Response of A Net Cage for Flatfish in Waves

    Institute of Scientific and Technical Information of China (English)

    桂福坤; 赵云鹏; 许条建; 关长涛

    2014-01-01

    A numerical model of flatfish cage is built based on the lumped mass method and the principle of rigid body kinematics. To validate the numerical model, a series of physical model tests are conducted in the wave flume. The numerical results correspond well with the data sets from physical model test. The effect of weight of bottom frame, height of fish net and net shape on motion responses of fish cage and tension force on mooring lines is then analyzed. The results indicate that the vertical displacements of float collar and bottom frame decrease with the increase in the weight of bottom frame; the maximum tension force on mooring lines increases with the increasing weight of bottom frame. The inclination angles of float collar and bottom frame decrease with the increasing net height; the maximum tension force increases obviously with the increase of net height.

  19. Numerical simulation of dynamic response of a net cage for flatfish in waves

    Science.gov (United States)

    Gui, Fu-kun; Zhao, Yun-peng; Xu, Tiao-jian; Guan, Chang-tao

    2014-03-01

    A numerical model of flatfish cage is built based on the lumped mass method and the principle of rigid body kinematics. To validate the numerical model, a series of physical model tests are conducted in the wave flume. The numerical results correspond well with the data sets from physical model test. The effect of weight of bottom frame, height of fish net and net shape on motion responses of fish cage and tension force on mooring lines is then analyzed. The results indicate that the vertical displacements of float collar and bottom frame decrease with the increase in the weight of bottom frame; the maximum tension force on mooring lines increases with the increasing weight of bottom frame. The inclination angles of float collar and bottom frame decrease with the increasing net height; the maximum tension force increases obviously with the increase of net height.

  20. Simulation of spatially coupling dynamic response of train-track time-variant system

    Institute of Scientific and Technical Information of China (English)

    向俊; 李德建; 曾庆元

    2003-01-01

    There exist three problems in the calculation of lateral vibration of the train-track time-variant system athome and abroad and the method to solve them is presented. Spatially coupling vibration analysis model of train-track time-variant system is put forward. Each vehicle is modeled as a multi-body system with 26 degrees of freedomand the action of coupler is also considered. The track structure is modeled as an assembly of track elements with 30degrees of freedom, then the spatially coupling vibration matrix equation of the train-track time-variant system is es-tablished on the basis of the principle of total potential energy with stationary value and the "set-in-right-position"rule. The track vertical geometric irregularity is considered as the excitation source of the vertical vibration of thesystem, and the hunting wave of car bogie frame is taken as the excitation source of lateral vibration of the system.The spatially coupling vibration matrix equation of the system is solved by Wilson-θ direct integration method. Theapproximation of the calculated results to the spot test results demonstrates the feasibility and effectiveness of thepresented analysis method. Finally, some other vibration responses of the system are also obtained.

  1. Application of bi-Helmholtz nonlocal elasticity and molecular simulations to the dynamical response of carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Koutsoumaris, C. Chr.; Tsamasphyros, G. J. [School of Applied Mathematical and Physical Sciences National Technical University of Athens (NTUA) 5 Iroon Polytechniou Str., Zografou, Zografou Campus, Athens, GR-157 73 (Greece); Vogiatzis, G. G.; Theodorou, D. N. [School of Chemical Engineering National Technical University of Athens (NTUA) 5 Iroon Polytechniou Str., Zografou, Zografou Campus, Athens, GR-157 73 (Greece)

    2015-12-31

    The nonlocal theory of elasticity is employed for the study of the free vibrations of carbon nanotubes (CNT). For the first time, a bi-Helmholtz operator has been used instead of the standard Helmholtz operator in a nonlocal beam model. Alongside the continuum formulation and its numerical solution, atomistic Molecular Dynamics (MD) simulations have been conducted in order to directly evaluate the eigenfrequencies of vibrating CNTs with a minimum of adjustable parameters. Our results show that the bi-Helmholtz operator is the most appropriate one to fit MD simulation results. However, the estimation of vibration eigenfrequencies from molecular simulations still remains an open (albeit well-posed) problem.

  2. Modeled response of the West Nile virus vector Culex quinquefasciatus to changing climate using the dynamic mosquito simulation model

    Science.gov (United States)

    Morin, Cory W.; Comrie, Andrew C.

    2010-09-01

    Climate can strongly influence the population dynamics of disease vectors and is consequently a key component of disease ecology. Future climate change and variability may alter the location and seasonality of many disease vectors, possibly increasing the risk of disease transmission to humans. The mosquito species Culex quinquefasciatus is a concern across the southern United States because of its role as a West Nile virus vector and its affinity for urban environments. Using established relationships between atmospheric variables (temperature and precipitation) and mosquito development, we have created the Dynamic Mosquito Simulation Model (DyMSiM) to simulate Cx. quinquefasciatus population dynamics. The model is driven with climate data and validated against mosquito count data from Pasco County, Florida and Coachella Valley, California. Using 1-week and 2-week filters, mosquito trap data are reproduced well by the model ( P climate projection data generated by the National Center for Atmospheric Research CCSM3 general circulation model, we applied temperature and precipitation offsets to the climate data at each location to evaluate mosquito population sensitivity to possible future climate conditions. We found that temperature and precipitation shifts act interdependently to cause remarkable changes in modeled mosquito population dynamics. Impacts include a summer population decline from drying in California due to loss of immature mosquito habitats, and in Florida a decrease in late-season mosquito populations due to drier late summer conditions.

  3. Assessing the detail needed to capture rainfall-runoff dynamics with physics-based hydrologic response simulation

    Science.gov (United States)

    Mirus, B.B.; Ebel, B.A.; Heppner, C.S.; Loague, K.

    2011-01-01

    Concept development simulation with distributed, physics-based models provides a quantitative approach for investigating runoff generation processes across environmental conditions. Disparities within data sets employed to design and parameterize boundary value problems used in heuristic simulation inevitably introduce various levels of bias. The objective was to evaluate the impact of boundary value problem complexity on process representation for different runoff generation mechanisms. The comprehensive physics-based hydrologic response model InHM has been employed to generate base case simulations for four well-characterized catchments. The C3 and CB catchments are located within steep, forested environments dominated by subsurface stormflow; the TW and R5 catchments are located in gently sloping rangeland environments dominated by Dunne and Horton overland flows. Observational details are well captured within all four of the base case simulations, but the characterization of soil depth, permeability, rainfall intensity, and evapotranspiration differs for each. These differences are investigated through the conversion of each base case into a reduced case scenario, all sharing the same level of complexity. Evaluation of how individual boundary value problem characteristics impact simulated runoff generation processes is facilitated by quantitative analysis of integrated and distributed responses at high spatial and temporal resolution. Generally, the base case reduction causes moderate changes in discharge and runoff patterns, with the dominant process remaining unchanged. Moderate differences between the base and reduced cases highlight the importance of detailed field observations for parameterizing and evaluating physics-based models. Overall, similarities between the base and reduced cases indicate that the simpler boundary value problems may be useful for concept development simulation to investigate fundamental controls on the spectrum of runoff generation

  4. Numerical Simulation of the Dynamic FSI Response and Stability of a Flapping Foil in a Dense Fluid

    Science.gov (United States)

    Chae, Eun Jung; Akcabay, Deniz Tolga; Young, Yin Lu

    2012-11-01

    To advance the understanding of fish locomotion, improve the design biological devices or marine propulsions or turbines, or to explore innovative ocean energy harvesting ideas, it is important to be able accurately predict the dynamic fluid structure interaction (FSI) response and stability of flexible structures in a dense fluid. The objectives of this research are to (1) present an efficient and stable algorithm for numerical modeling of the dynamic FSI response and stability of a flapping foil in dense fluid, and (2) investigate the influence of fluid-to-solid density ratio on the FSI response and stability of a flapping foil. The numerical model involves coupling an unsteady RANS solver with a 2DOF structural model using a new hybrid coupling approach. The results show that the new hybrid coupling approach converge much faster than traditional loosely and tightly coupled approaches, and is able to avoid numerical instability issues due to virtual added mass effects for light, flexible structures in incompressible flow. The influence of density ratio on the FSI response, divergence and flutter speeds are presented, along with comparisons between viscous and inviscid FSI computations.

  5. Simulating the Response of a Composite Honeycomb Energy Absorber. Part 1; Dynamic Crushing of Components and Multi-Terrain Impacts

    Science.gov (United States)

    Jackson, Karen E.; Fasanella, Edwin L.; Polanco, Michael A.

    2012-01-01

    This paper describes the experimental and analytical evaluation of an externally deployable composite honeycomb structure that is designed to attenuate impact energy during helicopter crashes. The concept, designated the Deployable Energy Absorber (DEA), utilizes an expandable Kevlar (Registered Trademark) honeycomb to dissipate kinetic energy through crushing. The DEA incorporates a unique flexible hinge design that allows the honeycomb to be packaged and stowed until needed for deployment. Experimental evaluation of the DEA included dynamic crush tests of multi-cell components and vertical drop tests of a composite fuselage section, retrofitted with DEA blocks, onto multi-terrain. Finite element models of the test articles were developed and simulations were performed using the transient dynamic code, LSDYNA (Registered Trademark). In each simulation, the DEA was represented using shell elements assigned two different material properties: Mat 24, an isotropic piecewise linear plasticity model, and Mat 58, a continuum damage mechanics model used to represent laminated composite fabrics. DEA model development and test-analysis comparisons are presented.

  6. Molecular dynamics simulation of diffusivity

    Institute of Scientific and Technical Information of China (English)

    Juanfang LIU; Danling ZENG; Qin LI; Hong GAO

    2008-01-01

    Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.

  7. Spatially-Explicit Simulation Modeling of Ecological Response to Climate Change: Methodological Considerations in Predicting Shifting Population Dynamics of Infectious Disease Vectors.

    Science.gov (United States)

    Dhingra, Radhika; Jimenez, Violeta; Chang, Howard H; Gambhir, Manoj; Fu, Joshua S; Liu, Yang; Remais, Justin V

    2013-09-01

    Poikilothermic disease vectors can respond to altered climates through spatial changes in both population size and phenology. Quantitative descriptors to characterize, analyze and visualize these dynamic responses are lacking, particularly across large spatial domains. In order to demonstrate the value of a spatially explicit, dynamic modeling approach, we assessed spatial changes in the population dynamics of Ixodes scapularis, the Lyme disease vector, using a temperature-forced population model simulated across a grid of 4 × 4 km cells covering the eastern United States, using both modeled (Weather Research and Forecasting (WRF) 3.2.1) baseline/current (2001-2004) and projected (Representative Concentration Pathway (RCP) 4.5 and RCP 8.5; 2057-2059) climate data. Ten dynamic population features (DPFs) were derived from simulated populations and analyzed spatially to characterize the regional population response to current and future climate across the domain. Each DPF under the current climate was assessed for its ability to discriminate observed Lyme disease risk and known vector presence/absence, using data from the US Centers for Disease Control and Prevention. Peak vector population and month of peak vector population were the DPFs that performed best as predictors of current Lyme disease risk. When examined under baseline and projected climate scenarios, the spatial and temporal distributions of DPFs shift and the seasonal cycle of key questing life stages is compressed under some scenarios. Our results demonstrate the utility of spatial characterization, analysis and visualization of dynamic population responses-including altered phenology-of disease vectors to altered climate.

  8. Uncertainty and Sensitivity of Neutron Kinetic Parameters in the Dynamic Response of a PWR Rod Ejection Accident Coupled Simulation

    Directory of Open Access Journals (Sweden)

    C. Mesado

    2012-01-01

    Full Text Available In nuclear safety analysis, it is very important to be able to simulate the different transients that can occur in a nuclear power plant with a very high accuracy. Although the best estimate codes can simulate the transients and provide realistic system responses, the use of nonexact models, together with assumptions and estimations, is a source of uncertainties which must be properly evaluated. This paper describes a Rod Ejection Accident (REA simulated using the coupled code RELAP5/PARCSv2.7 with a perturbation on the cross-sectional sets in order to determine the uncertainties in the macroscopic neutronic information. The procedure to perform the uncertainty and sensitivity (U&S analysis is a sampling-based method which is easy to implement and allows different procedures for the sensitivity analyses despite its high computational time. DAKOTA-Jaguar software package is the selected toolkit for the U&S analysis presented in this paper. The size of the sampling is determined by applying the Wilks’ formula for double tolerance limits with a 95% of uncertainty and with 95% of statistical confidence for the output variables. Each sample has a corresponding set of perturbations that will modify the cross-sectional sets used by PARCS. Finally, the intervals of tolerance of the output variables will be obtained by the use of nonparametric statistical methods.

  9. Spatially-Explicit Simulation Modeling of Ecological Response to Climate Change: Methodological Considerations in Predicting Shifting Population Dynamics of Infectious Disease Vectors

    Directory of Open Access Journals (Sweden)

    Justin V. Remais

    2013-07-01

    Full Text Available Poikilothermic disease vectors can respond to altered climates through spatial changes in both population size and phenology. Quantitative descriptors to characterize, analyze and visualize these dynamic responses are lacking, particularly across large spatial domains. In order to demonstrate the value of a spatially explicit, dynamic modeling approach, we assessed spatial changes in the population dynamics of Ixodes scapularis, the Lyme disease vector, using a temperature-forced population model simulated across a grid of 4 × 4 km cells covering the eastern United States, using both modeled (Weather Research and Forecasting (WRF 3.2.1 baseline/current (2001–2004 and projected (Representative Concentration Pathway (RCP 4.5 and RCP 8.5; 2057–2059 climate data. Ten dynamic population features (DPFs were derived from simulated populations and analyzed spatially to characterize the regional population response to current and future climate across the domain. Each DPF under the current climate was assessed for its ability to discriminate observed Lyme disease risk and known vector presence/absence, using data from the US Centers for Disease Control and Prevention. Peak vector population and month of peak vector population were the DPFs that performed best as predictors of current Lyme disease risk. When examined under baseline and projected climate scenarios, the spatial and temporal distributions of DPFs shift and the seasonal cycle of key questing life stages is compressed under some scenarios. Our results demonstrate the utility of spatial characterization, analysis and visualization of dynamic population responses—including altered phenology—of disease vectors to altered climate.

  10. Simulating growth dynamics and radiation response of avascular tumour spheroids-model validation in the case of an EMT6/Ro multicellular spheroid.

    Science.gov (United States)

    Zacharaki, Evangelia I; Stamatakos, Georgios S; Nikita, Konstantina S; Uzunoglu, Nikolaos K

    2004-12-01

    The goal of this paper is to provide both the basic scientist and the clinician with an advanced computational tool for performing in silico experiments aiming at supporting the process of biological optimisation of radiation therapy. Improved understanding and description of malignant tumour dynamics is an additional intermediate objective. To this end an advanced three-dimensional (3D) Monte-Carlo simulation model of both the avascular development of multicellular tumour spheroids and their response to radiation therapy is presented. The model is based upon a number of fundamental biological principles such as the transition between the cell cycle phases, the diffusion of oxygen and nutrients and the cell survival probabilities following irradiation. Efficient algorithms describing tumour expansion and shrinkage are proposed and applied. The output of the biosimulation model is introduced into the (3D) visualisation package AVS-Express, which performs the visualisation of both the external surface and the internal structure of the dynamically evolving tumour based on volume or surface rendering techniques. Both the numerical stability and the statistical behaviour of the simulation model have been studied and evaluated for the case of EMT6/Ro spheroids. Predicted histological structure and tumour growth rates have been shown to be in agreement with published experimental data. Furthermore, the underlying structure of the tumour spheroid as well as its response to irradiation satisfactorily agrees with laboratory experience.

  11. Dynamical response of the "GGG" rotor to test the Equivalence Principle: theory, simulation and experiment. Part I: the normal modes

    CERN Document Server

    Comandi, G L; Chiofalo, M L; Nobili, A M; Polacco, E; Toncelli, R

    2006-01-01

    Recent theoretical work suggests that violation of the Equivalence Principle might be revealed in a measurement of the fractional differential acceleration $\\eta$ between two test bodies -of different composition, falling in the gravitational field of a source mass- if the measurement is made to the level of $\\eta\\simeq 10^{-13}$ or better. This being within the reach of ground based experiments, gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in low orbit around the Earth is likely to provide a much better accuracy. We report on the progress made with the "Galileo Galilei on the Ground" (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following paper (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into superc...

  12. Dynamics modeling and simulation of flexible airships

    Science.gov (United States)

    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

  13. Vehicle dynamics modeling and simulation

    CERN Document Server

    Schramm, Dieter; Bardini, Roberto

    2014-01-01

    The authors examine in detail the fundamentals and mathematical descriptions of the dynamics of automobiles. In this context different levels of complexity will be presented, starting with basic single-track models up to complex three-dimensional multi-body models. A particular focus is on the process of establishing mathematical models on the basis of real cars and the validation of simulation results. The methods presented are explained in detail by means of selected application scenarios.

  14. Molecular dynamics simulation of pyridine

    Science.gov (United States)

    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.

  15. Dynamic simulation of flywheel-type fuses

    OpenAIRE

    Editorial Office

    1996-01-01

    Rounds of ammunition are normally armed with a fuse. In this study, a fuse is developed which uses a flywheel-type mechanism controlled by time or distance. Due to its simplicity of operation and construction, the concept is expected to have high reliabil­ity. The dynamic response of all the components of this flywheel-type fuse is mathematically modelled. Simulation software was developed which connects the mathematical models of the various components. With the definition of boundary value...

  16. Dynamic Simulation of the Harvester Boom Cylinder

    Directory of Open Access Journals (Sweden)

    Rongfeng Shen

    2017-04-01

    Full Text Available Based on the complete dynamic calculation method, the layout, force, and strength of harvester boom cylinders were designed and calculated. Closed simulations for the determination of the dynamic responses of the harvester boom during luffing motion considering the cylinder drive system and luffing angle position control have been realized. Using the ADAMS mechanical system dynamics analysis software, six different arm poses were selected and simulated based on the cylinder as the analysis object. A flexible model of the harvester boom luffing motion has been established. The movement of the oil cylinder under different conditions were analyzed, and the main operation dimensions of the harvester boom and the force condition of the oil cylinder were obtained. The calculation results show that the dynamic responses of the boom are more sensitive to the luffing acceleration, in comparison with the luffing velocity. It is seen that this method is very effective and convenient for boom luffing simulation. It is also reasonable to see that the extension of the distance of the bottom of the boom is shortened by adjusting the initial state of the boom in the working process, which can also effectively reduce the workload of the boom—thus improving the mechanical efficiency.

  17. Molecular dynamics simulation of benzene

    Science.gov (United States)

    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.

  18. Dynamic simulations of tissue welding

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-02-01

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

  19. Development of response models for the Earth Radiation Budget Experiment (ERBE) sensors. Part 1: Dynamic models and computer simulations for the ERBE nonscanner, scanner and solar monitor sensors

    Science.gov (United States)

    Halyo, Nesim; Choi, Sang H.; Chrisman, Dan A., Jr.; Samms, Richard W.

    1987-01-01

    Dynamic models and computer simulations were developed for the radiometric sensors utilized in the Earth Radiation Budget Experiment (ERBE). The models were developed to understand performance, improve measurement accuracy by updating model parameters and provide the constants needed for the count conversion algorithms. Model simulations were compared with the sensor's actual responses demonstrated in the ground and inflight calibrations. The models consider thermal and radiative exchange effects, surface specularity, spectral dependence of a filter, radiative interactions among an enclosure's nodes, partial specular and diffuse enclosure surface characteristics and steady-state and transient sensor responses. Relatively few sensor nodes were chosen for the models since there is an accuracy tradeoff between increasing the number of nodes and approximating parameters such as the sensor's size, material properties, geometry, and enclosure surface characteristics. Given that the temperature gradients within a node and between nodes are small enough, approximating with only a few nodes does not jeopardize the accuracy required to perform the parameter estimates and error analyses.

  20. Dynamic simulation of flywheel-type fuses

    Directory of Open Access Journals (Sweden)

    Editorial Office

    1996-07-01

    Full Text Available Rounds of ammunition are normally armed with a fuse. In this study, a fuse is developed which uses a flywheel-type mechanism controlled by time or distance. Due to its simplicity of operation and construction, the concept is expected to have high reliabil­ity. The dynamic response of all the components of this flywheel-type fuse is mathematically modelled. Simulation software was developed which connects the mathematical models of the various components. With the definition of boundary values, the response of the projectile, flywheel and other components can be determined continuously for firing and in-flight conditions.

  1. Using EnergyPlus to Simulate the Dynamic Response of a Residential Building to Advanced Cooling Strategies: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Booten, C.; Tabares-Velasco, P. C.

    2012-08-01

    This study demonstrates the ability of EnergyPlus to accurately model complex cooling strategies in a real home with a goal of shifting energy use off peak and realizing energy savings. The house was retrofitted through the Sacramento Municipal Utility District's (SMUD) deep energy retrofit demonstration program; field tests were operated by the National Renewable Energy Laboratory (NREL). The experimental data were collected as part of a larger study and are used here to validate simulation predictions.

  2. Human motion simulation predictive dynamics

    CERN Document Server

    Abdel-Malek, Karim

    2013-01-01

    Simulate realistic human motion in a virtual world with an optimization-based approach to motion prediction. With this approach, motion is governed by human performance measures, such as speed and energy, which act as objective functions to be optimized. Constraints on joint torques and angles are imposed quite easily. Predicting motion in this way allows one to use avatars to study how and why humans move the way they do, given specific scenarios. It also enables avatars to react to infinitely many scenarios with substantial autonomy. With this approach it is possible to predict dynamic motion without having to integrate equations of motion -- rather than solving equations of motion, this approach solves for a continuous time-dependent curve characterizing joint variables (also called joint profiles) for every degree of freedom. Introduces rigorous mathematical methods for digital human modelling and simulation Focuses on understanding and representing spatial relationships (3D) of biomechanics Develops an i...

  3. Development Of Dynamic Probabilistic Safety Assessment: The Accident Dynamic Simulator (ADS) Tool

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Y.H.; Mosleh, A.; Dang, V.N

    2003-03-01

    The development of a dynamic methodology for Probabilistic Safety Assessment (PSA) addresses the complex interactions between the behaviour of technical systems and personnel response in the evolution of accident scenarios. This paper introduces the discrete dynamic event tree, a framework for dynamic PSA, and its implementation in the Accident Dynamic Simulator (ADS) tool. Dynamic event tree tools generate and quantify accident scenarios through coupled simulation models of the plant physical processes, its automatic systems, the equipment reliability, and the human response. The current research on the framework, the ADS tool, and on Human Reliability Analysis issues within dynamic PSA, is discussed. (author)

  4. Grand canonical Molecular Dynamics Simulations

    CERN Document Server

    Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K

    2011-01-01

    For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.

  5. Dynamic simulator for PEFC propulsion plant

    Energy Technology Data Exchange (ETDEWEB)

    Hiraide, Masataka; Kaneda, Eiichi; Sato, Takao [Mitsui Engineering & Shipbuilding Co., Ltd., Tokyo (Japan)] [and others

    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.

  6. Humanoid robot simulator: a realistic dynamics approach

    OpenAIRE

    Lima, José; Gonçalves, José; Costa, Paulo; Moreira, António

    2008-01-01

    This paper describes a humanoid robot simulator with realistic dynamics. As simulation is a powerful tool for speeding up the control software development, the suggested accurate simulator allows to accomplish this goal. The simulator, based on the Open Dynamics Engine and GLScene graphics library, provides instant visual feedback and allows the user to test any control strategy without damaging the real robot in the early stages of the development. The proposed simulator also captures some c...

  7. Computational fluid dynamics simulation of the upper airway response to large incisor retraction in adult class I bimaxillary protrusion patients

    Science.gov (United States)

    Zheng, Zhe; Liu, Hong; Xu, Qi; Wu, Wei; Du, Liling; Chen, Hong; Zhang, Yiwen; Liu, Dongxu

    2017-04-01

    The changes of the upper airway after large retraction of the incisors in adult class I bimaxillary protrusion patients were assessed mainly focused on the anatomic variation and ignored the functional changes. This study aimed to investigate the changes of the upper airway in adult class I bimaxillary protrusion patients after extraction treatment using the functional images based on computational fluid dynamics (CFD). CFD was implemented after 3D reconstruction based on the CBCT of 30 patients who have completed extraction treatment. After treatment, pressure drop in the minimum area, oropharynx, and hypopharynx increased significantly. The minimum pressure and the maximum velocity mainly located in the hypopharynx in pre-treatment while they mostly occured in the oropharynx after treatment. Statistically significant correlation between pressure drop and anatomic parameters, pressure drop and treatment outcomes was found. No statistical significance changes in pressure drop and volume of nasopharynx was found. This study suggested that the risk of pharyngeal collapsing become higher after extraction treatment with maximum anchorage in bimaxillary protrusion adult patients. Those adverse changes should be taken into consideration especially for high-risk patients to avoid undesired weakening of the respiratory function in clinical treatment.

  8. Numerical simulation of dynamic response of explosive vessel in aqueous medium%水介质爆炸容器动力响应的数值模拟

    Institute of Scientific and Technical Information of China (English)

    钟冬望; 黄小武; 殷秀红; 李琳娜; 司剑峰

    2015-01-01

    采用有限元软件ANSYS/LS‐DYNA模拟水介质爆炸容器在不同 TNT 当量炸药于容器中心处爆炸时的动态响应,并与实测数据进行比较。结果表明,容器筒体爆心环面处的应变幅值在第一个周期内就达到最大值,并且其值大于筒体上其他点的最大应变;在容器椭圆封头处出现应变增长现象,封头顶端的最大主应变峰值大于筒体爆心环面处的应变峰值,且封头顶端的加速度峰值也明显大于爆心环面处的加速度峰值,仿真计算值与实测值吻合较好。在设计同类水介质爆炸容器时,应重点加强筒体爆心环面处和封头顶端。%When different TNT equivalent explosives blasted in the vessel center ,the dynamic response of explosive vessel in aqueous medium was simulated by finite element software ANSYS/LS‐DYNA . The simulation values were compared with the measured data .The results show that the strain ampli‐tude at cylindrical shell around the explosive center rises to its maximum value during the first cycle , w hich is larger than those at other parts of cylindrical shell ;the strain grow th phenomenon is found at the elliptical cover ;the peak values of the largest principal strain and acceleration at the top of ellipti‐cal cover are larger than those at cylindrical shell around the explosive center ,respectively ,and the simulation values agree well with the measured data .When designing the same explosive vessels used in aqueous medium ,designers should pay more attention to the elliptical cover of the vessel and the center part of cylindrical shell .

  9. Response of Vegetation Dynamics to Projected Climate Change based on NDVI Simulations using Stepwise Cluster Analysis in the Three-River Headwaters Region of China

    Science.gov (United States)

    Zheng, Y.; Lv, E.; Huang, Y.

    2016-12-01

    Located in the hinterland of the Qinghai-Tibetan Plateau, the Three-River Headwaters region (THR) features unique eco-environmental conditions and fragile ecosystems, and is very vulnerable to climate change. To investigate the effects of climate change on the ecosystem, the Normalized Difference Vegetation Index (NDVI) was employed as an indicator to reflect the vegetation dynamics in response to climate change. This study proposed a model based on Stepwise-cluster analysis to predict the temporal and spatial distributions of NDVI values for five future years according to Global Circulation Models (GCMs) climate projections under the RCP4.5 scenario. The obtained spatial results showed very good agreements between simulations and remote sensing observations of the NDVI value for both training and validation, and the developed model demonstrated its capability of predicting the monthly changes of NDVI through representing the relationships between it and various climatic factors, including remote sensed precipitation and temperature with no, 1 and 2-month lag period. The monthly average precipitation with one-month lag period was further found to be the most important climatic factor that drives the changes of NDVI in the THR. Compared with the values of NDVI in 2000 - 2013, the predicting results indicate the values of NDVI for the THR in growing season (May to October) will decrease by 15.74% in the next 100 years, suggesting that the THR is going to experience an environmental degradation. The results also show that precipitation is the primary driving factor relative to temperature, especially the one-month-lag precipitation. Findings from this study would help policy makers draw up effective water resource and eco-environmental management strategies for adapting to climate change in the THR.

  10. Dynamical response of the Galileo Galilei on the ground rotor to test the equivalence principle: Theory, simulation, and experiment. I. The normal modes

    Science.gov (United States)

    Comandi, G. L.; Chiofalo, M. L.; Toncelli, R.; Bramanti, D.; Polacco, E.; Nobili, A. M.

    2006-03-01

    Recent theoretical work suggests that violation of the equivalence principle might be revealed in a measurement of the fractional differential acceleration η between two test bodies—of different compositions, falling in the gravitational field of a source mass—if the measurement is made to the level of η ≃10-13 or better. This being within the reach of ground based experiments gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in a low orbit around the Earth is likely to provide a much better accuracy. We report on the progress made with the "Galileo Galilei on the ground" (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following articles (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into supercritical rotation—in particular, its normal modes (Part I) and rejection of common mode effects (Part II)—can be predicted by means of a simple but effective model that embodies all the relevant physics. Analytical solutions are obtained under special limits, which provide the theoretical understanding. A simulation environment is set up, obtaining a quantitative agreement with the available experimental data on the frequencies of the normal modes and on the whirling behavior. This is a needed and reliable tool for controlling and separating perturbative effects from the expected signal, as well as for planning the optimization of the apparatus.

  11. Sensitivity Analysis of Fire Dynamics Simulation

    DEFF Research Database (Denmark)

    Brohus, Henrik; Nielsen, Peter V.; Petersen, Arnkell J.

    2007-01-01

    equations require solution of the issues of combustion and gas radiation to mention a few. This paper performs a sensitivity analysis of a fire dynamics simulation on a benchmark case where measurement results are available for comparison. The analysis is performed using the method of Elementary Effects......In case of fire dynamics simulation requirements to reliable results are most often very high due to the severe consequences of erroneous results. At the same time it is a well known fact that fire dynamics simulation constitutes rather complex physical phenomena which apart from flow and energy...

  12. Simulations of coherent nonlinear optical response of molecular vibronic dimers

    CERN Document Server

    Perlík, Václav

    2016-01-01

    We have implemented vibronic dynamics for simulations of the third order coherent response of electronic dimers. In the present communication we provide the full and detailed description of the dynamical model, recently used for simulations of chlorophyll-carotenoid dyads, terylene dimers, or hypericin. We allow for explicit vibronic level structure, by including selected vibrational modes into a "system". Bath dynamics include the Landau-Teller vibrational relaxation, electronic dephasing, and nonlinear vibronic (to bath) coupling. Simulations combine effects of transport and dephasing between vibronic levels. Transport is described by master equation within secular approximation, phase is accumulated in cumulants and its calculation follows the transport pathways during waiting time period.

  13. Dynamic Simulation for Missile Erection System

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In order to study the dynamic characteristics of the missile erection system, it can be considered as a rigid-flexible coupling multi-body system. Firstly, the actual system is abstracted as an equal and simplified one and then the forces applied to it are analyzed. Secondly, the rigid-flexible coupling dynamic simulation for erection system is accomplished by use of the system simulation software, for example Pro/E, ADAMS, ANSYS, MATLAB/Simulink, etc. Finally, having the aid of simulation results, the kinetic and dynamic characteristics of the flexible bodies in erection system are analyzed.The simulation considering the erection system as a rigid-flexible coupling system can provide valuable results to the research of its kinetic, dynamic and vibrational characteristics.

  14. Dynamical response of vibrating ferromagnets

    CERN Document Server

    Gaganidze, E; Ziese, M

    2000-01-01

    The resonance frequency of vibrating ferromagnetic reeds in a homogeneous magnetic field can be substantially modified by intrinsic and extrinsic field-related contributions. Searching for the physical reasons of the field-induced resonance frequency change and to study the influence of the spin glass state on it, we have measured the low-temperature magnetoelastic behavior and the dynamical response of vibrating amorphous and polycrystalline ferromagnetic ribbons. We show that the magnetoelastic properties depend strongly on the direction of the applied magnetic field. The influence of the re-entrant spin glass transition on these properties is discussed. We present clear experimental evidence that for applied fields perpendicular to the main area of the samples the behavior of ferromagnetic reeds is rather independent of the material composition and magnetic state, exhibiting a large decrease of the resonance frequency. This effect can be very well explained with a model based on the dynamical response of t...

  15. Simulating protein dynamics: Novel methods and applications

    Science.gov (United States)

    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.

  16. Distributed Dynamic Condition Response Structures

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas; Mukkamala, Raghava Rao

    We present distributed dynamic condition response structures as a declarative process model inspired by the workflow language employed by our industrial partner and conservatively generalizing labelled event structures. The model adds to event structures the possibility to 1) finitely specify...... repeated, possibly infinite behavior, 2) finitely specify fine-grained acceptance conditions for (possibly infinite) runs based on the notion of responses and 3) distribute events via roles. We give a graphical notation inspired by related work by van der Aalst et al and formalize the execution semantics...

  17. Software life cycle dynamic simulation model: The organizational performance submodel

    Science.gov (United States)

    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.

  18. The Dynamic Responsiveness of Organizations

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    Organizational studies should address contemporary challenges of dealing effectively with the increasingly complex and dynamic business conditions. In this context we argue that structural features are linked to the corporate strategy process and affect the organization’s ability to respond...... to ongoing environmental changes. Sustainable performance arguably derives from integrative strategy-making where business opportunities are pursued as they emerge while being directed and coordinated through forward-looking analytics. This combination of decentralized responsiveness and central reasoning...

  19. Visualizing Structure and Dynamics of Disaccharide Simulations

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Simulating Flexible-Spacecraft Dynamics and Control

    Science.gov (United States)

    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.

  1. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

    Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

    1998-11-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  2. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    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.

  3. Object Oriented Modelling and Dynamical Simulation

    DEFF Research Database (Denmark)

    Wagner, Falko Jens; Poulsen, Mikael Zebbelin

    1998-01-01

    This report with appendix describes the work done in master project at DTU.The goal of the project was to develop a concept for simulation of dynamical systems based on object oriented methods.The result was a library of C++-classes, for use when both building componentbased models and when...... onduction simulation experiments....

  4. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    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.

  5. Multiscale Model Approach for Magnetization Dynamics Simulations

    CERN Document Server

    De Lucia, Andrea; Tretiakov, Oleg A; Kläui, Mathias

    2016-01-01

    Simulations of magnetization dynamics in a multiscale environment enable 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 f...

  6. Dynamic Metabolism in Immune Response

    Science.gov (United States)

    Al-Hommrani, Mazen; Chakraborty, Paramita; Chatterjee, Shilpak; Mehrotra, Shikhar

    2016-01-01

    Cell, the basic unit of life depends for its survival on nutrients and thereby energy to perform its physiological function. Cells of lymphoid and myeloid origin are key in evoking an immune response against “self” or “non-self” antigens. The thymus derived lymphoid cells called T cells are a heterogenous group with distinct phenotypic and molecular signatures that have been shown to respond against an infection (bacterial, viral, protozoan) or cancer. Recent studies have unearthed the key differences in energy metabolism between the various T cell subsets, natural killer cells, dendritic cells, macrophages and myeloid derived suppressor cells. While a number of groups are dwelling into the nuances of the metabolism and its role in immune response at various strata, this review focuses on dynamic state of metabolism that is operational within various cellular compartments that interact to mount an effective immune response to alleviate disease state.

  7. Numerical simulation of tulip flame dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. Numerical simulation of tulip flame dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Directory of Open Access Journals (Sweden)

    Ferenc Jordán

    Full Text Available 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

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

    Science.gov (United States)

    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

  11. Spin dynamics simulations at AGS

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Nested Dynamic Condition Response Graphs

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas; Mukkamala, Raghava Rao; Slaats, Tijs

    2012-01-01

    We present an extension of the recently introduced declarative process model Dynamic Condition Response Graphs ( DCR Graphs) to allow nested subgraphs and a new milestone relation between events. The extension was developed during a case study carried out jointly with our industrial partner...... Exformatics, a danish provider of case and workflow management systems. We formalize the semantics by giving first a map from Nested to (flat) DCR Graphs with milestones, and then extending the previously given mapping from DCR Graphs to Buchi-automata to include the milestone relation....

  13. The data system dynamic simulation /DSDS/

    Science.gov (United States)

    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.

  14. Multibody dynamic simulation of knee contact mechanics.

    Science.gov (United States)

    Bei, Yanhong; Fregly, Benjamin J

    2004-11-01

    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 multibody 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.

  15. Dynamical response of vibrating ferromagnets

    Science.gov (United States)

    Gaganidze, E.; Esquinazi, P.; Ziese, M.

    2000-02-01

    The resonance frequency of vibrating ferromagnetic reeds in a homogeneous magnetic field can be substantially modified by intrinsic and extrinsic field-related contributions. Searching for the physical reasons of the field-induced resonance frequency change and to study the influence of the spin glass state on it, we have measured the low-temperature magnetoelastic behavior and the dynamical response of vibrating amorphous and polycrystalline ferromagnetic ribbons. We show that the magnetoelastic properties depend strongly on the direction of the applied magnetic field. The influence of the re-entrant spin glass transition on these properties is discussed. We present clear experimental evidence that for applied fields perpendicular to the main area of the samples the behavior of ferromagnetic reeds is rather independent of the material composition and magnetic state, exhibiting a large decrease of the resonance frequency. This effect can be very well explained with a model based on the dynamical response of the reed and the magnetomechanical pole effect within a domain rotation model and is not related to magnetoelasticity.

  16. Dynamic Procedure for Filtered Gyrokinetic Simulations

    CERN Document Server

    Morel, Pierre; Albrecht-Marc, Michel; Carati, Daniele; Merz, Florian; Görler, Tobias; Jenko, Frank

    2011-01-01

    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 (DNS). Systematic comparisons are performed for different values of the temperature gradient and magnetic shear, parameters which are of prime importance in Ion Temperature Gradient (ITG) driven turbulence. Moreover, the degree of anisotropy of the problem, that can vary with parameters, can be adapted dynamically by the method that shows Gyrokinetic Large Eddy Simulation (GyroLES) to be a serious candidate to reduce numerical cost of gyrokinetic solvers.

  17. Induction generator models in dynamic simulation tools

    DEFF Research Database (Denmark)

    Knudsen, Hans; Akhmatov, Vladislav

    1999-01-01

    For AC network with large amount of induction generators (windmills) the paper demonstrates a significant discrepancy in the simulated voltage recovery after fault in weak networks when comparing dynamic and transient stability descriptions and the reasons of discrepancies are explained. It is fo......For AC network with large amount of induction generators (windmills) the paper demonstrates a significant discrepancy in the simulated voltage recovery after fault in weak networks when comparing dynamic and transient stability descriptions and the reasons of discrepancies are explained....... It is found to be possible to include a transient model in dynamic stability tools and, then, obtain correct results also in dynamic tools. The representation of the rotating system influences on the voltage recovery shape which is an important observation in case of windmills, where a heavy mill is connected...

  18. A Dynamical Simulation Facility for Hybrid Systems

    CERN Document Server

    Back, A; Myers, M; Back, Allen; Guckenheimer, John; Myers, Mark

    1993-01-01

    Abstract: This paper establishes a general framework for describing hybrid dynamical systems which is particularly suitable for numerical simulation. In this context, the data structures used to describe the sets and functions which comprise the dynamical system are crucial since they provide the link between a natural mathematical formulation of a problem and the correct application of standard numerical algorithms. We describe a partial implementation of the design methodology and use this simulation tool for a specific control problem in robotics as an illustration of the utility of the approach for practical applications.

  19. Dynamic Fracture Simulations of Explosively Loaded Cylinders

    Energy Technology Data Exchange (ETDEWEB)

    Arthur, Carly W. [Univ. of California, Davis, CA (United States). Dept. of Civil and Environmental Engineering; Goto, D. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    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.

  20. Towards Four-Flavour Dynamical Simulations

    CERN Document Server

    Herdoiza, Gregorio

    2010-01-01

    The inclusion of physical effects from sea quarks has been one of the main advances in lattice QCD simulations over the last few years. We report on recent studies with four flavours of dynamical quarks and address some of the potential issues arising in this new setup. First results for physical observables in the light, strange and charm sectors are presented together with the status of dedicated simulations to perform the non-perturbative renormalisation in mass-independent schemes.

  1. Towards four-flavour dynamical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Herdoiza, Gregorio [DESY, Zeuthen (Germany). John von Neumann-Institut fuer Computing NIC; Univ. Autonoma de Madrid (Spain). Dept. de Fisica Teorica e Inst. de Fiscia Teorica

    2011-03-15

    The inclusion of physical effects from sea quarks has been one of the main advances in lattice QCD simulations over the last few years. We report on recent studies with four flavours of dynamical quarks and address some of the potential issues arising in this new setup. First results for physical observables in the light, strange and charm sectors are presented together with the status of dedicated simulations to perform the non-perturbative renormalisation in mass-independent schemes. (orig.)

  2. Testing dynamic stabilisation in complex Langevin simulations

    CERN Document Server

    Attanasio, Felipe

    2016-01-01

    Complex Langevin methods have been successfully applied in theories that suffer from a sign problem such as QCD with a chemical potential. We present and illustrate a novel method (dynamic stabilisation) that ensures that Complex Langevin simulations stay close to the SU(3) manifold, which lead to correct and improved results in the framework of pure Yang-Mills simulations and QCD in the limit of heavy quarks.

  3. Quantum Simulation for Open-System Dynamics

    Science.gov (United States)

    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.

  4. Molecular dynamic simulations of ocular tablet dissolution.

    Science.gov (United States)

    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.

  5. Dynamical response near quantum critical points

    CERN Document Server

    Lucas, Andrew; Podolsky, Daniel; Witczak-Krempa, William

    2016-01-01

    We study high frequency response functions, notably the optical conductivity, in the vicinity of quantum critical points (QCPs) by allowing for both detuning from the critical coupling and finite temperature. We consider general dimensions and dynamical exponents. This leads to a unified understanding of sum rules. In systems with emergent Lorentz invariance, powerful methods from conformal field theory allow us to fix the high frequency response in terms of universal coefficients. We test our predictions analytically in the large-N O(N) model and using the gauge-gravity duality, and numerically via Quantum Monte Carlo simulations on a lattice model hosting the interacting superfluid-insulator QCP. In superfluid phases, interacting Goldstone bosons qualitatively change the high frequency optical conductivity, and the corresponding sum rule.

  6. Dynamical Response near Quantum Critical Points

    Science.gov (United States)

    Lucas, Andrew; Gazit, Snir; Podolsky, Daniel; Witczak-Krempa, William

    2017-02-01

    We study high-frequency response functions, notably the optical conductivity, in the vicinity of quantum critical points (QCPs) by allowing for both detuning from the critical coupling and finite temperature. We consider general dimensions and dynamical exponents. This leads to a unified understanding of sum rules. In systems with emergent Lorentz invariance, powerful methods from quantum field theory allow us to fix the high-frequency response in terms of universal coefficients. We test our predictions analytically in the large-N O (N ) model and using the gauge-gravity duality and numerically via quantum Monte Carlo simulations on a lattice model hosting the interacting superfluid-insulator QCP. In superfluid phases, interacting Goldstone bosons qualitatively change the high-frequency optical conductivity and the corresponding sum rule.

  7. Induction generator models in dynamic simulation tools

    DEFF Research Database (Denmark)

    Knudsen, Hans; Akhmatov, Vladislav

    1999-01-01

    . It is found to be possible to include a transient model in dynamic stability tools and, then, obtain correct results also in dynamic tools. The representation of the rotating system influences on the voltage recovery shape which is an important observation in case of windmills, where a heavy mill is connected......For AC network with large amount of induction generators (windmills) the paper demonstrates a significant discrepancy in the simulated voltage recovery after fault in weak networks when comparing dynamic and transient stability descriptions and the reasons of discrepancies are explained...

  8. Fluid dynamics theory, computation, and numerical simulation

    CERN Document Server

    Pozrikidis, C

    2001-01-01

    Fluid Dynamics Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes Two distinguishing features of the discourse are solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty Matlab codes are presented and discussed for a broad...

  9. Fluid Dynamics Theory, Computation, and Numerical Simulation

    CERN Document Server

    Pozrikidis, Constantine

    2009-01-01

    Fluid Dynamics: Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner. The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming. This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice. There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes. Two distinguishing features of the discourse are: solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty. Matlab codes are presented and discussed for ...

  10. Monte carlo simulation for soot dynamics

    KAUST Repository

    Zhou, Kun

    2012-01-01

    A new Monte Carlo method termed Comb-like frame Monte Carlo is developed to simulate the soot dynamics. Detailed stochastic error analysis is provided. Comb-like frame Monte Carlo is coupled with the gas phase solver Chemkin II to simulate soot formation in a 1-D premixed burner stabilized flame. The simulated soot number density, volume fraction, and particle size distribution all agree well with the measurement available in literature. The origin of the bimodal distribution of particle size distribution is revealed with quantitative proof.

  11. Object Oriented Modelling and Dynamical Simulation

    DEFF Research Database (Denmark)

    Wagner, Falko Jens; Poulsen, Mikael Zebbelin

    1998-01-01

    This report with appendix describes the work done in master project at DTU.The goal of the project was to develop a concept for simulation of dynamical systems based on object oriented methods.The result was a library of C++-classes, for use when both building componentbased models and when...

  12. Dynamic rod worth simulation study for a sodium-cooled TRU burner

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Ji; Ha, Pham Nhu Viet, E-mail: phamha@kaeri.re.kr; Lee, Min Jae; Kang, Chang Mu

    2015-12-15

    Highlights: • Dynamic rod worth calculation methodology for a sodium-cooled TRU burner was developed. • The spatial weighting functions were relatively insensitive to control rods position. • The simulated pseudo detector response agreed well with the calculated core power. • The simulated dynamic rod worths compared well against the simulated static values. • Impact of individual detector on the simulated dynamic worth was evaluated. - Abstract: This paper presents a preliminary dynamic rod worth simulation study for a TRU burner core mockup of the PGSFR (Korean Prototype Gen-IV Sodium-cooled Fast Reactor) named BFS-76-1A so as to establish a calculation methodology for evaluating the rod worth of the PGSFR. The simulation method was mainly based on a three-dimensional multi-group nodal diffusion transient code for fast reactors in which the rod drop simulation for the BFS-76-1A was performed and all the fuel assemblies were taken into account for the detector response calculation. Then the dynamic rod worths were inferred from the simulated detector responses using an inverse point kinetics model and compared against the simulated static worths. The results show good agreement between the simulated pseudo detector response and the calculated core power as well as between the simulated dynamic and static rod worths, and thus indicate that the dynamic rod worth simulation method developed in this work can be applied to the rod worth estimation and validation for the PGSFR.

  13. Molecular dynamics simulations of magnetized dusty plasmas

    Science.gov (United States)

    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)

  14. Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow

    CERN Document Server

    Archereau, Aurelien Y M; Willmott, Geoff R

    2016-01-01

    We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.

  15. Probing Cellular Dynamics with Mesoscopic Simulations

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2010-01-01

    Cellular processes span a huge range of length and time scales from the molecular to the near-macroscopic. Understanding how effects on one scale influence, and are themselves influenced by, those on lower and higher scales is a critical issue for the construction of models in Systems Biology....... Advances in computing hardware and software now allow explicit simulation of some aspects of cellular dynamics close to the molecular scale. Vesicle fusion is one example of such a process. Experiments, however, typically probe cellular behavior from the molecular scale up to microns. Standard particle...... soon be coupled to Mass Action models allowing the parameters in such models to be continuously tuned according to the finer resolution simulation. This will help realize the goal of a computational cellular simulation that is able to capture the dynamics of membrane-associated processes...

  16. Computer simulation of confined liquid crystal dynamics

    CERN Document Server

    Webster, R E

    2001-01-01

    are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results...

  17. General regularity of dynamic responses of slopes under dynamic input

    Institute of Scientific and Technical Information of China (English)

    QI Shengwen; WU Faquan; SUN Jinzhong

    2003-01-01

    Through lots of numerical simulations with FLAC3D, dynamic responses of slopes are comprehensively studied in this paper and the general regularities of the isoline of the coefficient of the displacement, velocity and acceleration of the slope section are reached. Given a certain material slope, if the height of the slope is less than a certain value, the displacement, velocity and acceleration linearly enlarge with elevation in the vertical direction; if the height of the slope surpasses the certain value, the displacement,velocity and acceleration do not linearly enlarge with elevation any more, on the other hand, they fluctuate with a certain rhythm. At the same time, the rhythm appears in the horizontal direction, and the displacement, velocity and acceleration of the slope surface enlarge near the slope surface. The distribution form of the isoline of the coefficient of displacement, velocity and acceleration in the section of the slope is remarkably affected by the slope angle. In the certain area near the slope surface, the isoline of displacement,velocity and acceleration is parallel to the surface of the slope; in the mean time the strike direction of the extremum area is parallel to the surface of the slope, too. The charts of the slope dynamic responses can be depicted with two indexes, one is the strike direction of the isoline, and the other is the number of the rhythm extremum area of the direction parallel to the surface of the slope.

  18. Accelerated molecular dynamics simulations of protein folding.

    Science.gov (United States)

    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.

  19. Simulation of Stimuli-Responsive Polymer Networks

    Directory of Open Access Journals (Sweden)

    Thomas Gruhn

    2013-11-01

    Full Text Available The structure and material properties of polymer networks can depend sensitively on changes in the environment. There is a great deal of progress in the development of stimuli-responsive hydrogels for applications like sensors, self-repairing materials or actuators. Biocompatible, smart hydrogels can be used for applications, such as controlled drug delivery and release, or for artificial muscles. Numerical studies have been performed on different length scales and levels of details. Macroscopic theories that describe the network systems with the help of continuous fields are suited to study effects like the stimuli-induced deformation of hydrogels on large scales. In this article, we discuss various macroscopic approaches and describe, in more detail, our phase field model, which allows the calculation of the hydrogel dynamics with the help of a free energy that considers physical and chemical impacts. On a mesoscopic level, polymer systems can be modeled with the help of the self-consistent field theory, which includes the interactions, connectivity, and the entropy of the polymer chains, and does not depend on constitutive equations. We present our recent extension of the method that allows the study of the formation of nano domains in reversibly crosslinked block copolymer networks. Molecular simulations of polymer networks allow the investigation of the behavior of specific systems on a microscopic scale. As an example for microscopic modeling of stimuli sensitive polymer networks, we present our Monte Carlo simulations of a filament network system with crosslinkers.

  20. Neutron Star Crust and Molecular Dynamics Simulation

    CERN Document Server

    Horowitz, C J; Schneider, A; Berry, D K

    2011-01-01

    In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.

  1. Atomic dynamics of alumina melt: A molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    S.Jahn

    2008-03-01

    Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.

  2. Mesoscopic Simulation Methods for Polymer Dynamics

    Science.gov (United States)

    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.

  3. A Modal Model to Simulate Typical Structural Dynamic Nonlinearity

    Energy Technology Data Exchange (ETDEWEB)

    Pacini, Benjamin Robert [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mayes, Randall L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Roettgen, Daniel R [Univ. of Wisconsin, Madison, WI (United States)

    2015-10-01

    Some initial investigations have been published which simulate nonlinear response with almost traditional modal models: instead of connecting the modal mass to ground through the traditional spring and damper, a nonlinear Iwan element was added. This assumes that the mode shapes do not change with amplitude and there are no interactions between modal degrees of freedom. This work expands on these previous studies. An impact experiment is performed on a structure which exhibits typical structural dynamic nonlinear response, i.e. weak frequency dependence and strong damping dependence on the amplitude of vibration. Use of low level modal test results in combination with high level impacts are processed using various combinations of modal filtering, the Hilbert Transform and band-pass filtering to develop response data that are then fit with various nonlinear elements to create a nonlinear pseudo-modal model. Simulations of forced response are compared with high level experimental data for various nonlinear element assumptions.

  4. Simulation of Gas-Surface Dynamical Interactions

    Science.gov (United States)

    2007-07-01

    Brenig, Z. Phys. B 36, 81 (1979). [39] J. Böheim and W. Brenig, Z. Phys. B 41, 243 (1981). [40] G. B. Arfken and H. J. Weber, Mathematical Methods for...excitation of the substrate have to be taken into account. In this lecture, the quantum and classical methods required for the simulation of gas-surface...well-defined conditions [2]. In this chapter, I will briefly review the theoretical methods necessary to determine the dynamics of processes at surfaces

  5. Study of Nanowires Using Molecular Dynamics Simulations

    OpenAIRE

    Monk, Joshua D

    2007-01-01

    In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...

  6. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  7. Simulation of dynamics of a permanent magnet linear actuator

    DEFF Research Database (Denmark)

    Yatchev, Ivan; Ritchie, Ewen

    2010-01-01

    Comparison of two approaches for the simulation of the dynamic behaviour of a permanent magnet linear actuator is presented. These are full coupled model, where the electromagnetic field, electric circuit and mechanical motion problems are solved simultaneously, and decoupled model, where first...... flexibility when the actuator response is required to be estimated for different external conditions, e.g. external circuit parameters or mechanical loads....

  8. IGCC Dynamic Simulator and Training Center

    Energy Technology Data Exchange (ETDEWEB)

    Zitney, S.E.; Erbes, M.R. (Enginomix, LLC)

    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.

  9. SIMULATION OF INTERLINE DYNAMIC VOLTAGE RESTORER

    Directory of Open Access Journals (Sweden)

    J.Singaravelan

    2011-08-01

    Full Text Available This paper presents a new approach for the dynamic control of a current source inverter (CSI using Super Conductive Magnetic energy storage (SMES based Interline DVR. The dynamic voltage restorer (DVR provides a technically advanced and economical solution to voltage-sag problem. As the voltage-restoration process involves the real-power injection into the distribution system, the capability ofa DVR, especially for compensating long-duration voltage sags, it depends on the energy storage capacity of the DVR. The interline DVR proposed in this paper provides a way to replenish Dc-link energy storage dynamically. The IDVR consists of several DVRs connected to different distribution feeders in the power system. The DVRs in the IDVR system shares the common energy storage. When one of the DVRcompensates for voltage sag appearing in that feeder, the other DVRs replenish the energy in the common dc-link dynamically. Thus, one DVR in the IDVR system works in voltage-sag compensation mode whilethe other DVRs in the IDVR system operate in power-flow control mode. The proposed topology is simulated using Matlab/Simulink and total IDVR system is simulated using Matlab/Simulink.

  10. Molecular Dynamics Simulations of Network Glasses

    Science.gov (United States)

    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

  11. Simulations of fusion chamber dynamics and first wall response in a Z-pinch driven fusion–fission hybrid power reactor (Z-FFR)

    Energy Technology Data Exchange (ETDEWEB)

    Qi, J.M., E-mail: qjm06@sina.com [Laboratory of Advanced Nuclear Energy (LANE), Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999 (China); Center for Fusion Energy Science and Technology (CFEST), China Academy of Engineering Physics, Mianyang 621999 (China); Wang, Z., E-mail: wangz_es@caep.cn [Laboratory of Advanced Nuclear Energy (LANE), Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999 (China); Center for Fusion Energy Science and Technology (CFEST), China Academy of Engineering Physics, Mianyang 621999 (China); Chu, Y.Y., E-mail: chuyanyun@caep.cn [Laboratory of Advanced Nuclear Energy (LANE), Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999 (China); Center for Fusion Energy Science and Technology (CFEST), China Academy of Engineering Physics, Mianyang 621999 (China); Li, Z.H., E-mail: lee_march@sina.com [Laboratory of Advanced Nuclear Energy (LANE), Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999 (China)

    2016-03-15

    Highlights: • Z-FFR utilizes DT neutrons to drive a sub-critical fission blanket to produce energy. • A metal shell and Ar gas are employed in the fusion chamber for shock mitigation. • Massive materials can effectively mitigate the thermal heats on the chamber wall. • The W-coated Zr-alloy first wall exhibits good viability as a long-lived component. - Abstract: In a Z-pinch driven fusion–fission hybrid power reactor (Z-FFR), the fusion target will produce enormous energy of ∼1.5 GJ per pulse at a frequency of 0.1 Hz. Almost 20% of the fusion energy yield, approximately 300 MJ, is released in forms of pulsed X-rays. To prevent the first wall from fatal damages by the intense X-rays, a thin spherical metal shell and rare Ar buffer gas are introduced to mitigate the transient X-ray bursts. Radiation hydrodynamics in the fusion chamber were investigated by MULTI-1D simulations, and the corresponding thermal and mechanical loads on the first wall were also obtained. The simulations indicated that by optimizing the design parameters of the metal shell and Ar buffer gas, peak power flux of the thermal heats on the first wall could be mitigated to less than 10{sup 4} W/cm{sup 2} within a time scale of several milliseconds, while peak overpressures of the mechanical loads varying from 0.6 to 0.7 MPa. In addition, the thermomechanical response in a W–coated Zr-alloy first wall was performed by FWDR1D calculations using the derived thermal and mechanical loads as inputs. The temperature and stress fields were analyzed, and the corresponding elastic strains were conducted for primary lifetime estimations by using the Coffin–Manson relationships of both W and Zr-alloy. It was shown that the maximum temperature rises and stresses in the first wall were less than 50 K and 130 MPa respectively, and lifetime of the first wall would be in excess of 10{sup 9} cycles. The chamber exhibits good viability as a long-lived component to sustain the Z-FFR conceptual

  12. DYNAMIC SIMULATION OF ROTATING SHELLS COUPLED WITH LIQUID

    Institute of Scientific and Technical Information of China (English)

    Wei Fayuan; Li Shiqi; Zhong Yifang; Huang Yuying

    2001-01-01

    The dynamic behaviors of rotating shells coupled with liquid are shown. The shell under consideration has arbitrary boundary conditions and a complex shape. A modified boundary element method and finite strip technique are used to improve the computing efficiency and to guarantee the continuity conditions on the liquid-shell interaction plane. The effects of various parameters such as shell's thickness and liquid depth are investigated. Dynamic simulations are applied to several typical shell-liquid systems, and the natural frequencies, mode shapes and response of vibration are calculated numerically.

  13. Nanodrop contact angles from molecular dynamics simulations

    Science.gov (United States)

    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.

  14. The simulation of the swelling and deswelling dynamics of gels

    Science.gov (United States)

    Yamaue, Tatsuya; Taniguchi, Takashi; Doi, Masao

    We have formulated the dynamics and the simulation scheme for large deformation of gels using the stress-diffusion coupling model [Yamaue, T., Taniguchi, T., and Doi, M., 2000, AIP Conference Proceedings, Vol. 519 (AIP), p. 584]. Using this model, we have simulated the deswelling process of 2D slab thermo-responsive gels undergoing spinodal decomposition, in comparison with the conventional collective diffusion model of gel networks. We reproduced the 'plateau period' due to the surface skin formation and the pattern formations in the inner region of gels by the stress-diffusion coupling model.

  15. Dynamic simulation of regulatory networks using SQUAD

    Directory of Open Access Journals (Sweden)

    Xenarios Ioannis

    2007-11-01

    Full Text Available Abstract 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

  16. Roadway dynamic response analysis under mining rockburst condition

    Institute of Scientific and Technical Information of China (English)

    LI Chun-rui; QI Qing-xin; PAN Jun-feng; LAN Hang

    2009-01-01

    In order to determine how a roadway withstands a momentum wave and de-termine the extent of damage to rock surrounding the roadway under different force wave peak impacts, the roadway dynamic response state was analysed using numerical simula-tion method. The roadway's critical peak force wave and fracture region under dynamic wave action were put forward. It is concluded that the method has practical value to road-way support and rockburst prevention.

  17. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Dislocation dynamics simulations of plasticity at small scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Caizhi [Iowa State Univ., Ames, IA (United States)

    2010-01-01

    As metallic structures and devices are being created on a dimension comparable to the length scales of the underlying dislocation microstructures, the mechanical properties of them change drastically. Since such small structures are increasingly common in modern technologies, there is an emergent need to understand the critical roles of elasticity, plasticity, and fracture in small structures. Dislocation dynamics (DD) simulations, in which the dislocations are the simulated entities, offer a way to extend length scales beyond those of atomistic simulations and the results from DD simulations can be directly compared with the micromechanical tests. The primary objective of this research is to use 3-D DD simulations to study the plastic deformation of nano- and micro-scale materials and understand the correlation between dislocation motion, interactions and the mechanical response. Specifically, to identify what critical events (i.e., dislocation multiplication, cross-slip, storage, nucleation, junction and dipole formation, pinning etc.) determine the deformation response and how these change from bulk behavior as the system decreases in size and correlate and improve our current knowledge of bulk plasticity with the knowledge gained from the direct observations of small-scale plasticity. Our simulation results on single crystal micropillars and polycrystalline thin films can march the experiment results well and capture the essential features in small-scale plasticity. Furthermore, several simple and accurate models have been developed following our simulation results and can reasonably predict the plastic behavior of small scale materials.

  19. A Fault Evolution Model Including the Rupture Dynamic Simulation

    Science.gov (United States)

    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

  20. Dynamic Response Analysis of Motorized Spindle System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Li; LUO Yi-chao; XU Juan; XIAO Ru-feng; LI Xian-hui

    2013-01-01

    As to motorized spindle system, this paper builds a simplified 3D model of spindle and bearing, performs structure modal analysis, reveals its dynamic characteristics under the free model;furthermore, modifies bearing radial stiffness and number of model, and studies the change of modal parameters. On this basis, through the harmonic response analysis of the finite element model, dy-namic response characteristic caused by imbalance of monitored spindle system and law of vibration response to different amount of unbalance is analyzed.

  1. Monoamine transporters: Insights from molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Julie eGrouleff

    2015-10-01

    Full Text Available The human monoamine transporters 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 monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters 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 monoamine transporters, 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.

  2. Monoamine transporters: insights from molecular dynamics simulations

    Science.gov (United States)

    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

  3. DYNAMICS OF THE ESCAPE RESPONSE.

    Science.gov (United States)

    requirements. It has been shown that force is a lawful response measure under positive reinforcement (Notterman and Mintz, 1965). Subjects will adjust...concluded that response force in an escape situation is a lawful response measure, and that it operates in a manner similar to force under positive reinforcement .

  4. Dynamic modeling of cellular response to DNA damage based on p53 stress response networks

    Institute of Scientific and Technical Information of China (English)

    Jinpeng Qi; Yongsheng Ding; Shihuang Shao

    2009-01-01

    Under acute perturbations from the outside, cells can trigger self-defensive mechanisms to fight against genome stress. To investigate the cellular response to continuous ion radiation (IR), a dynamic model for p53 stress response networks at the cellular level is proposed. The model can successfully be used to simulate the dynamic processes of double-strand breaks (DSBs) generation and their repair, switch-like ataxia telangiectasia mutated (ATM) activation, oscillations occurring in the p53-MDM2 feedback loop, as well as toxins elimination triggered by p53 stress response networks. Especially, the model can predict the plausible outcomes of cellular response under different IR dose regimes.

  5. Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations

    Science.gov (United States)

    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.

  6. Molecular Dynamics Simulations of Polyelectrolyte Solutions

    Science.gov (United States)

    Dobrynin, Andrey

    2014-03-01

    Polyelectrolytes are polymers with ionizable groups. In polar solvents, these groups dissociate releasing counterions into solution and leaving uncompensated charges on the polymer backbone. Examples of polyelectrolytes include biopolymers such as DNA and RNA, and synthetic polymers such as poly(styrene sulfonate) and poly(acrylic acids). In this talk I will discuss recent molecular dynamics simulations of static and dynamic properties of polyelectrolyte solutions. These simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I - 1 / 2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ~ I- 1 / 5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ~ I- 1 / 2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ~ cp-1 / 4 . While at high salt concentrations one observes a weaker dependence of the chain size on the solution ionic strength, R ~ I- 1 / 8. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X (I) in salt solutions and corresponding quantities X (I0) in salt-free solutions, X (I) = X (I0) (I /I0) β . The exponent β = -1/2 for chain persistence length lp , β = 1/4 for solution correlation length, β = -1/5 and β = -1/8 for chain size R in dilute and semidilute solution regimes respectively. Furthermore, the analysis of the spectrum and of the relaxation times of Rouse modes confirms existence of the single length scale (correlation length) that controls both static and dynamic properties of semidilute polyelectrolyte solutions. These findings

  7. Traffic flow dynamics data, models and simulation

    CERN Document Server

    Treiber, Martin

    2013-01-01

    This textbook provides a comprehensive and instructive coverage of vehicular traffic flow dynamics and modeling. It makes this fascinating interdisciplinary topic, which to date was only documented in parts by specialized monographs, accessible to a broad readership. Numerous figures and problems with solutions help the reader to quickly understand and practice the presented concepts. This book is targeted at students of physics and traffic engineering and, more generally, also at students and professionals in computer science, mathematics, and interdisciplinary topics. It also offers material for project work in programming and simulation at college and university level. The main part, after presenting different categories of traffic data, is devoted to a mathematical description of the dynamics of traffic flow, covering macroscopic models which describe traffic in terms of density, as well as microscopic many-particle models in which each particle corresponds to a vehicle and its driver. Focus chapters on ...

  8. Molecular dynamics simulations of classical stopping power.

    Science.gov (United States)

    Grabowski, Paul E; Surh, Michael P; Richards, David F; Graziani, Frank R; Murillo, Michael S

    2013-11-22

    Molecular dynamics can provide very accurate tests of classical kinetic theory; for example, unambiguous comparisons can be made for classical particles interacting via a repulsive 1/r potential. The plasma stopping power problem, of great interest in its own right, provides an especially stringent test of a velocity-dependent transport property. We have performed large-scale (~10(4)-10(6) particles) molecular dynamics simulations of charged-particle stopping in a classical electron gas that span the weak to moderately strong intratarget coupling regimes. Projectile-target coupling is varied with projectile charge and velocity. Comparisons are made with disparate kinetic theories (both Boltzmann and Lenard-Balescu classes) and fully convergent theories to establish regimes of validity. We extend these various stopping models to improve agreement with the MD data and provide a useful fit to our results.

  9. Hybrid simulation theory for a classical nonlinear dynamical system

    Science.gov (United States)

    Drazin, Paul L.; Govindjee, Sanjay

    2017-03-01

    Hybrid simulation is an experimental and computational technique which allows one to study the time evolution of a system by physically testing a subset of it while the remainder is represented by a numerical model that is attached to the physical portion via sensors and actuators. The technique allows one to study large or complicated mechanical systems while only requiring a subset of the complete system to be present in the laboratory. This results in vast cost savings as well as the ability to study systems that simply can not be tested due to scale. However, the errors that arise from splitting the system in two requires careful attention, if a valid simulation is to be guaranteed. To date, efforts to understand the theoretical limitations of hybrid simulation have been restricted to linear dynamical systems. In this work we consider the behavior of hybrid simulation when applied to nonlinear dynamical systems. As a model problem, we focus on the damped, harmonically-driven nonlinear pendulum. This system offers complex nonlinear characteristics, in particular periodic and chaotic motions. We are able to show that the application of hybrid simulation to nonlinear systems requires a careful understanding of what one expects from such an experiment. In particular, when system response is chaotic we advocate the need for the use of multiple metrics to characterize the difference between two chaotic systems via Lyapunov exponents and Lyapunov dimensions, as well as correlation exponents. When system response is periodic we advocate the use of L2 norms. Further, we are able to show that hybrid simulation can falsely predict chaotic or periodic response when the true system has the opposite characteristic. In certain cases, we are able to show that control system parameters can mitigate this issue.

  10. Molecular Dynamics Simulations for Predicting Surface Wetting

    Directory of Open Access Journals (Sweden)

    Jing Chen

    2014-06-01

    Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.

  11. Molecular Dynamics Simulations of Hypervelocity Impacts

    Science.gov (United States)

    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.

  12. Nano-tribology through molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    王慧; 胡元中; 邹鲲; 冷永胜

    2001-01-01

    The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.

  13. [Oligoglycine surface structures: molecular dynamics simulation].

    Science.gov (United States)

    Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V

    2010-01-01

    The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

  14. Molecular Dynamics Simulations of Interface Failure

    Science.gov (United States)

    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.

  15. Schwinger model simulations with dynamical overlap fermions

    CERN Document Server

    Bietenholz, W; Volkholz, J

    2007-01-01

    We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate Sigma vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the lowest eigenvalues in different topological sectors with chiral RMT in unitary ensemble we obtain -- for the very light fermion masses -- values for $\\Sigma$ that follow closely the analytical predictions in the continuum.

  16. Schwinger model simulations with dynamical overlap fermions

    Energy Technology Data Exchange (ETDEWEB)

    Bietenholz, W. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Shcheredin, S. [Bielefeld Univ. (Germany). Fakultaet fuer Physik; Volkholz, J. [Humboldt-Universitaet, Berlin (Germany). Inst. fuer Physik

    2007-11-15

    We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate {sigma} vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the lowest eigenvalues in different topological sectors with chiral RMT in unitary ensemble we obtain - for the very light fermion masses - values for {sigma} that follow closely the analytical predictions in the continuum. (orig.)

  17. Osmosis : a molecular dynamics computer simulation study

    Science.gov (United States)

    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..

  18. Dynamical response to a stationary tidal field

    CERN Document Server

    Landry, Philippe

    2015-01-01

    We demonstrate that a slowly rotating compact body subjected to a stationary tidal field undergoes a dynamical response, in which the fluid variables and the interior metric vary on the time scale of the rotation period. This dynamical response requires the tidal field to have a gravitomagnetic component generated by external mass currents; the response to a gravitoelectric tidal field is stationary. We confirm that in a calculation carried out to first order in the body's rotation, the exterior geometry bears no trace of this internal dynamics; it remains stationary in spite of the time-dependent interior.

  19. Effect of Conductor Verbalization, Dynamic Markings, Conductor Gesture, and Choir Dynamic Level on Singers' Dynamic Responses.

    Science.gov (United States)

    Skadsem, Julie A.

    1997-01-01

    Examines the effects of conductor verbalization, dynamic markings, conductor gesture, and choir dynamic level on individual singers' dynamic responses. Indicates that verbal instructions from the conductor elicited significantly stronger dynamic performance responses than did the other instructional conditions. Suggests that additional research…

  20. Parallel Monte Carlo Simulation of Aerosol Dynamics

    Directory of Open Access Journals (Sweden)

    Kun Zhou

    2014-02-01

    Full Text Available A highly efficient Monte Carlo (MC algorithm is developed for the numerical simulation of aerosol dynamics, that is, nucleation, surface growth, and coagulation. Nucleation and surface growth are handled with deterministic means, while coagulation is simulated with a stochastic method (Marcus-Lushnikov stochastic process. Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI. The parallel computing efficiency is investigated through numerical examples. Near 60% parallel efficiency is achieved for the maximum testing case with 3.7 million MC particles running on 93 parallel computing nodes. The algorithm is verified through simulating various testing cases and comparing the simulation results with available analytical and/or other numerical solutions. Generally, it is found that only small number (hundreds or thousands of MC particles is necessary to accurately predict the aerosol particle number density, volume fraction, and so forth, that is, low order moments of the Particle Size Distribution (PSD function. Accurately predicting the high order moments of the PSD needs to dramatically increase the number of MC particles.

  1. Parallel Monte Carlo simulation of aerosol dynamics

    KAUST Repository

    Zhou, K.

    2014-01-01

    A highly efficient Monte Carlo (MC) algorithm is developed for the numerical simulation of aerosol dynamics, that is, nucleation, surface growth, and coagulation. Nucleation and surface growth are handled with deterministic means, while coagulation is simulated with a stochastic method (Marcus-Lushnikov stochastic process). Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI). The parallel computing efficiency is investigated through numerical examples. Near 60% parallel efficiency is achieved for the maximum testing case with 3.7 million MC particles running on 93 parallel computing nodes. The algorithm is verified through simulating various testing cases and comparing the simulation results with available analytical and/or other numerical solutions. Generally, it is found that only small number (hundreds or thousands) of MC particles is necessary to accurately predict the aerosol particle number density, volume fraction, and so forth, that is, low order moments of the Particle Size Distribution (PSD) function. Accurately predicting the high order moments of the PSD needs to dramatically increase the number of MC particles. 2014 Kun Zhou et al.

  2. Dynamic Response Testing in an Electrically Heated Reactor Test Facility

    Science.gov (United States)

    Bragg-Sitton, Shannon M.; Morton, T. J.

    2006-01-01

    Non-nuclear testing can be a valuable tool in development of a space nuclear power or propulsion system. In a non-nuclear test bed, electric heaters are used to simulate the heat from nuclear fuel. Standard testing allows one to fully assess thermal, heat transfer, and stress related attributes of a given system, but fails to demonstrate the dynamic response that would be present in an integrated, fueled reactor system. The integration of thermal hydraulic hardware tests with simulated neutronic response provides a bridge between electrically heated testing and full nuclear testing. By implementing a neutronic response model to simulate the dynamic response that would be expected in a fueled reactor system, one can better understand system integration issues, characterize integrated system response times and response characteristics, and assess potential design improvements at a relatively small fiscal investment. Initial system dynamic response testing was demonstrated on the integrated SAFE-100a heat pipe cooled, electrically heated reactor and heat exchanger hardware, utilizing a one-group solution to the point kinetics equations to simulate the expected neutronic response of the system (Bragg-Sitton, 2005). The current paper applies the same testing methodology to a direct drive gas cooled reactor system, demonstrating the applicability of the testing methodology to any reactor type and demonstrating the variation in system response characteristics in different reactor concepts. In each testing application, core power transients were controlled by a point kinetics model with reactivity feedback based on core average temperature; the neutron generation time and the temperature feedback coefficient are provided as model inputs. Although both system designs utilize a fast spectrum reactor, the method of cooling the reactor differs significantly, leading to a variable system response that can be demonstrated and assessed in a non-nuclear test facility.

  3. http://www.phrp.com.au/issues/february-2017-volume-27-issue-1-2/dynamic-simulation-modelling-of-policy-responses-to-reduce-alcohol-related-harms-rationale-and-procedure-for-a-participatory-approach/

    Directory of Open Access Journals (Sweden)

    Jo-An Atkinson

    2017-02-01

    Full Text Available Development of effective policy responses to address complex public health problems can be challenged by a lack of clarity about the interaction of risk factors driving the problem, differing views of stakeholders on the most appropriate and effective intervention approaches, a lack of evidence to support commonly implemented and acceptable intervention approaches, and a lack of acceptance of effective interventions. Consequently, political considerations, community advocacy and industry lobbying can contribute to a hotly contested debate about the most appropriate course of action; this can hinder consensus and give rise to policy resistance. The problem of alcohol misuse and its associated harms in New South Wales (NSW, Australia, provides a relevant example of such challenges. Dynamic simulation modelling is increasingly being valued by the health sector as a robust tool to support decision making to address complex problems. It allows policy makers to ask ‘what-if’ questions and test the potential impacts of different policy scenarios over time, before solutions are implemented in the real world. Participatory approaches to modelling enable researchers, policy makers, program planners, practitioners and consumer representatives to collaborate with expert modellers to ensure that models are transparent, incorporate diverse evidence and perspectives, are better aligned to the decision-support needs of policy makers, and can facilitate consensus building for action. This paper outlines a procedure for embedding stakeholder engagement and consensus building in the development of dynamic simulation models that can guide the development of effective, coordinated and acceptable policy responses to complex public health problems, such as alcohol-related harms in NSW.

  4. Voltage Controlled Dynamic Demand Response

    DEFF Research Database (Denmark)

    Bhattarai, Bishnu Prasad; Bak-Jensen, Birgitte; Mahat, Pukar

    2013-01-01

    . An adaptive dynamic model has been developed to determine composite voltage dependency of an aggregated load on feeder level. Following the demand dispatch or control signal, optimum voltage setting at the LV substation is determined based on the voltage dependency of the load. Furthermore, a new technique...

  5. Analog circuit design designing dynamic circuit response

    CERN Document Server

    Feucht, Dennis

    2010-01-01

    This second volume, Designing Dynamic Circuit Response builds upon the first volume Designing Amplifier Circuits by extending coverage to include reactances and their time- and frequency-related behavioral consequences.

  6. Nano-tribology through molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    WANG; Hui(

    2001-01-01

    [1]Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.[2]Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.[3]Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.[4]Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.[5]Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.[6]Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.[7]Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.[8]Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.[9]Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.[10]Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.[11]Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.[12]Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.[13]Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.

  7. Simulating the Immune Response on a Distributed Parallel Computer

    Science.gov (United States)

    Castiglione, F.; Bernaschi, M.; Succi, S.

    The application of ideas and methods of statistical mechanics to problems of biological relevance is one of the most promising frontiers of theoretical and computational mathematical physics.1,2 Among others, the computer simulation of the immune system dynamics stands out as one of the prominent candidates for this type of investigations. In the recent years immunological research has been drawing increasing benefits from the resort to advanced mathematical modeling on modern computers.3,4 Among others, Cellular Automata (CA), i.e., fully discrete dynamical systems evolving according to boolean laws, appear to be extremely well suited to computer simulation of biological systems.5 A prominent example of immunological CA is represented by the Celada-Seiden automaton, that has proven capable of providing several new insights into the dynamics of the immune system response. To date, the Celada-Seiden automaton was not in a position to exploit the impressive advances of computer technology, and notably parallel processing, simply because no parallel version of this automaton had been developed yet. In this paper we fill this gap and describe a parallel version of the Celada-Seiden cellular automaton aimed at simulating the dynamic response of the immune system. Details on the parallel implementation as well as performance data on the IBM SP2 parallel platform are presented and commented on.

  8. Dynamic Response of Embedded Structures.

    Science.gov (United States)

    1991-07-15

    1 (202) 767-6963 AFOSR/Nh 00 FORM 1473, 83 APR EDITION OF I JAN 73 IS OBSOLETE. Uwc A ____________ SECURITY CLASSIFICATION OF THIS PAGE...4. Baker W. E., Westine P. S., Dodge F. T., "Similarity Methods in Engineering Dynamics", Hayden Book Company, Inc., New Jerset, 1978. 5. Bazant , Z...P., "Size Effect in Blunt Fracture: Concrete, Rock, Metal", ASCE, Journal of Engineering Mechanics, Vol. 110, No. 4, April 1984. 6. Bazant , Z. P

  9. Quantum molecular dynamics simulations of dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)

    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.

  10. Dynamics simulations for engineering macromolecular interactions

    Science.gov (United States)

    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

  11. Dynamic Response Testing in an Electrically Heated Reactor Test Facility

    Science.gov (United States)

    Bragg-Sitton, Shannon M.; Morton, T. J.

    2006-01-01

    Non-nuclear testing can be a valuable tool in the development of a space nuclear power or propulsion system. In a non-nuclear test bed, electric heaters are used to simulate the heat from nuclear fuel. Standard testing allows one to fully assess thermal, heat transfer, and stress related attributes of a given system, but fails to demonstrate the dynamic response that would be present in an integrated, fueled reactor system. The integration of thermal hydraulic hardware tests with simulated neutronic response provides a bridge between electrically heated testing and fueled nuclear testing. By implementing a neutronic response model to simulate the dynamic response that would be expected in a fueled reactor system, one can better understand system integration issues, characterize integrated system response times and response characteristics, and assess potential design improvements at a relatively small fiscal investment. Initial system dynamic response testing was demonstrated on the integrated SAFE-100a heat pipe (HP) cooled, electrically heated reactor and heat exchanger hardware, utilizing a one-group solution to the point kinetics equations to simulate the expected neutronic response of the system. Reactivity feedback calculations were then based on a bulk reactivity feedback coefficient and measured average core temperature. This paper presents preliminary results from similar dynamic testing of a direct drive gas cooled reactor system (DDG), demonstrating the applicability of the testing methodology to any reactor type and demonstrating the variation in system response characteristics in different reactor concepts. Although the HP and DDG designs both utilize a fast spectrum reactor, the method of cooling the reactor differs significantly, leading to a variable system response that can be demonstrated and assessed in a non-nuclear test facility. Planned system upgrades to allow implementation of higher fidelity dynamic testing are also discussed. Proposed DDG

  12. On sequential dynamical systems and simulation

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. Dynamic response of cavitating turbomachines

    Science.gov (United States)

    Ng, S. L.

    1976-01-01

    Stimulated by the pogo instability encountered in many liquid propellant rockets, the dynamic behavior of cavitating inducers is discussed. An experimental facility where the upstream and downstream flows of a cavitating inducer could be perturbed was constructed and tested. The upstream and downstream pressure and mass flow fluctuations were measured. Matrices representing the transfer functions across the inducer pump were calculated from these measurements and from the hydraulic system characteristics for two impellers in various states of cavitation. The transfer matrices when plotted against the perturbing frequency showed significant departure from steady state or quasi-steady predictions especially at higher frequencies.

  14. Dynamical response of the Galileo Galilei on the ground rotor to test the equivalence principle: Theory, simulation, and experiment. II. The rejection of common mode forces

    Science.gov (United States)

    Comandi, G. L.; Toncelli, R.; Chiofalo, M. L.; Bramanti, D.; Nobili, A. M.

    2006-03-01

    "Galileo Galilei on the ground" (GGG) is a fast rotating differential accelerometer designed to test the equivalence principle (EP). Its sensitivity to differential effects, such as the effect of an EP violation, depends crucially on the capability of the accelerometer to reject all effects acting in common mode. By applying the theoretical and simulation methods reported in Part I of this work, and tested therein against experimental data, we predict the occurrence of an enhanced common mode rejection of the GGG accelerometer. We demonstrate that the best rejection of common mode disturbances can be tuned in a controlled way by varying the spin frequency of the GGG rotor.

  15. Computational methods for coupling microstructural and micromechanical materials response simulations

    Energy Technology Data Exchange (ETDEWEB)

    HOLM,ELIZABETH A.; BATTAILE,CORBETT C.; BUCHHEIT,THOMAS E.; FANG,HUEI ELIOT; RINTOUL,MARK DANIEL; VEDULA,VENKATA R.; GLASS,S. JILL; KNOROVSKY,GERALD A.; NEILSEN,MICHAEL K.; WELLMAN,GERALD W.; SULSKY,DEBORAH; SHEN,YU-LIN; SCHREYER,H. BUCK

    2000-04-01

    Computational materials simulations have traditionally focused on individual phenomena: grain growth, crack propagation, plastic flow, etc. However, real materials behavior results from a complex interplay between phenomena. In this project, the authors explored methods for coupling mesoscale simulations of microstructural evolution and micromechanical response. In one case, massively parallel (MP) simulations for grain evolution and microcracking in alumina stronglink materials were dynamically coupled. In the other, codes for domain coarsening and plastic deformation in CuSi braze alloys were iteratively linked. this program provided the first comparison of two promising ways to integrate mesoscale computer codes. Coupled microstructural/micromechanical codes were applied to experimentally observed microstructures for the first time. In addition to the coupled codes, this project developed a suite of new computational capabilities (PARGRAIN, GLAD, OOF, MPM, polycrystal plasticity, front tracking). The problem of plasticity length scale in continuum calculations was recognized and a solution strategy was developed. The simulations were experimentally validated on stockpile materials.

  16. A Dynamical Training and Design Simulator for Active Catheters

    Directory of Open Access Journals (Sweden)

    Georges Dumont

    2008-11-01

    Full Text Available This work addresses the design of an active multi-link micro-catheter actuated by Shape Memory Alloy (SMA micro actuators. This may be a response to one medical major demand on such devices, which will be useful for surgical explorations and interventions. In this paper, we focus on a training and design simulator dedicated to such catheters. This simulator is based on an original simulation platform (OpenMASK. The catheter is a robotic system, which is evaluated by a dynamical simulation addressing a navigation task in its environment. The design of the prototype and its mechanical model are presented. We develop an interaction model for contact. This model uses a real medical database for which distance cartography is proposed. Then we focus on an autonomous control model based on a multi-agent approach and including the behaviour description of the SMA actuators. Results of mechanical simulations including interaction with the ducts are presented. Furthermore, the interest of such a simulator is presented by applying virtual prototyping techniques for the design optimization. This optimization process is achieved by using genetic algorithms at different stages with respect to the specified task.

  17. Simulation of Operators' Response in Emergencies

    DEFF Research Database (Denmark)

    Rasmussen, Jens

    1986-01-01

    For the simulation of the accidental course of events in industrial process plants, a model is needed of operators' response to the cues presented by the system. A model is proposed, based on the simplifications which can be made when restricting attention to the operator functions having...

  18. Simulated impacts of insect defoliation on forest carbon dynamics

    Science.gov (United States)

    Medvigy, D.; Clark, K. L.; Skowronski, N. S.; Schäfer, K. V. R.

    2012-12-01

    Many temperate and boreal forests are subject to insect epidemics. In the eastern US, over 41 million meters squared of tree basal area are thought to be at risk of gypsy moth defoliation. However, the decadal-to-century scale implications of defoliation events for ecosystem carbon dynamics are not well understood. In this study, the effects of defoliation intensity, periodicity and spatial pattern on the carbon cycle are investigated in a set of idealized model simulations. A mechanistic terrestrial biosphere model, ecosystem demography model 2, is driven with observations from a xeric oak-pine forest located in the New Jersey Pine Barrens. Simulations indicate that net ecosystem productivity (equal to photosynthesis minus respiration) decreases linearly with increasing defoliation intensity. However, because of interactions between defoliation and drought effects, aboveground biomass exhibits a nonlinear decrease with increasing defoliation intensity. The ecosystem responds strongly with both reduced productivity and biomass loss when defoliation periodicity varies from 5 to 15 yr, but exhibits a relatively weak response when defoliation periodicity varies from 15 to 60 yr. Simulations of spatially heterogeneous defoliation resulted in markedly smaller carbon stocks than simulations with spatially homogeneous defoliation. These results show that gypsy moth defoliation has a large effect on oak-pine forest biomass dynamics, functioning and its capacity to act as a carbon sink.

  19. A Novel Dynamic Co-Simulation Analysis for Overall Closed Loop Operation Control of a Large Wind Turbine

    Directory of Open Access Journals (Sweden)

    Ching-Sung Wang

    2016-08-01

    Full Text Available A novel dynamic co-simulation methodology of overall wind turbine systems is presented. This methodology combines aerodynamics, mechanism dynamics, control system dynamics, and subsystems dynamics. Aerodynamics and turbine properties were modeled in FAST (Fatigue, Aerodynamic, Structures, and Turbulence, and ADAMS (Automatic Dynamic Analysis of Mechanical Systems performed the mechanism dynamics; control system dynamics and subsystem dynamics such as generator, pitch control system, and yaw control system were modeled and built in MATLAB/SIMULINK. Thus, this comprehensive integration of methodology expands both the flexibility and controllability of wind turbines. The dynamic variations of blades, rotor dynamic response, and tower vibration can be performed under different inputs of wind profile, and the control strategies can be verified in the different closed loop simulation. Besides, the dynamic simulation results are compared with the measuring results of SCADA (Supervisory Control and Data Acquisition of a 2 MW wind turbine for ensuring the novel dynamic co-simulation methodology.

  20. CADS:Cantera Aerosol Dynamics Simulator.

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. Simulating the dynamics of complex plasmas

    CERN Document Server

    Schwabe, Mierk

    2014-01-01

    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.

  2. Kinetic Simulations of Plasmoid Chain Dynamics

    CERN Document Server

    Markidis, Stefano; Lapenta, Giovanni; Divin, Andrey; Goldman, Martin; Newman, David; Laure, Erwin

    2013-01-01

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

  3. Astrophysical Fluid Dynamics via Direct Statistical Simulation

    CERN Document Server

    Tobias, S M; Marston, J B

    2010-01-01

    In this paper we introduce the concept of Direct Statistical Simulation (DSS) for astrophysical flows. This technique may be appropriate for problems in astrophysical fluids where the instantaneous dynamics of the flows are of secondary importance to their statistical properties. We give examples of such problems including mixing and transport in planets, stars and disks. The method is described for a general set of evolution equations, before we consider the specific case of a spectral method optimised for problems on a spherical surface. The method is illustrated for the simplest non-trivial example of hydrodynamics and MHD on a rotating spherical surface. We then discuss possible extensions of the method both in terms of computational methods and the range of astrophysical problems that are of interest.

  4. Dynamic wind turbine models in power system simulation tool

    DEFF Research Database (Denmark)

    Hansen, Anca D.; Iov, Florin; Sørensen, Poul

    This report presents a collection of models and control strategies developed and implemented in the power system simulation tool PowerFactory DIgSILENT for different wind turbine concepts. It is the second edition of Risø-R-1400(EN) and it gathers and describes a whole wind turbine model database...... strategies have different goals e.g. fast response over disturbances, optimum power efficiency over a wider range of wind speeds, voltage ride-through capability including grid support. A dynamic model of a DC connection for active stall wind farms to the grid including the control is also implemented...

  5. Dynamic computer simulation of the Fort St. Vrain steam turbines

    Energy Technology Data Exchange (ETDEWEB)

    Conklin, J.C.

    1983-01-01

    A computer simulation is described for the dynamic response of the Fort St. Vrain nuclear reactor regenerative intermediate- and low-pressure steam turbines. The fundamental computer-modeling assumptions for the turbines and feedwater heaters are developed. A turbine heat balance specifying steam and feedwater conditions at a given generator load and the volumes of the feedwater heaters are all that are necessary as descriptive input parameters. Actual plant data for a generator load reduction from 100 to 50% power (which occurred as part of a plant transient on November 9, 1981) are compared with computer-generated predictions, with reasonably good agreement.

  6. In silico FRET from simulated dye dynamics

    Science.gov (United States)

    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

  7. Coarse-grained protein molecular dynamics simulations

    Science.gov (United States)

    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.

  8. Dynamical simulation of tether in orbit deployment

    Science.gov (United States)

    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.

  9. Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Shuangshuang; Chen, Yousu; Wu, Di; Diao, Ruisheng; Huang, Zhenyu

    2015-12-09

    Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.

  10. Dynamic Responsive Systems for Catalytic Function.

    Science.gov (United States)

    Vlatković, Matea; Collins, Beatrice S L; Feringa, Ben L

    2016-11-21

    Responsive systems have recently gained much interest in the scientific community in attempts to mimic dynamic functions in biological systems. One of the fascinating potential applications of responsive systems lies in catalysis. Inspired by nature, novel responsive catalytic systems have been built that show analogy with allosteric regulation of enzymes. The design of responsive catalytic systems allows control of catalytic activity and selectivity. In this Review, advances in the field over the last four decades are discussed and a comparison is made amongst the dynamic responsive systems based on the principles underlying their catalytic mechanisms. The catalyst systems are sorted according to the triggers used to achieve control of the catalytic activity and the distinct catalytic reactions illustrated. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Molecular dynamics simulations of lipid membranes with lateral force: rupture and dynamic properties.

    Science.gov (United States)

    Xie, Jun Yu; Ding, Guang Hong; Karttunen, Mikko

    2014-03-01

    Membranes' response to lateral tension, and eventual rupture, remains poorly understood. In this study, pure dipalmitoylphosphatidylcholine (DPPC) lipid bilayers, under tension/pressure, were studied using molecular dynamics (MD) simulations. The irreversible membrane breakdown is demonstrated to depend on the amplitude of lateral tension, loading rate, and the size of the bilayer. In all of our simulations, -200bar lateral pressure was found to be enough to rupture lipid membrane regardless of the loading rate or the membrane size. Loading rate and membrane size had a significant impact on rupture. A variety of dynamic properties of lipid molecules, probability distribution of area per lipid particularly, have been determined, and found to be fundamental for describing membrane behavior in detail, thus providing the quantitative description for the requirement of membrane rupture.

  12. Accurate direct Eulerian simulation of dynamic elastic-plastic flow

    Energy Technology Data Exchange (ETDEWEB)

    Kamm, James R [Los Alamos National Laboratory; Walter, John W [Los Alamos National Laboratory

    2009-01-01

    The simulation of dynamic, large strain deformation is an important, difficult, and unsolved computational challenge. Existing Eulerian schemes for dynamic material response are plagued by unresolved issues. We present a new scheme for the first-order system of elasto-plasticity equations in the Eulerian frame. This system has an intrinsic constraint on the inverse deformation gradient. Standard Godunov schemes do not satisfy this constraint. The method of Flux Distributions (FD) was devised to discretely enforce such constraints for numerical schemes with cell-centered variables. We describe a Flux Distribution approach that enforces the inverse deformation gradient constraint. As this approach is new and novel, we do not yet have numerical results to validate our claims. This paper is the first installment of our program to develop this new method.

  13. A Hardware Transverse Beam Frequency Response Simulator

    CERN Document Server

    Ning, Jia

    2005-01-01

    We build an electronical instrument to get the frequency response close to the pattern of transverse beam frequency response. The method is to apply 1)a time delay circuit with ADC, FIFO RAM and DAC; 2)a phase shift circuit which is an all pass filter with adjustable phase shift in the frequency range of 25kHz to 30kHz; in a feedback loop of 3)a commutating filter which is a high Q band pass filter. We can dynamically adjust the center frequency, the side band distance during the testing. With this instrument, some beam instruments can be tested without using the real beam.

  14. Rotational Brownian Dynamics simulations of clathrin cage formation

    Energy Technology Data Exchange (ETDEWEB)

    Ilie, Ioana M.; Briels, Wim J. [Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Otter, Wouter K. den, E-mail: w.k.denotter@utwente.nl [Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Multi Scale Mechanics, Faculty of Engineering Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)

    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.

  15. Rotational Brownian dynamics simulations of clathrin cage formation.

    Science.gov (United States)

    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.

  16. Roadway dynamic response analysis under mining rockburst condition

    Energy Technology Data Exchange (ETDEWEB)

    Chun-rui Li; Qing-xin Qi; Jun-feng Pan; Hang Lan [China Coal Research Institute, Beijing (China). Mining Design and Research Institute

    2009-09-15

    In order to determine how a roadway withstands a momentum wave and determine the extent of damage to rock surrounding the roadway under different force wave peak impacts, the roadway dynamic response state was analysed using numerical simulation method. The roadway's critical peak force wave and fracture region under dynamic wave action were put forward. It is concluded that the method has practical value to roadway support and rockburst prevention.The article is based on the anaysis of Xinwen Mining Group's geologic condition of Xiezhuang 4-2 mine. 4 refs., 4 figs., 1 tab.

  17. Nanoscale deicing by molecular dynamics simulation

    Science.gov (United States)

    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

  18. Computation simulation of the nonlinear response of suspension bridges

    Energy Technology Data Exchange (ETDEWEB)

    McCallen, D.B.; Astaneh-Asl, A.

    1997-10-01

    Accurate computational simulation of the dynamic response of long- span bridges presents one of the greatest challenges facing the earthquake engineering community The size of these structures, in terms of physical dimensions and number of main load bearing members, makes computational simulation of transient response an arduous task. Discretization of a large bridge with general purpose finite element software often results in a computational model of such size that excessive computational effort is required for three dimensional nonlinear analyses. The aim of the current study was the development of efficient, computationally based methodologies for the nonlinear analysis of cable supported bridge systems which would allow accurate characterization of a bridge with a relatively small number of degrees of freedom. This work has lead to the development of a special purpose software program for the nonlinear analysis of cable supported bridges and the methodologies and software are described and illustrated in this paper.

  19. Dynamic epigenetic responses to muscle contraction

    DEFF Research Database (Denmark)

    Rasmussen, Morten; Zierath, Juleen R; Barrès, Romain

    2014-01-01

    Skeletal muscle is a malleable organ that responds to a single acute exercise bout by inducing the expression of genes involved in structural, metabolic and functional adaptations. Several epigenetic mechanisms including histone H4 deacetylation and loss of promoter methylation have been implicated...... in modifying exercise-responsive gene expression. These transient changes suggest that epigenetic mechanisms are not restricted to early stages of human development but are broad dynamic controllers of genomic plasticity in response to environmental factors....

  20. Simulating Silicon Photomultiplier Response to Scintillation Light

    Science.gov (United States)

    Jha, Abhinav K.; van Dam, Herman T.; Kupinski, Matthew A.; Clarkson, Eric

    2015-01-01

    The response of a Silicon Photomultiplier (SiPM) to optical signals is affected by many factors including photon-detection efficiency, recovery time, gain, optical crosstalk, afterpulsing, dark count, and detector dead time. Many of these parameters vary with overvoltage and temperature. When used to detect scintillation light, there is a complicated non-linear relationship between the incident light and the response of the SiPM. In this paper, we propose a combined discrete-time discrete-event Monte Carlo (MC) model to simulate SiPM response to scintillation light pulses. Our MC model accounts for all relevant aspects of the SiPM response, some of which were not accounted for in the previous models. We also derive and validate analytic expressions for the single-photoelectron response of the SiPM and the voltage drop across the quenching resistance in the SiPM microcell. These analytic expressions consider the effect of all the circuit elements in the SiPM and accurately simulate the time-variation in overvoltage across the microcells of the SiPM. Consequently, our MC model is able to incorporate the variation of the different SiPM parameters with varying overvoltage. The MC model is compared with measurements on SiPM-based scintillation detectors and with some cases for which the response is known a priori. The model is also used to study the variation in SiPM behavior with SiPM-circuit parameter variations and to predict the response of a SiPM-based detector to various scintillators. PMID:26236040

  1. Dynamics Modeling of Heavy Special Driving Simulator

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Based on the dynamical characteristic parameters of the real vehicle, the modeling approach and procedure of dynamics of vehicles are expatiated. The layout of vehicle dynamics is proposed, and the sub-models of the diesel engine, drivetrain system and vehicle multi-body dynamics are introduced. Finally, the running characteristic data of the virtual and real vehicles are compared, which shows that the dynamics model is similar closely to the real vehicle system.

  2. Nanoscale deicing by molecular dynamics simulation.

    Science.gov (United States)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-08-14

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

  3. Annual Report 1999 Environmental Dynamics and Simulation

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. MOLECULAR DYNAMIC SIMULATION OF PEPTIDE POLYELECTROLYTES

    Directory of Open Access Journals (Sweden)

    I. M. Neelov

    2014-07-01

    Full Text Available The paper deals with investigation of the conformational properties of some charged homopolypeptides in dilute aqueous solutions by computer simulation. A method of molecular dynamics for the full-atomic models of polyaspartic acid and polylysine with explicit account of water and counter-ions is used for this purpose. For systems containing these polypeptides we calculated time trajectories and the size, shape, distribution functions and time correlation functions of inertia radius and the distances between the ends of peptide chains. We have also calculated the solvatation characteristics of considered polyelectrolytes. We have found out that polyaspartic acid in dilute aqueous solution has more compact structure and more spherical shape than polylysine. We have shown that these differences are due to different interaction between the polypeptides and water molecules (in particular, the quality and quantity of hydrogen bonds formed by these peptides with water, and the difference in an amount of ion pairs formed by the charged groups of the peptides and counter-ions. The obtained results should be taken into account for elaboration of new products based on the investigated peptides and their usage in various industrial and biomedical applications.

  5. Molecular dynamics simulations of vibrated granular gases.

    Science.gov (United States)

    Barrat, Alain; Trizac, Emmanuel

    2002-11-01

    We present molecular dynamics simulations of monodisperse or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met experimentally, density and temperature fields display heterogeneous profiles in the direction perpendicular to the walls. A general equation of state for an arbitrary mixture of fluidized inelastic hard spheres is derived and successfully tested against numerical data. Single-particle velocity distribution functions with non-Gaussian features are also obtained, and the influence of various parameters (inelasticity coefficients, density, etc.) are analyzed. The validity of a recently proposed random restitution coefficient model is assessed through the study of projected collisions onto the direction perpendicular to that of energy injection. For the binary mixture, the nonequipartition of translational kinetic energy is studied and compared both to experimental data and to the case of homogeneous energy injection ("stochastic thermostat"). The rescaled velocity distribution functions are found to be very similar for both species.

  6. Expansion techniques for collisionless stellar dynamical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Meiron, Yohai [Kavli Institute for Astronomy and Astrophysics at Peking University, Beijing 100871 (China); Li, Baile; Holley-Bockelmann, Kelly [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States); Spurzem, Rainer, E-mail: ymeiron@pku.edu.cn [National Astronomical Observatories of China, Chinese Academy of Sciences, Beijing 100012 (China)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Concepcion, Ricky James [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Elliott, Ryan Thomas [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    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.

  8. Swimming patterns and dynamics of simulated Escherichia coli bacteria.

    Science.gov (United States)

    Zonia, Laura; Bray, Dennis

    2009-11-06

    A spatially and temporally realistic simulation of Escherichia coli chemotaxis was used to investigate the swimming patterns of wild-type and mutant bacteria within a rectangular arena in response to chemoattractant gradients. Swimming dynamics were analysed during long time series with phase-space trajectories, power spectra and estimations of fractal dimensions (FDs). Cell movement displayed complex trajectories in the phase space owing to interaction of multiple attractors that captured runs and tumbles. Deletion of enzymes responsible for adaptation (CheR and CheB) restricted the pattern of bacterial swimming in the absence of a gradient. In the presence of a gradient, there was a strong increase in trajectories arising from runs and attenuation of those arising from tumbles. Similar dynamics were observed for mutants lacking CheY, which are unable to tumble. The deletion of CheR, CheB and CheY also caused significant shifts in chemotaxis spectral frequencies. Rescaled range analysis and estimation of FD suggest that wild-type bacteria display characteristics of fractional Brownian motion with positive correlation between past and future events. These results reveal an underlying order in bacterial swimming dynamics, which enables a chemotactic search strategy conforming to a fractal walk.

  9. 汽车炸弹作用下球罐动力学响应的模拟研究%Simulation Research on Dynamic Response of Speherical Tank Effected on Car Bomb

    Institute of Scientific and Technical Information of China (English)

    冯伟涛; 方向; 谢立军; 刘金川; 陈刊

    2011-01-01

    The numerical simulation on dynamic response of spherical tank effeeted on the car bomb was researched. The ANSYS/LS-DYNA software was used to calculate the relationship among equivalent stress, dispalcement and time on a 5 000 m butylene spherical tank body when a 1 600 kg TNT car bomb exploded. The simulation results show that the metamorphosis of the spherical tank happens earlier and the effective stress and displacement is bigger when the spherical tank closer to the explosion center,then the damage on tank body is more obvious. So,on the effect of the car bombs, the partial damage is very likely to happen on the spherical tank, therefore, it is necessary to adopt some protection measures mound the spherical tanks.%针对球形储罐在汽车炸弹作用下的动力学响应进行了数值模拟研究.采用ANSYS/LS-DYNA软件模拟计算了装药量为1 600 kg TNT汽车炸弹爆炸后在1 m、5 m和10 m距离内5000m3丁烯球罐罐体上的等效应力和位移随时间的变化关系.模拟结果表明,炸药边界距离球罐距离越近,罐体发生变形的时间越早,观察点的应力和位移值越大,汽车炸弹对罐体的破坏作用越明显.因此,在汽车炸弹作用下,球罐极有可能发生局部破坏,有必要在罐区周围采取一定的防护措施.

  10. How Dynamic Consumer Response, Competitor Response, Company Support, and Company Inertia Shape Long-Term Marketing Effectiveness

    OpenAIRE

    Koen Pauwels

    2004-01-01

    Long-term marketing effectiveness is a high-priority research topic for managers, and emerges from the complex interplay among dynamic reactions of several market players. This paper introduces restricted policy simulations to distinguish four dynamic forces: consumer response, competitor response, company inertia, and company support. A rich marketing dataset allows the analysis of price, display, feature, advertising, and product-line extensions. The first finding is that consumer response ...

  11. Experiences on dynamic simulation software in chemical engineering education

    DEFF Research Database (Denmark)

    Komulainen, Tiina M.; Enemark-rasmussen, Rasmus; Sin, Gürkan

    2012-01-01

    Commercial process simulators are increasing interest in the chemical engineer education. In this paper, the use of commercial dynamic simulation software, D-SPICE® and K-Spice®, for three different chemical engineering courses is described and discussed. The courses cover the following topics......: basic chemical engineering, operability and safety analysis and process control. User experiences from both teachers and students are presented. The benefits of dynamic simulation as an additional teaching tool are discussed and summarized. The experiences confirm that commercial dynamic simulators...

  12. Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence

    OpenAIRE

    Ferenc Jordán; Nerta Gjata; Shu Mei; 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...

  13. Experiences on dynamic simulation software in chemical engineering education

    OpenAIRE

    Komulainen, Tiina M.; Enemark-Rasmussen, Rasmus; Sin, Gürkan; John P Fletcher; Cameron, David

    2012-01-01

    Commercial process simulators are increasing interest in the chemical engineer education. In this paper, the use of commercial dynamic simulation software, D-SPICE® and K-Spice®, for three different chemical engineering courses is described and discussed. The courses cover the following topics: basic chemical engineering, operability and safety analysis and process control. User experiences from both teachers and students are presented. The benefits of dynamic simulation as an additional teac...

  14. 电力需求侧响应利益联动机制的系统动力学模拟%Simulating the electric demand response profit linkage mechanism by system dynamics

    Institute of Scientific and Technical Information of China (English)

    王建军; 李莉; 谭忠富; 牛东晓

    2011-01-01

    Because implementing demand response in China is not conductive for the electric power supply company to recover their costs, it is necessary to establish a profit linkage mechanism for linking the electric power generators' profits and electric power supply companies' loss. This will greatly promote the enthusiasm of electric power supply company. A system dynamics model is established to simulate the effects of this profit linkage mechanism on the whole electric power system. The simulating system divided the demand response profit chain into customer subsystem, electric power grid subsystem and electric power generators subsystem. The internal and external relationship among the relating factors was researched by modeling layer by layer. The simulation results show that if the profit linkage mechanism is designed rationally, demand response will play its largest role, and all the related bodies in the electric power system will be benefited, the electric power generators should also actively support this mechanism, for their negative response will not only hurt other bodies, but also hurt themselves.%考虑到在我国实施需求侧响应可能使得电网企业不能有效回收需求侧响应的成本,且由于发电公司实际上是需求侧响应的最大受益者,因此需要在电网企业和发电公司之间建立一个利益联动机制.运用系统动力学模型模拟发电公司和电网公司联动的行为对电力系统产生的效果,来证明这种利益联动机制存在的必要性.模拟系统将需求侧响应的利益链条分为用户子系统、电网子系统和发电子系统三个部分,通过层层建模剖析了各子系统内部和外部影响因素之间的关系.以某市电网的基础数据为例进行模型,模拟结果表明,如果设计合理,需求侧响应将为整个电力系统带来巨大的效益,而且发电公司应该积极参与到该机制中,因为他们的消极对待不仅会给其它主体带来不利影响,

  15. Dynamic Response of Flexible Wind Turbine Blade

    Directory of Open Access Journals (Sweden)

    Yu-qiao Zheng

    2013-07-01

    Full Text Available Aiming at the non-stationary and stall flutter problems of wind turbine blade caused by transient load fluctuations, the dynamic properties of wind turbine were studied, the blade was simplify to a cantilever beam in case of the action of shear deformation and cross section rotating effect were considered in this analysis, equations of the blade were established based on D'Alemberts' principle and the principle of virtual displacement. The dynamic response of the wind turbine was solved by using the finite element method under the transient load environment. A 29.2 m rotor blade, previously reported in specialized literature, was chosen as a case study to validate dynamic behaviour predicted by a Timoshenko beam model. It is concluded that despite its simplicity, The cross-sectional shear-deformation  has great influence on  dynamic response of the blade.Dynamic model is sufficiently accurate to serve as a design tool for the recursive analyses required during design and optimization stages of wind turbines using only readily available computational tools.

  16. Dynamic-tensile-extrusion response of fluoropolymers

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Eric N [Los Alamos National Laboratory; Trujillo, Carl P [Los Alamos National Laboratory; Gray, George T [Los Alamos National Laboratory

    2009-01-01

    The current work applies the recently developed Dynamic-Tensile-Extrusion (Dyn-Ten-Ext) technique to polytetrafluoroethylene (PTFE) and polychlorotrifluoroethylene (PCTFE). Similar to the Taylor Impact Rod, Dynamic-Tensile-Extrusion is a strongly integrated test, probing a wide range of strain rates and stress states. However, the stress state is primarily tensile enabling investigation of dynamic tensile failure modes. Here we investigate the influence of this propensity to neck or not between PCTFE and PTFE on their response under dynamic tensile extrusion loading. The results of the Dyn-Ten-Ext technique are compared with two classic techniques. Both polymers have been investigated using Tensile Split Hopkinson Pressure Bar. The quasistatic and dynamic responses of both fluoro-polymers have been extensively characterized. The two polymers exhibit significantly different failure behavior under tensile loading at moderate strain rates. Polytetrafluoroethylene resists formation of a neck and exhibits significant strain hardening. Independent of temperature or strain rate, PTFE sustains true strains to failure of approximately 1.5. Polychlorotrifluoroethylene, on the other hand, consistently necks at true strains of approximately 0.05.

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

    Science.gov (United States)

    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…

  18. Simulations of boundary migration during recrystallization using molecular dynamics

    DEFF Research Database (Denmark)

    Godiksen, Rasmus Brauner; Trautt, Z.T.; Upmanyu, M.

    2007-01-01

    We have applied an atomistic simulation methodology based on molecular dynamics to study grain boundary migration in crystalline materials, driven by the excess energy of dislocation arrangements. This method is used to simulate recrystallization in metals. The simulations reveal that the migration...

  19. Weak simulated extratropical responses to complete tropical deforestation

    Science.gov (United States)

    Findell, K.L.; Knutson, T.R.; Milly, P.C.D.

    2006-01-01

    The Geophysical Fluid Dynamics Laboratory atmosphere-land model version 2 (AM2/LM2) coupled to a 50-m-thick slab ocean model has been used to investigate remote responses to tropical deforestation. Magnitudes and significance of differences between a control run and a deforested run are assessed through comparisons of 50-yr time series, accounting for autocorrelation and field significance. Complete conversion of the broadleaf evergreen forests of South America, central Africa, and the islands of Oceania to grasslands leads to highly significant local responses. In addition, a broad but mild warming is seen throughout the tropical troposphere (deforested run and the control run are similar in magnitude and area to the differences between nonoverlapping segments of the control run. These simulations suggest that extratropical responses to complete tropical deforestation are unlikely to be distinguishable from natural climate variability.

  20. Mathematical Modeling Social Responsibility for Dynamic Organizations

    Directory of Open Access Journals (Sweden)

    Farzaneh Chavoshbashi

    2012-03-01

    Full Text Available Dynamic organizations as accountable organizations, for transparency and accountability to its stakeholders to stakeholders for their toward performance there should express their commitment to social responsibility are through their values and ensure that this commitment throughout the organization are now and thus will have a social responsibility for their mutual benefit, so there is more and more coherent in their ethical approach takes advantage and the community and stakeholders and the organization will have better performance and strengths. Because of interest in social responsibility, in this paper dynamic model is presented for Corporate Social Responsibility of Bionic organization. Model presented a new model is inspired by chaos theory and natural systems theory based on bifurcation in creation to be all natural systems, realizing the value of responsibility as one of the fundamental values of social and institutional development that the relationship between business and work environment in the global market economy and range will be specified. First Social Responsibility factors identified, then experts and scholars determine the weight of the components and technical coefficient for modeling and paired comparison has been done using MATLAB mathematical Software.

  1. A Dynamic Remote Sensing Data-Driven Approach for Oil Spill Simulation in the Sea

    Directory of Open Access Journals (Sweden)

    Jining Yan

    2015-05-01

    Full Text Available In view of the fact that oil spill remote sensing could only generate the oil slick information at a specific time and that traditional oil spill simulation models were not designed to deal with dynamic conditions, a dynamic data-driven application system (DDDAS was introduced. The DDDAS entails both the ability to incorporate additional data into an executing application and, in reverse, the ability of applications to dynamically steer the measurement process. Based on the DDDAS, combing a remote sensor system that detects oil spills with a numerical simulation, an integrated data processing, analysis, forecasting and emergency response system was established. Once an oil spill accident occurs, the DDDAS-based oil spill model receives information about the oil slick extracted from the dynamic remote sensor data in the simulation. Through comparison, information fusion and feedback updates, continuous and more precise oil spill simulation results can be obtained. Then, the simulation results can provide help for disaster control and clean-up. The Penglai, Xingang and Suizhong oil spill results showed our simulation model could increase the prediction accuracy and reduce the error caused by empirical parameters in existing simulation systems. Therefore, the DDDAS-based detection and simulation system can effectively improve oil spill simulation and diffusion forecasting, as well as provide decision-making information and technical support for emergency responses to oil spills.

  2. Effect of the Longitudinal Contact Location on Vehicle Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    N. Burgelman

    2016-01-01

    Full Text Available This paper investigates the effect of the calculation of the longitudinal location of a wheel rail contact point on the wheelset’s motion in a vehicle dynamic simulation. All current vehicle dynamic software programs assume that the contact between wheel and rail takes place in the vertical plane through the wheelset’s rolling axis. However, when the yaw angle of the wheelset is nonzero, the contact point is situated up to 10 mm from that plane. This difference causes a difference in the yaw moment on the wheelset which is used in the vehicle dynamic simulation. To such an end, an existing analytical method to determine the longitudinal method was validated using a numerical approach. Then vehicle dynamic simulations with both the classic and the new contact location were performed, concluding that using a more accurate contact point location results in a smaller wheelset yaw angle in a vehicle dynamic simulation, although the effect is small.

  3. Anomalous Dynamical Responses in a Driven System

    CERN Document Server

    Dutta, Suman

    2016-01-01

    The interplay between structure and dynamics in non-equilibrium steady-state is far from understood. We address this interplay by tracking Brownian Dynamics trajectories of particles in a binary colloid of opposite charges in an external electric field, undergoing cross-over from homogeneous to lane state, a prototype of heterogeneous structure formation in non-equilibrium systems. We show that the length scale of structural correlations controls heterogeneity in diffusion and consequent anomalous dynamic responses, like the exponential tail in probability distributions of particle displacements and stretched exponential structural relaxation. We generalise our observations using equations for steady state density which may aid to understand microscopic basis of heterogeneous diffusion in condensed matter systems.

  4. Two Dynamic Discrete Choice Estimation Problems and Simulation Method Solutions

    OpenAIRE

    Steven Stern

    1994-01-01

    This paper considers two problems that frequently arise in dynamic discrete choice problems but have not received much attention with regard to simulation methods. The first problem is how to simulate unbiased simulators of probabilities conditional on past history. The second is simulating a discrete transition probability model when the underlying dependent variable is really continuous. Both methods work well relative to reasonable alternatives in the application discussed. However, in bot...

  5. Dynamic lateral response of suction caissons

    DEFF Research Database (Denmark)

    Latini, Chiara; Zania, Varvara

    2017-01-01

    Deeper water installations of offshore wind turbines may be supported by jacket structures. This study investigates the dynamic response of suction caissons for jackets by analysing 3D finite element models in the frequency domain. The numerical modelling was firstly validated by analytical...... solutions for pile foundations. Groups of crucial dimensionless parameters related to the soil profile and the foundation geometry are identified and their effects on the response of suction caissons are studied. Static stiffness coefficients are presented in a form of mathematical formulas obtained...... by fitting the numerical results, pertaining foundations with different slenderness ratios and embedded in different soil profiles. Sensitivity of the dynamic impedances of suction caissons on the skirt length was showed in this study. Moreover, the results for the suction caissons indicated that the overall...

  6. Dynamic response of visco-elastic plates

    Science.gov (United States)

    Kadıoǧlu, Fethi; Tekin, Gülçin

    2016-12-01

    In this study, a comprehensive analysis about the dynamic response characteristics of visco-elastic plates is given. To construct the functional in the Laplace-Carson domain for the analysis of visco-elastic plates based on the Kirchhoff hypothesis, functional analysis method is employed. By using this new energy functional in the Laplace-Carson domain, moment values that are important for engineers can be obtained directly with excellent accuracy and element equations can be written explicitly. Three-element model is considered for modelling the visco-elastic material behavior. The solutions obtained in the Laplace-Carson domain by utilizing mixed finite element formulation are transformed to the time domain using the Durbin's inverse Laplace transform technique. The proposed mixed finite element formulation is shown to be simple to implement and gives satisfactory results for dynamic response of visco-elastic plates.

  7. Dynamic Deformation of Thermosetting Polymers---All Atomistic Simulations

    Science.gov (United States)

    Tsige, Mesfin; Shenogina, Natalia; Mukhopadhyay, Sharmila; Patnaik, Soumya

    2013-03-01

    We are using all-atom molecular dynamics simulations to investigate the interconnection between structural and mechanical properties of highly cross-linked polymer networks. In this study we focused on the widely used resin-hardener system composed of DGEBA epoxy oligomers and aromatic amine hardener DETDA. Accurate cross-linked models were developed using the effective cross-linking procedure that enables to generate thermoset structures with realistic structural characteristics. These models were used to examine the elastic properties of thermosetting networks with various degrees of curing and length of resin strands both in glassy and rubbery states. In our recent study we employed static deformation approach to estimate potential energy contribution to the mechanical response. In the present work we are using dynamic deformation approach which takes into account both potential energy and thermal motions in the structure. Uniaxial, volumetric and shear dynamic deformation modes were used to obtain Young's, bulk, shear moduli and Poisson's ratio directly. We also calculated elastic constants using formulae of linear elasticity and analyzed the results obtained by direct deformation and interconversion methods. The elastic properties determined from these two approaches are in good agreement with each other and also with experimental data.

  8. Quasimolecular Dynamic Simulation for Bending Fracture of Laminar Composite Materials

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Recently, quasimolecular dynamics has been successfully used to simulate the deformation characteristics of actual size solid materials. In quasimolecular dynamics, which is an attempt to bridge the gap between atomistic and continuum simulations, molecules are aggregated into large units, called quasimolecules, to evaluate large scale material behavior. In this paper, a 2-dimensional numerical simulation using quasimolecular dynamics was performed to investigate laminar composite material fractures and crack propagation behavior in the uniform bending of laminar composite materials. It was verified that under bending deformation laminar composite materials deform quite differently from homogeneous materials

  9. Numerical Simulation of Blasting Dynamic Response of Small Spacing Tunnel Expansion%小净距隧道扩建爆破动力响应数值模拟方法研究

    Institute of Scientific and Technical Information of China (English)

    李秀地; 蒋树屏; 刘元雪; 黄伦海

    2014-01-01

    With the rapid economic development in China,an increasing number of highway tun-nels require reconstruction and expansion because the road traffic volume is increasing exponen-tially.The original Damaoshan highway tunnel is a separated four-lane expressway located be-tween Fuzhou city and Xiamen city,Fujian province,southeastern China.The expansion scheme of this tunnel includes new construction of a four-lane tunnel between the original two tunnels and expansion of the right-hand original tunnel into a four-lane structure.Thus,the expanded Damaos-han highway tunnel will comprise a series of closely spaced tunnels.The newly constructed four-lane tunnel,22 m long and 255 m2 wide,will be merely 5.89 m from the original tunnel.Moreo-ver,the structure safety of the nearby original tunnel must be ensured to maintain effective traffic flow during the explosions for the construction of the new tunnel.Thus,the blasting vibration must be strictly controlled.In this study,semi-empirical theory and direct initiation method are used to determine blasting loads in numerical simulation of blasting dynamic response.With the project background of the first application of the Damaoshan highway four-lane tunnel expansion, a numerical analysis model is established using LS-DYNA3D software from the direct initiation of explosives to simulate blasting effects on an adjacent operation tunnel.The numerical analysis model is based on a multi-material unit and fluid-structure interaction technique to simulate the explosive detonation and the dynamic response of the nearby structure,respectively.The element type is SOLID1 64,and the non-reflected boundary condition is used.Influences of the rock calcula-tion range,mesh size,material hardening condition,and failure strain on the numerical simulation are analyzed.The rock failure strain value in this study is obtained by comparing the explosive cavity radius between the numerical simulation and experience formula.The simulation results show

  10. Dynamic response analysis of DFB fibre lasers

    DEFF Research Database (Denmark)

    Yujun, Qian; Varming, Poul; Povlsen, Jørn Hedegaard

    1998-01-01

    We present a model for relative intensity noise (RIN) in DFB fibre lasers which predicts measured characteristics accurately. Calculation results implies that the RIN decreases rapidly with stronger Bragg grating and higher pump power. We propose here a simplified model based on three spatially...... independent rate equations to describe the dynamic response of erbium doped DFB fibre lasers on pump power fluctuations, using coupled-mode theory to calculate the steady-state hole-burning of the erbium ion inversion...

  11. Dynamic fault simulation of wind turbines using commercial simulation tools

    DEFF Research Database (Denmark)

    Lund, Torsten; Eek, Jarle; Uski, Sanna

    2005-01-01

    . The deviations and the reasons for the deviations between the tools are stated. The simulation models are imple-mented using the built-in library components of the simulation tools with exception of the mechanical drive-train model, which had to be user-modeled in PowerFactory and PSS/E.......This paper compares the commercial simulation tools: PSCAD/EMTDC, PowerFactory, SIMPOW and PSS/E for analysing fault sequences defined in the Danish grid code requirements for wind turbines connected to a voltage level below 100 kV. Both symmetrical and unsymmetrical faults are analysed...

  12. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    Science.gov (United States)

    Radak, Brian K.; Roux, Benoît

    2016-10-01

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Finally, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.

  13. Hypervelocity impact properties of graphene armor via molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Wang W.

    2012-08-01

    Full Text Available Hypervelocity impact properties of two different graphene armor systems are investigated using molecular dynamics simulations. One system is the so-called spaced armor which consists of a number of graphene plates spaced certain distance apart. Its response under normal impact of a spherical projectile is studied, focusing on the effect of the number of graphene monolayers per plate (denoted by n on the penetration resistance of the armor. We find that under normal impact by a spherical projectile the penetration resistance increases with decreasing number of monolayers per plate (n, and the best penetration resistance is achieved in the system with one graphene layer for each plate. Note that the monolayers in all the simulated multilayer graphene plates were AB-stacked. The second system being studied is the laminated copper/graphene composites with the graphene layers inside copper, on impact or back surface, or on both the impact and back surfaces. The simulation results show that under normal impact by a spherical projectile the laminated copper/graphene composite has much higher penetration resistance than the monolithic copper plate. The best efficiency is achieved when the graphene layers are on both the impact and back surfaces.

  14. A Study on Dynamic Response of Cable-Seabed Interaction

    Institute of Scientific and Technical Information of China (English)

    WANG Fei; HUANG Guo-liang; DENG De-heng; TU Xing-hua

    2009-01-01

    A numerical method is developed to investigate the dynamic response of cable-seabed interaction in this paper. The motion of cable is described by the Lumped Parameter Method, while the seabed, unlike the prevailing simplified model of elastic foundation, is modeled as an irregular continuous rigid surface with rebound and friction existing, and the forces exerted by the seabed consist of normal counterforce and isotropic tangential Coulomb friction resistance. To describe the detailed dynamic response, two coefficients are introduced by analogy with the theory of rigid body collision with friction. The cable-seabed kinematic and dynamic contact conditions are formulated subsequently, and are used to incorporate the seabed effect into the cable dynamics to produce a set of ordinary differential governing equations. In this paper, we employ 4th order Runge-Kutta method to solve these equations. Several simulation cases are presented to illustrate the seabed effect. The results show that friction and impact have a prominent influence on the statics and dynamics of the cable.

  15. Kinematics and dynamics analysis of a novel serial-parallel dynamic simulator

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Bo; Zhang, Lian Dong; Yu, Jingjing [Parallel Robot and Mechatronic System Laboratory of Hebei Province, Yanshan University, Qinhuangdao, Hebei (China)

    2016-11-15

    A serial-parallel dynamics simulator based on serial-parallel manipulator is proposed. According to the dynamics simulator motion requirement, the proposed serial-parallel dynamics simulator formed by 3-RRS (active revolute joint-revolute joint-spherical joint) and 3-SPR (Spherical joint-active prismatic joint-revolute joint) PMs adopts the outer and inner layout. By integrating the kinematics, constraint and coupling information of the 3-RRS and 3-SPR PMs into the serial-parallel manipulator, the inverse Jacobian matrix, velocity, and acceleration of the serial-parallel dynamics simulator are studied. Based on the principle of virtual work and the kinematics model, the inverse dynamic model is established. Finally, the workspace of the (3-RRS)+(3-SPR) dynamics simulator is constructed.

  16. Rare event simulation for dynamic fault trees

    NARCIS (Netherlands)

    Ruijters, Enno Jozef Johannes; Reijsbergen, D.P.; de Boer, Pieter-Tjerk; Stoelinga, Mariëlle Ida Antoinette

    2017-01-01

    Fault trees (FT) are a popular industrial method for reliability engineering, for which Monte Carlo simulation is an important technique to estimate common dependability metrics, such as the system reliability and availability. A severe drawback of Monte Carlo simulation is that the number of

  17. Coarse-grained molecular dynamics simulations of biomolecules

    Directory of Open Access Journals (Sweden)

    Ken Takahashi

    2014-03-01

    Full Text Available Coarse-grained molecular dynamics (CGMD simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.

  18. Mosquito population dynamics from cellular automata-based simulation

    Science.gov (United States)

    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.

  19. Dynamic response of flexible retaining walls

    Energy Technology Data Exchange (ETDEWEB)

    Younan, A.H.; Veletsos, A.S.; Bandyopadhyay, K.

    1997-01-01

    Making use of an extension of a recently proposed, relatively simple, approximate method of analysis, a critical evaluation is made of the response to horizontal ground shaking of flexible walls retaining a uniform, linear, viscoelastic stratum of constant thickness and semiinfinite extent in the horizontal direction. Both cantilever and top-supported walls are examined. Following a detailed description of the method and of its rate of convergence, comprehensive numerical solutions are presented that elucidate the action of the system and the effects of the various parameters involved. The parameters varied include the flexibility of the wall, the condition of top support, and the characteristics of the ground motion. The effects of both harmonic base motions and an actual earthquake record are examined. Special attention is paid to the effects of long-period, effectively static excitations. A maximum dynamic response is then expressed as the product of the corresponding static response and an appropriate amplification or deamplification factor. The response quantities examined include the displacements of the wall relative to the moving base, the dynamic wall pressures, and the total wall force, base shear and base moment.

  20. Unified Nonlinear Flight Dynamics and Aeroelastic Simulator Tool Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology, Inc. (ZONA) proposes a R&D effort to develop a Unified Nonlinear Flight Dynamics and Aeroelastic Simulator (UNFDAS) Tool that will combine...

  1. The framework for simulation of dynamics of mechanical aggregates

    OpenAIRE

    Ivankov, Petr R.; Ivankov, Nikolay P.

    2007-01-01

    A framework for simulation of dynamics of mechanical aggregates has been developed. This framework enables us to build model of aggregate from models of its parts. Framework is a part of universal framework for science and engineering.

  2. Molecular Dynamics Simulations and XAFS (MD-XAFS)

    Energy Technology Data Exchange (ETDEWEB)

    Schenter, Gregory K.; Fulton, John L.

    2017-01-20

    MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.

  3. Dynamical simulations of strongly correlated electron materials

    Science.gov (United States)

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

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

  4. Structural optimization for nonlinear dynamic response

    DEFF Research Database (Denmark)

    Dou, Suguang; Strachan, B. Scott; Shaw, Steven W.

    2015-01-01

    condition, thereby providing a means for tailoring its nonlinear response. The method is applied to the fundamental nonlinear resonance of a clamped–clamped beam and to the coupled mode response of a frame structure, and the results show that one can modify essential normal form coefficients by an order...... resonant behaviour is being used for a variety of applications in sensing and signal conditioning. In this work, we describe a computational method that provides a systematic means for manipulating and optimizing features of nonlinear resonant responses of mechanical structures that are described...... by a single vibrating mode, or by a pair of internally resonant modes. The approach combines techniques from nonlinear dynamics, computational mechanics and optimization, and it allows one to relate the geometric and material properties of structural elements to terms in the normal form for a given resonance...

  5. Visual Dynamic Simulation and Optimization of Zhangjiuhe Diversion Project

    Institute of Scientific and Technical Information of China (English)

    ZHONG Denghua; LIU Jianmin; XIONG Kaizhi; FU Jinqiang

    2008-01-01

    With the aim of visualizing the real-time simulation calculation of water delivery system (WDS), a structural drawing-oriented (SDO) simulation technique was presented, and applied to Zhangjiuhe Diversion Project, which is a long-distance water delivery system constructed for drawing water from the Zhangjiuhe River to Kunming city. Taking SIMULINK software as simulating platform, the technique established a visual dynamic simulation model for the system. The simulation procedure of the system was simplified, and the efficiency of modeling was also enhanced according to the modularization and reutilization of the simulation program. Furthermore, a selfoptimization model was presented. Based on the digital simulation models, the on line controlled optimization link was added, and the input data can be continually optimized according to the feedback information of simulating output. The system was thus optimized automatically. Built upon MATLAB software, simulation optimization of the Zhangjiuhe Diversion Project was achieved, which provides a new way for the research of optimal operation of WDS.

  6. Dynamic modelling of an adsorption storage tank using a hybrid approach combining computational fluid dynamics and process simulation

    Science.gov (United States)

    Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.

    2004-01-01

    A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.

  7. Perspective: Computer simulations of long time dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Elber, Ron [Department of Chemistry, The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712 (United States)

    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.

  8. DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results

    Directory of Open Access Journals (Sweden)

    Gizzatkulov Nail M

    2010-08-01

    Full Text Available Abstract Background Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting. Results We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle. Conclusion DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Simulation of capillary flow with a dynamic contact angle

    NARCIS (Netherlands)

    van Mourik, S; Veldman, AEP; Dreyer, ME

    2005-01-01

    A number of theoretical and empirical dynamic contact angle (DCA) models have been tested in a numerical simulation of liquid reorientation in microgravity for which experimental validation data are available. It is observed that the DCA can have a large influence on liquid dynamics in microgravity.

  11. Molecular dynamics simulation of a polysorbate 80 micelle in water

    NARCIS (Netherlands)

    Amani, Amir; York, Peter; de Waard, Hans; Anwar, Jamshed

    2011-01-01

    The structure and dynamics of a single molecule of the nonionic surfactant polysorbate 80 (POE (20) sorbitan monooleate; Tween 80 (R)) as well as a micelle comprising sixty molecules of polysorbate 80 in water have been investigated by molecular dynamics simulation. In its free state in water the po

  12. Simulating market dynamics : Interactions between consumer psychology and social networks

    NARCIS (Netherlands)

    Janssen, MA; Jager, W

    2003-01-01

    Markets can show different types of dynamics, from quiet markets dominated by one or a few products, to markets with continual penetration of new and reintroduced products. in a previous article we explored the dynamics of markets from a psychological perspective using a multi-agent simulation model

  13. Effect of the Longitudinal Contact Location on Vehicle Dynamics Simulation

    NARCIS (Netherlands)

    Burgelman, N.; Li, Z.; Dollevoet, R.

    2016-01-01

    This paper investigates the effect of the calculation of the longitudinal location of a wheel rail contact point on the wheelset’s motion in a vehicle dynamic simulation. All current vehicle dynamic software programs assume that the contact between wheel and rail takes place in the vertical plane th

  14. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  15. Stability of dynamic response of suspension bridges

    Science.gov (United States)

    Capsoni, Antonio; Ardito, Raffaele; Guerrieri, Andrea

    2017-04-01

    The potential occurrence of internal parametric resonance phenomena has been recently indicated as a potential contributory cause of the appearance of critical dynamic states in long-span suspension bridges. At the same time, suspension bridges, in view of their flexibility, are prone to aeroelastic response, such as vortex shedding, torsional divergence and flutter. In this paper, a non-linear dynamic model of a suspension bridge is devised, with the purpose of providing a first attempt toward a unified framework for the study of aeroelastic and internal resonance instabilities. Inspired by the pioneering work of Herrmann and Hauger, the analyses have been based on a linearized formulation that is able to represent the main structural non-linear effects and the coupling given by aerodynamic forces. The results confirm that the interaction between aeroelastic effects and non-linear internal resonance leads to unstable conditions for wind speeds which can be lower than the critical threshold for standard aeroelastic predictions.

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

    Science.gov (United States)

    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.

  17. Food supply and demand, a simulation model of the functional response of grazing ruminants

    NARCIS (Netherlands)

    Smallegange, I.M.; Brunsting, A.M.H.

    2002-01-01

    A dynamic model of the functional response is a first prerequisite to be able to bridge the gap between local feeding ecology and grazing rules that pertain to larger scales. A mechanistic model is presented that simulates the functional response, growth and grazing time of ruminants. It is based on

  18. Food supply and demand, a simulation model of the functional response of grazing ruminants

    NARCIS (Netherlands)

    Smallegange, I.M.; Brunsting, A.M.H.

    2002-01-01

    A dynamic model of the functional response is a first prerequisite to be able to bridge the gap between local feeding ecology and grazing rules that pertain to larger scales. A mechanistic model is presented that simulates the functional response, growth and grazing time of ruminants. It is based on

  19. Speed-accuracy trade-offs in computing spatial impulse responses for simulating medical ultrasound imaging

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt

    2001-01-01

    Medical ultrasound imaging can be simulated realistically using linear acoustics. One of the most powerful approaches is to employ spatial impulse responses. Hereby both emitted fields and pulse-echo responses from point scatterers can be determined. Also any kind of dynamic focusing...

  20. N-body simulations in modified Newtonian dynamics

    Science.gov (United States)

    Nipoti, C.; Londrillo, P.; Ciotti, L.

    2011-01-01

    We describe some results obtained with N-MODY, a code for N-body simulations of collisionless stellar systems in modified Newtonian dynamics (MOND). We found that a few fundamental dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter. In particular, violent relaxation, phase mixing and galaxy merging take significantly longer in MOND than in Newtonian gravity, while dynamical friction is more effective in a MOND system than in an equivalent Newtonian system with dark matter.

  1. Active site modeling in copper azurin molecular dynamics simulations

    NARCIS (Netherlands)

    Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R

    2004-01-01

    Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po

  2. Rotational Brownian Dynamics simulations of clathrin cage formation

    NARCIS (Netherlands)

    Ilie, I.M.; Otter, den W.K.; Briels, W.J.

    2014-01-01

    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 assem

  3. Rotational Brownian Dynamics simulations of clathrin cage formation

    NARCIS (Netherlands)

    Ilie, Ioana Mariuca; den Otter, Wouter K.; Briels, Willem J.

    2014-01-01

    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

  4. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations

    NARCIS (Netherlands)

    De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut

    2011-01-01

    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 c

  5. The use of system dynamics for EROI simulation

    DEFF Research Database (Denmark)

    Atlason, Reynir Smari

    to construct a systems dynamics model to represent a geothermal power plant and calculate the EROI3,i. The benefits of such models are their simplicity, and simulation power. The system simulated is adapted from Atlason et al. (2013) where the EROI for the Nesjavellir geothermal power plant was calculated...

  6. Responses of Haloarchaea to Simulated Microgravity

    Science.gov (United States)

    Dornmayr-Pfaffenhuemer, Marion; Legat, Andrea; Schwimbersky, Karin; Fendrihan, Sergiu; Stan-Lotter, Helga

    2011-04-01

    Various effects of microgravity on prokaryotes have been recognized in recent years, with the focus on studies of pathogenic bacteria. No archaea have been investigated yet with respect to their responses to microgravity. For exposure experiments on spacecrafts or on the International Space Station, halophilic archaea (haloarchaea) are usually embedded in halite, where they accumulate in fluid inclusions. In a liquid environment, these cells will experience microgravity in space, which might influence their viability and survival. Two haloarchaeal strains, Haloferax mediterranei and Halococcus dombrowskii, were grown in simulated microgravity (SMG) with the rotary cell culture system (RCCS, Synthecon). Initially, salt precipitation and detachment of the porous aeration membranes in the RCCS were observed, but they were avoided in the remainder of the experiment by using disposable instead of reusable vessels. Several effects were detected, which were ascribed to growth in SMG: Hfx. mediterranei's resistance to the antibiotics bacitracin, erythromycin, and rifampicin increased markedly; differences in pigmentation and whole cell protein composition (proteome) of both strains were noted; cell aggregation of Hcc. dombrowskii was notably reduced. The results suggest profound effects of SMG on haloarchaeal physiology and cellular processes, some of which were easily observable and measurable. This is the first report of archaeal responses to SMG. The molecular mechanisms of the effects induced by SMG on prokaryotes are largely unknown; haloarchaea could be used as nonpathogenic model systems for their elucidation and in addition could provide information about survival during lithopanspermia (interplanetary transport of microbes inside meteorites).

  7. Fluid dynamics theory, computation, and numerical simulation

    CERN Document Server

    Pozrikidis, C

    2017-01-01

    This book provides an accessible introduction to the basic theory of fluid mechanics and computational fluid dynamics (CFD) from a modern perspective that unifies theory and numerical computation. Methods of scientific computing are introduced alongside with theoretical analysis and MATLAB® codes are presented and discussed for a broad range of topics: from interfacial shapes in hydrostatics, to vortex dynamics, to viscous flow, to turbulent flow, to panel methods for flow past airfoils. The third edition includes new topics, additional examples, solved and unsolved problems, and revised images. It adds more computational algorithms and MATLAB programs. It also incorporates discussion of the latest version of the fluid dynamics software library FDLIB, which is freely available online. FDLIB offers an extensive range of computer codes that demonstrate the implementation of elementary and advanced algorithms and provide an invaluable resource for research, teaching, classroom instruction, and self-study. This ...

  8. Structural optimization for nonlinear dynamic response.

    Science.gov (United States)

    Dou, Suguang; Strachan, B Scott; Shaw, Steven W; Jensen, Jakob S

    2015-09-28

    Much is known about the nonlinear resonant response of mechanical systems, but methods for the systematic design of structures that optimize aspects of these responses have received little attention. Progress in this area is particularly important in the area of micro-systems, where nonlinear resonant behaviour is being used for a variety of applications in sensing and signal conditioning. In this work, we describe a computational method that provides a systematic means for manipulating and optimizing features of nonlinear resonant responses of mechanical structures that are described by a single vibrating mode, or by a pair of internally resonant modes. The approach combines techniques from nonlinear dynamics, computational mechanics and optimization, and it allows one to relate the geometric and material properties of structural elements to terms in the normal form for a given resonance condition, thereby providing a means for tailoring its nonlinear response. The method is applied to the fundamental nonlinear resonance of a clamped-clamped beam and to the coupled mode response of a frame structure, and the results show that one can modify essential normal form coefficients by an order of magnitude by relatively simple changes in the shape of these elements. We expect the proposed approach, and its extensions, to be useful for the design of systems used for fundamental studies of nonlinear behaviour as well as for the development of commercial devices that exploit nonlinear behaviour.

  9. Dynamic Responses of Truss Spar Due to Wave Actions

    Directory of Open Access Journals (Sweden)

    V.J. Kurian

    2013-01-01

    Full Text Available Spar platforms have been used for drilling, production and storage of oil and gas in the offshore deepwater region. The structure is installed at the deepwater locations in the sea and is exposed to continuous action of wind, wave, current and other environmental forces. Wave force constitutes about 70% of the total environmental force and could be considered as the most significant force affecting the dynamic responses needed for the design of these structures. In this study, the dynamic responses of the truss spar due to wave actions including the wave force theories and wave propagation directions are investigated. Numerical simulations are developed to investigate the accuracy of the wave force theories i.e., Morison equation and Diffraction theory, for large structure such as truss spar. The investigation is further expanded to study responses of the truss spar due to variations directions of the wave propagated. The truss spar is modelled as a rigid body with three degrees of freedom restrained by mooring lines. In the simulation, the mass, damping and stiffness matrices are evaluated at every time step. The equations of motion are formulated for the platform dynamic equilibrium and solved by using Newmark Beta method. To compute the wave force for truss spar, which is large compared to the wave length, Diffraction theory was found to be more appropriate. The Morison equation was found applicable only at the high frequency range. Short crested waves resulted in smaller responses in all the motions than that for long crested waves. Hence, it would be appropriate to consider the short crested wave statistics for the optimum design.

  10. Dynamic response of dry and water-saturated sand systems

    Science.gov (United States)

    LaJeunesse, J. W.; Hankin, M.; Kennedy, G. B.; Spaulding, D. K.; Schumaker, M. G.; Neel, C. H.; Borg, J. P.; Stewart, S. T.; Thadhani, N. N.

    2017-07-01

    The effect of grain size and moisture content on the dynamic macroscopic response of granular geological materials was explored by performing uniaxial planar impact experiments on high purity, Oklahoma #1, sand samples composed of either fine (75-150 μm) or coarse (425-500 μm) grain sizes in either dry or fully water-saturated conditions. Oklahoma #1 sand was chosen for its smooth, quasi-spherical grain shapes, narrow grain size distributions, and nearly pure SiO2 composition (99.8 wt. %). The water-saturated samples were completely saturated ensuring a two-phase mixture with roughly 65% sand and 35% water. Sand samples were dynamically loaded to pressures between 1 and 11 GPa. Three-dimensional meso-scale simulations using an Eulerian hydrocode, CTH, were created to model the response of each sand sample. Multi-phase equations of state were used for both silicon dioxide, which comprised individual sand grains, and water, which surrounded individual grains. Particle velocity profiles measured from the rear surface of the sand, both experimentally and computationally, reveal that fine grain samples have steeper rise characteristics than coarse grain samples and water-saturated samples have an overall much stiffer response than dry samples. The experimentally determined particle velocity vs. shock velocity response of dry sand was linear over this pressure range, with little difference between the two grain sizes investigated. The experimental response for the water saturated sand exhibited a piecewise continuous response with a transition region between particle velocities of 0.6 km s-1 and 0.8 km s-1 and a pressure of 4.5-6 GPa. Hypotheses for the cause of this transition region are drawn based on results of the meso-scale simulations.

  11. Reducing ambulance response times using discrete event simulation.

    Science.gov (United States)

    Wei Lam, Sean Shao; Zhang, Zhong Cheng; Oh, Hong Choon; Ng, Yih Ying; Wah, Win; Hock Ong, Marcus Eng

    2014-01-01

    The objectives of this study are to develop a discrete-event simulation (DES) model for the Singapore Emergency Medical Services (EMS), and to demonstrate the utility of this DES model for the evaluation of different policy alternatives to improve ambulance response times. A DES model was developed based on retrospective emergency call data over a continuous 6-month period in Singapore. The main outcome measure is the distribution of response times. The secondary outcome measure is ambulance utilization levels based on unit hour utilization (UHU) ratios. The DES model was used to evaluate different policy options in order to improve the response times, while maintaining reasonable fleet utilization. Three policy alternatives looking at the reallocation of ambulances, the addition of new ambulances, and alternative dispatch policies were evaluated. Modifications of dispatch policy combined with the reallocation of existing ambulances were able to achieve response time performance equivalent to that of adding 10 ambulances. The median (90th percentile) response time was 7.08 minutes (12.69 minutes). Overall, this combined strategy managed to narrow the gap between the ideal and existing response time distribution by 11-13%. Furthermore, the median UHU under this combined strategy was 0.324 with an interquartile range (IQR) of 0.047 versus a median utilization of 0.285 (IQR of 0.051) resulting from the introduction of additional ambulances. Response times were shown to be improved via a more effective reallocation of ambulances and dispatch policy. More importantly, the response time improvements were achieved without a reduction in the utilization levels and additional costs associated with the addition of ambulances. We demonstrated the effective use of DES as a versatile platform to model the dynamic system complexities of Singapore's national EMS systems for the evaluation of operational strategies to improve ambulance response times.

  12. Generator dynamics in aeroelastic analysis and simulations

    DEFF Research Database (Denmark)

    Larsen, Torben J.; Hansen, Morten Hartvig; Iov, F.

    2003-01-01

    This report contains a description of a dynamic model for a doubly-fed induction generator. The model has physical input parameters (voltage, resistance, reactance etc.) and can be used to calculate rotor and stator currents, hence active and reactivepower. A perturbation method has been used...... to reduce the original generator model equations to a set of equations which can be solved with the same time steps as a typical aeroelastic code. The method is used to separate the fast transients of the modelfrom the slow variations and deduce a reduced order expression for the slow part. Dynamic effects...

  13. Long-term dynamics simulation: Modeling requirements

    Energy Technology Data Exchange (ETDEWEB)

    Morched, A.S.; Kar, P.K.; Rogers, G.J.; Morison, G.K. (Ontario Hydro, Toronto, ON (Canada))

    1989-12-01

    This report details the required performance and modelling capabilities of a computer program intended for the study of the long term dynamics of power systems. Following a general introduction which outlines the need for long term dynamic studies, the modelling requirements for the conduct of such studies is discussed in detail. Particular emphasis is placed on models for system elements not normally modelled in power system stability programs, which will have a significant impact in the long term time frame of minutes to hours following the initiating disturbance. The report concludes with a discussion of the special computational and programming requirements for a long term stability program. 43 refs., 36 figs.

  14. Multiscale mathematical modeling and simulation of cellular dynamical process.

    Science.gov (United States)

    Nakaoka, Shinji

    2014-01-01

    Epidermal homeostasis is maintained by dynamic interactions among molecules and cells at different spatiotemporal scales. Mathematical modeling and simulation is expected to provide clear understanding and precise description of multiscaleness in tissue homeostasis under systems perspective. We introduce a stochastic process-based description of multiscale dynamics. Agent-based modeling as a framework of multiscale modeling to achieve consistent integration of definitive subsystems is proposed. A newly developed algorithm that particularly aims to perform stochastic simulations of cellular dynamical process is introduced. Finally we review applications of multiscale modeling and quantitative study to important aspects of epidermal and epithelial homeostasis.

  15. An attempt toward the generalized Langevin dynamics simulation

    Directory of Open Access Journals (Sweden)

    B.Kim

    2008-03-01

    Full Text Available An attempt to generalize the Langevin dynamics simulation method is presented based on the generalized Langevin theory of liquids, in which the dynamics of both solute and solvent is treated by the generalized Langevin equations, but the integration of the equation of motion of solute is made in the manner similar to the ordinary molecular dynamics simulation with discretized time steps along a trajectory. A preliminary result is derived based on an assumption of the uniform solvent density. The result is regarded to be a microscopic generalization of the phenomenological Langevin theory for the harmonic oscillator immersed in a continuum solvent developed by Wang and Uhlenbeck.

  16. Modular simulation of reefer container dynamics

    DEFF Research Database (Denmark)

    Sørensen, Kresten Kjær; Nielsen, Jens Frederik Dalsgaard; Stoustrup, Jakob

    2014-01-01

    The amount of food transported long distances in reefer containers is constantly increasing and so is the cost per mile because of rising fuel prices. One way to reduce the cost is to minimize the energy consumed by reefer containers through a better controller but in order to achieve this a fast...... and flexible simulation model is needed for controller development. The simulation model may also be used for developing fault diagnosis methods for the reefer container and thereby further lowering costs by reducing the amount of functioning spare parts that is replaced and by providing early warning...... that ensures numerical stability and that the error is bounded using a minimum of calculations. The reefer container model is simulated using both ode15s and the proposed method both in multi-rate and monolithic configurations. The results are analyzed and compared with respect to speed and accuracy....

  17. Dynamic modeling and simulation of power transformer maintenance costs

    Directory of Open Access Journals (Sweden)

    Ristić Olga

    2016-01-01

    Full Text Available The paper presents the dynamic model of maintenance costs of the power transformer functional components. Reliability is modeled combining the exponential and Weibull's distribution. The simulation was performed with the aim of corrective maintenance and installation of the continuous monitoring system of the most critical components. Simulation Dynamic System (SDS method and VENSIM PLE software was used to simulate the cost. In this way, significant savings in maintenance costs will be achieved with a small initial investment. [Projekat Ministarstva nauke Republike Srbije, br. III 41025 i br. OI 171007

  18. Dynamic Modeling and Simulation of a Commercial Naphtha Catalytic Reforming Process

    Institute of Scientific and Technical Information of China (English)

    胡永有; 徐巍华; 侯卫锋; 苏宏业; 褚健

    2005-01-01

    A first principles-based dynamic model for a continuous catalyst regeneration (CCR) platforming process, the UOP commercial naphtha catalytic reforming process, is developed in this paper. The lumping details of the naphtha feed and reaction scheme of the reaction model are given. The process model is composed of the reforming reaction model with catalyst deactivation, the furnace model and the separator model, which is capable of capturing the major dynamics that occurs in this process system. Dynamic simulations are performed based on Gear numerical algorithm and method of lines (MOL), a numerical technique dealing with partial differential equations (PDEs). The results of simulation are also presented. Dynamic responses caused by disturbances in the process system can be correctly predicted through simulations.

  19. Probing Cellular Dynamics with Mesoscopic Simulations

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2010-01-01

    . But these models struggle to represent processes that are localized in space and time or involve the transport of material through a crowded environment. A novel class of mesoscopic simulation techniques are now able to span length and time scales from nanometers to microns for hundreds of microseconds, and may......-based simulation techniques cannot capture such a broad range. Consequently, at long length scales, models have often been of the Mass Action variety, in which molecular constituents are represented by density fields that vary continuously in space and time, rather than involving discrete molecules...

  20. Simulation of dynamic behavior in bubbling fluidization

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Both the behavior of bubbles in the distributor with several orifices and the sensitive dependence of bubbling fluidization on initial condition have been simulated by particle-motion-resolved discrete model in which the gas flow is obtained by solving the Navier-Stokes equation including two-phase interaction, and the motion of solid phase is obtained by decomposing the motion of each particle into collision process and suspension process. Compared with the pseudo-fluid models and previous discrete models, this model is authentic and can be widely used for simulating bubbling fluidization.

  1. Topology in dynamical lattice QCD simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gruber, Florian

    2012-08-20

    Lattice simulations of Quantum Chromodynamics (QCD), the quantum field theory which describes the interaction between quarks and gluons, have reached a point were contact to experimental data can be made. The underlying mechanisms, like chiral symmetry breaking or the confinement of quarks, are however still not understood. This thesis focuses on topological structures in the QCD vacuum. Those are not only mathematically interesting but also closely related to chiral symmetry and confinement. We consider methods to identify these objects in lattice QCD simulations. Based on this, we explore the structures resulting from different discretizations and investigate the effect of a very strong electromagnetic field on the QCD vacuum.

  2. Computer simulation of multiple dynamic photorefractive gratings

    DEFF Research Database (Denmark)

    Buchhave, Preben

    1998-01-01

    The benefits of a direct visualization of space-charge grating buildup are described. The visualization is carried out by a simple repetitive computer program, which simulates the basic processes in the band-transport model and displays the result graphically or in the form of numerical data. The....... The simulation sheds light on issues that are not amenable to analytical solutions, such as the spectral content of the wave forms, cross talk in three-beam interaction, and the range of applications of the band-transport model. (C) 1998 Optical Society of America....

  3. Path-integral molecular dynamics simulation of diamond

    Science.gov (United States)

    Ramírez, Rafael; Herrero, Carlos P.; Hernández, Eduardo R.

    2006-06-01

    Diamond is studied by path-integral molecular dynamics simulations of the atomic nuclei in combination with a tight-binding Hamiltonian to describe its electronic structure and total energy. This approach allows us to quantify the influence of quantum zero-point vibrations and finite temperatures on both the electronic and vibrational properties of diamond. The electron-phonon coupling mediated by the zero-point vibration reduces the direct electronic gap of diamond by 10%. The calculated decrease of the direct gap with temperature shows good agreement with the experimental data available up to 700K . Anharmonic vibrational frequencies of the crystal have been obtained from a linear-response approach based on the path integral formalism. In particular, the temperature dependence of the zone-center optical phonon has been derived from the simulations. The anharmonicity of the interatomic potential produces a red shift of this phonon frequency. At temperatures above 500K , this shift is overestimated in comparison to available experimental data. The predicted temperature shift of the elastic constant c44 displays reasonable agreement with the available experimental results.

  4. Ensemble simulations with discrete classical dynamics

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2013-01-01

    For discrete classical Molecular dynamics (MD) obtained by the "Verlet" algorithm (VA) with the time increment $h$ there exist a shadow Hamiltonian $\\tilde{H}$ with energy $\\tilde{E}(h)$, for which the discrete particle positions lie on the analytic trajectories for $\\tilde{H}$. $\\tilde...

  5. NVU dynamics. III. Simulating molecules at constant potential energy

    DEFF Research Database (Denmark)

    Ingebrigtsen, Trond; Dyre, J. C.

    2012-01-01

    This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B....... In this paper, the NVU algorithm for atomic systems is extended to be able to simulate the geodesic motion of molecules at constant potential energy. We derive an algorithm for simulating rigid bonds and test this algorithm on three different systems: an asymmetric dumbbell model, Lewis-Wahnström o......-terphenyl (OTP) and rigid SPC/E water. The rigid bonds introduce additional constraints beyond that of constant potential energy for atomic systems. The rigid-bond NVU algorithm conserves potential energy, bond lengths, and step length for indefinitely long runs. The quantities probed in simulations give results...

  6. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-06

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  7. Molecular Dynamics Simulation of Amyloid Beta Dimer Formation

    CERN Document Server

    Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V

    2004-01-01

    Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...

  8. Simulations of Energetic Particles Interacting with Dynamical Magnetic Turbulence

    Science.gov (United States)

    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.

  9. Studies of climate dynamics with innovative global-model simulations

    Science.gov (United States)

    Shi, Xiaoming

    Climate simulations with different degrees of idealization are essential for the development of our understanding of the climate system. Studies in this dissertation employ carefully designed global-model simulations for the goal of gaining theoretical and conceptual insights into some problems of climate dynamics. Firstly, global warming-induced changes in extreme precipitation are investigated using a global climate model with idealized geography. The precipitation changes over an idealized north-south mid-latitude mountain barrier at the western margin of an otherwise flat continent are studied. The intensity of the 40 most intense events on the western slopes increases by about ~4°C of surface warming. In contrast, the intensity of the top 40 events on the eastern mountain slopes increases at about ~6°C. This higher sensitivity is due to enhanced ascent during the eastern-slope events, which can be explained in terms of linear mountain-wave theory relating to global warming-induced changes in the upper-tropospheric static stability and the tropopause level. Dominated by different dynamical factors, changes in the intensity of extreme precipitation events over plains and oceans might differ from changes over mountains. So the response of extreme precipitation over mountains and flat areas are further compared using larger data sets of simulated extreme events over the two types of surfaces. It is found that the sensitivity of extreme precipitation to increases in global mean surface temperature is 3% per °C lower over mountains than over the oceans or the plains. The difference in sensitivity among these regions is not due to thermodynamic effects, but rather to differences between the gravity-wave dynamics governing vertical velocities over the mountains and the cyclone dynamics governing vertical motions over the oceans and plains. The strengthening of latent heating in the storms over oceans and plains leads to stronger ascent in the warming climate

  10. Dynamic Process Simulation for Analysis and Design.

    Science.gov (United States)

    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…

  11. New ways to boost molecular dynamics simulations

    NARCIS (Netherlands)

    Krieger, E.; Vriend, G.

    2015-01-01

    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 A cutoff, correct

  12. Responsive Guest Encapsulation of Dynamic Conjugated Microporous Polymers.

    Science.gov (United States)

    Xu, Lai; Li, Youyong

    2016-06-30

    The host-guest complexes of conjugated microporous polymers encapsulating C60 and dye molecules have been investigated systematically. The orientation of guest molecules inside the cavities, have different terms: inside the open cavities of the polymer, or inside the cavities formed by packing different polymers. The host backbone shows responsive dynamic behavior in order to accommodate the size and shape of incoming guest molecule or guest aggregates. Simulations show that the host-guest binding of conjugated polymers is stronger than that of non-conjugated polymers. This detailed study could provide a clear picture for the host-guest interaction for dynamic conjugated microporous polymers. The mechanism obtained could guide designing new conjugated microporous polymers.

  13. Dynamic characteristics of nanoindentation in Ni:A molecular dynamics simulation study

    Institute of Scientific and Technical Information of China (English)

    Muhammad Imran; Fayyaz Hussain; Muhammad Rashid; S.A.Ahmad

    2012-01-01

    In this work,three-dimensional molecular dynamics simulation is carried out to elucidate the nanoindentation behaviour of single crystal Ni.The substrate indenter system is modelled using hybrid interatomic potentials including the manybody potential (embedded atom method) and two-body Morse potential.The spherical indenter is chosen,and the simulation is performed for different loading rates from 10 m/s to 200 m/s.Results show that the maximum indentation load and hardness of the system increase with the increase of velocity.The effect of indenter size on the nanoindentation response is also analysed.It is found that the maximum indentation load is higher for the large indenter whereas the hardness is higher for the smaller indenter.Dynamic nanoindentation is carried out to investigate the behaviour of Ni substrate to multiple loading-unloading cycles.It is observed from the results that the increase in the number of loading unloading cycles reduces the maximum load and hardness of the Ni substrate.This is attributed to the decrease in recovery force due to defects and dislocations produced after each indentation cycle.

  14. DESIGN AND DYNAMICAL SIMULATION TO NEW VIBRATING CENTRIFUGE WITH WIDER FREQUENCY RANGE

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A new type of vibrating centrifuge with wider frequency range is designed instead of the traditional one with a single frequency to improve the vibrating effect. With the aid of a new dynamical model, one simulation without considering the visco-elasticity of basis is presented, then the dynamical responses of time and frequency in different scheme are given. The computational results show that the improved vibrating centrifuge possesses a remarkably widened frequency range.

  15. Dynamics of active cellular response under stress

    Science.gov (United States)

    de, Rumi; Zemel, Assaf; Safran, Samuel

    2008-03-01

    Forces exerted by and on adherent cells are important for many physiological processes such as wound healing and tissue formation. In addition, recent experiments have shown that stem cell differentiation is controlled, at least in part, by the elasticity of the surrounding matrix. Using a simple theoretical model that includes the forces due to both the mechanosensitive nature of cells and the elastic response of the matrix, we predict the dynamics of orientation of cells. The model predicts many features observed in measurements of cellular forces and orientation including the increase with time of the forces generated by cells in the absence of applied stress and the consequent decrease of the force in the presence of quasi-static stresses. We also explain the puzzling observation of parallel alignment of cells for static and quasi-static stresses and of nearly perpendicular alignment for dynamically varying stresses. In addition, we predict the response of the cellular orientation to a sinusoidally varying applied stress as a function of frequency. The dependence of the cell orientation angle on the Poisson ratio of the surrounding material can be used to distinguish systems in which cell activity is controlled by stress from those where cell activity is controlled by strain. Reference: Nature Physics, vol. 3, pp 655 (2007).

  16. Dynamic Responses of Mobile Offshore Base Connectors

    Institute of Scientific and Technical Information of China (English)

    余澜; 李润培; 舒志

    2003-01-01

    A Mobile Offshore Base (MOB) is a multi-purpose logistics base, which can be stationed in coastal or international waters. In the conceptual design of the MOB, attention should be paid to the dynamic responses of the inter-module connectors because tremendous loads occur in the connectors. In this paper, a study on dynamic responses of the MOB connectors is carried out by use of the Rigid Module Flexible Connector (RMFC) model which assumes that the module stiffness is significantly larger than that of the connector. In the analysis, the connector is modeled as a linear spring, which restricts relative translations but allows for relative rotations of modules. The 3-D source distribution method is adopted to determine the hydrodynamic forces of the modules, and the hydrodynamic interaction between modules is taken into account. The module motions and connector loads for 12 connector stiffness cases in regular and irregular waves are calculated with the multi-rigid-body motion equations. And the calculated results are compared with those from relative references. It is shown that the results obtained by different methods are in good agreement.

  17. Classical trajectory simulations of post-transition state dynamics

    Science.gov (United States)

    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.

  18. Dynamical Transition of Myoglobin and Cu/Zn Superoxide Dismutase Revealed by Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    张莉莉; 张建华; 周林祥

    2002-01-01

    We have carried out parallel molecular dynamics simulations of solvated and non-solvated myoglobin and solvated Cu/Zn superoxide dismutase at different temperatures. By analysis of several methods, the simulations reproduce the quasielastic neutron scattering experimental results. Below 200 K these two proteins behave as harmonic solids with essentially only vibrational motion, while above this temperature, there is a striking dynamic transition into anharmonic motion. Moreover, the simulations further show that water molecules play an important role for this dynamical transition. There is no such sharp dynamical transition in non-solvated proteins and the higher the solvate density is, the steeper at transition point the curve of mean square displacement versus temperature will be. The simulations also display that the dynamical transition is a general property for globular protein and this transition temperature is a demarcation of enzyme activity.

  19. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    CERN Document Server

    Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver

    2015-01-01

    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 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 (GLE), which can be rigorously derived by means of a linear projection (LP) 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 most 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. Importa...

  20. A Grid-Based Cyber Infrastructure for High Performance Chemical Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Khadka Prashant

    2008-10-01

    Full Text Available Chemical dynamics simulation is an effective means to study atomic level motions of molecules, collections of molecules, liquids, surfaces, interfaces of materials, and chemical reactions. To make chemical dynamics simulations globally accessible to a broad range of users, recently a cyber infrastructure was developed that provides an online portal to VENUS, a popular chemical dynamics simulation program package, to allow people to submit simulation jobs that will be executed on the web server machine. In this paper, we report new developments of the cyber infrastructure for the improvement of its quality of service by dispatching the submitted simulations jobs from the web server machine onto a cluster of workstations for execution, and by adding an animation tool, which is optimized for animating the simulation results. The separation of the server machine from the simulation-running machine improves the service quality by increasing the capacity to serve more requests simultaneously with even reduced web response time, and allows the execution of large scale, time-consuming simulation jobs on the powerful workstation cluster. With the addition of an animation tool, the cyber infrastructure automatically converts, upon the selection of the user, some simulation results into an animation file that can be viewed on usual web browsers without requiring installation of any special software on the user computer. Since animation is essential for understanding the results of chemical dynamics simulations, this animation capacity provides a better way for understanding simulation details of the chemical dynamics. By combining computing resources at locations under different administrative controls, this cyber infrastructure constitutes a grid environment providing physically and administratively distributed functionalities through a single easy-to-use online portal

  1. Stereochemical errors and their implications for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Freddolino Peter L

    2011-05-01

    Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.

  2. Fast simulation of Brownian dynamics in a crowded environment

    CERN Document Server

    Smith, Stephen

    2016-01-01

    Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed 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 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 simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the case where the reactive particles are point particles, and where they themselves occupy a volume. We use simulations of simple chemical reaction networks to confirm that our simplification is just as accurate as the original algorithm, and that it corresponds to a large spee...

  3. Strong Analog Classical Simulation of Coherent Quantum Dynamics

    Science.gov (United States)

    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

  4. Simulating sub-Milankovitch climate variations associated with vegetation dynamics

    Directory of Open Access Journals (Sweden)

    E. Tuenter

    2007-01-01

    Full Text Available Climate variability at sub-Milankovitch periods (between 2 and 15 kyr is studied in a set of transient simulations with a coupled atmosphere/ocean/vegetation model of intermediate complexity (CLIMBER-2. Focus is on the region influenced by the African and Asian summer monsoon. Pronounced variations at periods of about 10 kyr (Asia and Africa and about 5 kyr (Asia are found in the monsoonal runoff in response to the precessional forcing. In the model this is due to the following mechanism. For low summer insolation (precession maximum precipitation is low and desert expands at the expense of grass, while for high insolation (precession minimum precipitation is high and the tree fraction increases also reducing the grass fraction. This induces sub-Milankovitch variations in the grass fraction and associated variations in the water holding capacity of the soil. The runoff does not exhibit sub-Milankovitch variability when vegetation is kept fixed. High-latitude vegetation also exhibits sub-Milankovitch variability under both obliquity and precessional forcing. We thus hypothesize that sub-Milankovitch variability can occur due to the dynamic response of the vegetation. However, this mechanism should be further tested with more sophisticated climate/vegetation models.

  5. Molecular dynamics simulation of propagating cracks

    Science.gov (United States)

    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.

  6. Gas dynamics for accretion disk simulations

    Science.gov (United States)

    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.

  7. Computer Simulation of Turbulent Reactive Gas Dynamics

    Directory of Open Access Journals (Sweden)

    Bjørn H. Hjertager

    1984-10-01

    Full Text Available A simulation procedure capable of handling transient compressible flows involving combustion is presented. The method uses the velocity components and pressure as primary flow variables. The differential equations governing the flow are discretized by integration over control volumes. The integration is performed by application of up-wind differencing in a staggered grid system. The solution procedure is an extension of the SIMPLE-algorithm accounting for compressibility effects.

  8. Molecular dynamics simulation of propagating cracks

    Science.gov (United States)

    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.

  9. Transforming Healthcare Delivery: Integrating Dynamic Simulation Modelling and Big Data in Health Economics and Outcomes Research

    NARCIS (Netherlands)

    Marshall, Deborah A.; Burgos-Liz, Lina; Pasupathy, Kalyan S.; Padula, William V.; IJzerman, Maarten J.; Wong, Peter K.; Higashi, Mitchell K.; Engbers, Jordan; Wiebe, Samuel; Crown, William; Osgood, Nathaniel D.

    2016-01-01

    In the era of the Information Age and personalized medicine, healthcare delivery systems need to be efficient and patient-centred. The health system must be responsive to individual patient choices and preferences about their care, while considering the system consequences. While dynamic simulation

  10. Dynamic Factor Method of Computing Dynamic Mathematical Model for System Simulation

    Institute of Scientific and Technical Information of China (English)

    老大中; 吴娟; 杨策; 蒋滋康

    2003-01-01

    The computational methods of a typical dynamic mathematical model that can describe the differential element and the inertial element for the system simulation are researched. The stability of numerical solutions of the dynamic mathematical model is researched. By means of theoretical analysis, the error formulas, the error sign criteria and the error relationship criterion of the implicit Euler method and the trapezoidal method are given, the dynamic factor affecting the computational accuracy has been found, the formula and the methods of computing the dynamic factor are given. The computational accuracy of the dynamic mathematical model like this can be improved by use of the dynamic factor.

  11. Molecular dynamics simulation of Ni3Al melting

    Institute of Scientific and Technical Information of China (English)

    Rongshan Wang; Huaiyu Hou; Xiaodong Ni; Guoliang Chen

    2008-01-01

    With the Voter-Chert version of embedded-atom model (EAM) potential and molecular dynamics, the melting of Ni3A1 alloy was simulated by one-phase (conventional) and two-phase approaches. It is shown that the simulated melting point is dependent on the potential and the simulation method. The structures of the melts obtained by different simulation methods were analyzed by the pair correlation function, the coordination number, and the distribution of atom pair type (indexed by the Honeycutt-Andersen pair analysis technique). The results show that the structures are very similar.

  12. Molecular Dynamics Simulation of Glass Transition Behavior of Polyimide Ensemble

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The effect of chromophores to the glass transition temperature of polyimide ensemble has been investigated by means of molecular dynamics simulation in conjunction with barrier analysis. Simulated Tg results indicated a good agreement with experimental value. This study showed the MD simulation could estimate the effect of chromophores to the Tg of polyimide ensemble conveniently and an estimation approach method had a surprising deviation of Tg from experiment. At the same time, a polyimide structure with higher barrier energy was designed and validated by MD simulation.

  13. Insights from molecular dynamics simulations for computational protein design.

    Science.gov (United States)

    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.

  14. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    Science.gov (United States)

    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.

  15. Dynamic computer simulations of electrophoresis: three decades of active research.

    Science.gov (United States)

    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.

  16. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori

    2011-09-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

  17. Multiscale simulation of microbe structure and dynamics.

    Science.gov (United States)

    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.

  18. Evolution of taxis responses in virtual bacteria: non-adaptive dynamics.

    Directory of Open Access Journals (Sweden)

    Richard A Goldstein

    2008-05-01

    Full Text Available Bacteria are able to sense and respond to a variety of external stimuli, with responses that vary from stimuli to stimuli and from species to species. The best-understood is chemotaxis in the model organism Escherichia coli, where the dynamics and the structure of the underlying pathway are well characterised. It is not clear, however, how well this detailed knowledge applies to mechanisms mediating responses to other stimuli or to pathways in other species. Furthermore, there is increasing experimental evidence that bacteria integrate responses from different stimuli to generate a coherent taxis response. We currently lack a full understanding of the different pathway structures and dynamics and how this integration is achieved. In order to explore different pathway structures and dynamics that can underlie taxis responses in bacteria, we perform a computational simulation of the evolution of taxis. This approach starts with a population of virtual bacteria that move in a virtual environment based on the dynamics of the simple biochemical pathways they harbour. As mutations lead to changes in pathway structure and dynamics, bacteria better able to localise with favourable conditions gain a selective advantage. We find that a certain dynamics evolves consistently under different model assumptions and environments. These dynamics, which we call non-adaptive dynamics, directly couple tumbling probability of the cell to increasing stimuli. Dynamics that are adaptive under a wide range of conditions, as seen in the chemotaxis pathway of E. coli, do not evolve in these evolutionary simulations. However, we find that stimulus scarcity and fluctuations during evolution results in complex pathway dynamics that result both in adaptive and non-adaptive dynamics depending on basal stimuli levels. Further analyses of evolved pathway structures show that effective taxis dynamics can be mediated with as few as two components. The non-adaptive dynamics

  19. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    Science.gov (United States)

    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.

  20. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  1. Computational fluid dynamics for sport simulation

    CERN Document Server

    2009-01-01

    All over the world sport plays a prominent role in society: as a leisure activity for many, as an ingredient of culture, as a business and as a matter of national prestige in such major events as the World Cup in soccer or the Olympic Games. Hence, it is not surprising that science has entered the realm of sports, and, in particular, that computer simulation has become highly relevant in recent years. This is explored in this book by choosing five different sports as examples, demonstrating that computational science and engineering (CSE) can make essential contributions to research on sports topics on both the fundamental level and, eventually, by supporting athletes’ performance.

  2. Numerical simulations of blobs with ion dynamics

    Science.gov (United States)

    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.

  3. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... an improved stability with a factor of , but the overhead of computer time is a factor of at least two. The conclusion is that the second-order “Verlet”-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated...

  4. Dynamical simulation of non-abelian cosmic strings

    CERN Document Server

    McGraw, P

    1996-01-01

    We describe a method for simulating the dynamics of an S_3 cosmic string network. We use a lattice Monte Carlo to generate initial conditions for the network, which subsequently is allowed to relax continuously according to a simplified model of string dynamics. The dynamics incorporates some novel features which, to our knowledge, have not been studied in previous numerical simulations: The existence of two types of string which may have different tensions, and the possibility that two non-commuting strings may intersect. Simulation of the non-commuting fluxes presents a computational challenge as it requires a rather complex gauge-fixing procedure. The flux definitions change as strings change their positions and orientations relative to each other and must be carefully updated as the network evolves. The method is described here in some detail, with results to be presented elsewhere.

  5. A dynamic simulation model of desertification in Egypt

    Directory of Open Access Journals (Sweden)

    M. Rasmy

    2010-12-01

    Full Text Available This paper presents the development of a system dynamic model to simulate and analyze potential future state of desertification in Egypt. The presented model enhances the MEDALUS methodology developed by European Commission. It illustrates the concept of desertification through different equations and simulation output graphs. It is supplemented with a causal loop diagram showing the feedback between different variables. For the purpose of testing and measuring the effect of different policy scenarios on desertification in Egypt, a simulation model using stock and flow diagram was designed. Multi-temporal data were used to figure out the dynamic changes in desertification sensitivity related to the dynamic nature of desert environment. The model was applied to Al Bihira governorate in western Nile Delta, Egypt, as the study area, and the results showed that the urban expansion, salinization, and not applying the policy enforcement are considered the most variables provoking the desertification.

  6. Photonic water dynamically responsive to external stimuli

    Science.gov (United States)

    Sano, Koki; Kim, Youn Soo; Ishida, Yasuhiro; Ebina, Yasuo; Sasaki, Takayoshi; Hikima, Takaaki; Aida, Takuzo

    2016-08-01

    Fluids that contain ordered nanostructures with periodic distances in the visible-wavelength range, anomalously exhibit structural colours that can be rapidly modulated by external stimuli. Indeed, some fish can dynamically change colour by modulating the periodic distance of crystalline guanine sheets cofacially oriented in their fluid cytoplasm. Here we report that a dilute aqueous colloidal dispersion of negatively charged titanate nanosheets exhibits structural colours. In this `photonic water', the nanosheets spontaneously adopt a cofacial geometry with an ultralong periodic distance of up to 675 nm due to a strong electrostatic repulsion. Consequently, the photonic water can even reflect near-infrared light up to 1,750 nm. The structural colour becomes more vivid in a magnetic flux that induces monodomain structural ordering of the colloidal dispersion. The reflective colour of the photonic water can be modulated over the entire visible region in response to appropriate physical or chemical stimuli.

  7. Simulation of nanofractal dynamics with MBN Explorer

    Science.gov (United States)

    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.

  8. Molecular dynamics simulation of laser shock phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).

    2001-10-01

    Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)

  9. Dynamic response of Hovercraft lift fans

    Science.gov (United States)

    Moran, D. D.

    1981-08-01

    Hovercraft lift fans are subjected to varying back pressure due to wave action and craft motions when these vehicles are operating in a seaway. The oscillatory back pressure causes the fans to perform dynamically, exhibiting a hysteresis type of response and a corresponding degradation in mean performance. Since Hovercraft motions are influenced by variations in lift fan pressure and discharge, it is important to understand completely the nature of the dynamic performance of lift fans in order to completely solve the Hovercraft seakeeping problem. The present study was performed to determine and classify the instabilities encountered in a centrifugal fan operating against time-varying back pressure. A model-scale experiment was developed in which the fan discharge was directed into a flow-measuring device, terminating in a rotating valve which produced an oscillatory back pressure superimposed upon a mean aerodynamic resistance. Pressure and local velocity were measured as functions of time at several locations in the fan volute. The measurements permitted the identification of rotating (or propagating) stall in the impeller. One cell and two cell configurations were classified and the transient condition connecting these two configurations was observed. The mechanisms which lead to rotating stall in a centrifugal compressor are presented and discussed with specific reference to Hovercraft applications.

  10. Dynamics modeling and simulation of mechanism with joint clearance

    Institute of Scientific and Technical Information of China (English)

    BAI Zheng-feng; TIAN Hao; ZHAO Yang

    2010-01-01

    The existence of clearance in the joints of mechanisms system is inevitable.The movements of the real mechanism are deftection from the ideal mechanism due to the clearances and the motion accuracv is decreased.The effects of the hinge clearance on the crank and rocker mechanism system are studied.The svstem dynamics equation with clearance is presented.The contact dynamics model is established using the nonlinear equivalent spring-damp model and the friction effect is considered by using Coulomb friction model.Then the models are incorporated into ADAMS,and based on the model,large numbers numeric simulations are made.The regularity of contact forces in clearance are studied in detail.And the effects of clearance size.clearance friction on the mechanism dynamics characteristic are analyzed.The simulation resuhs Can predict the effects of clearance on the mechanism dynamics characteristic preferably.

  11. A dynamic skull model for simulation of cerebral cortex folding.

    Science.gov (United States)

    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.

  12. Dynamic Multiscale Quantum Mechanics/Electromagnetics Simulation Method.

    Science.gov (United States)

    Meng, Lingyi; Yam, ChiYung; Koo, SiuKong; Chen, Quan; Wong, Ngai; Chen, GuanHua

    2012-04-10

    A newly developed hybrid quantum mechanics and electromagnetics (QM/EM) method [Yam et al. Phys. Chem. Chem. Phys.2011, 13, 14365] is generalized to simulate the real time dynamics. Instead of the electric and magnetic fields, the scalar and vector potentials are used to integrate Maxwell's equations in the time domain. The TDDFT-NEGF-EOM method [Zheng et al. Phys. Rev. B2007, 75, 195127] is employed to simulate the electronic dynamics in the quantum mechanical region. By allowing the penetration of a classical electromagnetic wave into the quantum mechanical region, the electromagnetic wave for the entire simulating region can be determined consistently by solving Maxwell's equations. The transient potential distributions and current density at the interface between quantum mechanical and classical regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. Charge distribution, current density, and potentials at different temporal steps and spatial scales are integrated seamlessly within a unified computational framework.

  13. Simulation of Naval Guns' Breechblock System Dynamics Based on ADAMS

    Science.gov (United States)

    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.

  14. Simulation of Dynamic Recrystallization Using Cellular Automaton Method

    Institute of Scientific and Technical Information of China (English)

    XIAO Hong; XIE Hong-biao; YAN Yan-hong; Jun YANAGIMOTO

    2004-01-01

    A new modeling approach that couples fundamental metallurgical principles of dynamical recrystallization with the cellular automaton method was developed to simulate the microstructural evolution linking with the plastic flow behavior during thermomechanical processing. The driving force for the nucleation and growth of dynamically recrystallized grain is the volume free energy due to the stored dislocation density of a deformation matrix. The growth terminates the impingement. The model is capable of simulating kinetics, microstructure and texture evolution during recrystallization. The predictions of microstructural evolution agree with the experimental results.

  15. Dynamic Simulation Analysis of Forest-fruit Vibratory Harvester Arm

    Directory of Open Access Journals (Sweden)

    Jian Zhou

    2014-01-01

    Full Text Available For obtaining excellent properties of vibration type picking machine of oil tea fruit, two and three dimensional virtual prototype of forest-fruit vibratory harvester was established by CAD and Pro/E software, then the dynamic prototype was converted and the dynamics simulation was worked out by the Adams system simulation software for the arm. The mechanical characteristics of arm were measured during positioning and vibrating the end of arm and they provide a theoretical references to optimize the physical prototype.

  16. Dynamic modeling, simulation and control of energy generation

    CERN Document Server

    Vepa, Ranjan

    2013-01-01

    This book addresses the core issues involved in the dynamic modeling, simulation and control of a selection of energy systems such as gas turbines, wind turbines, fuel cells and batteries. The principles of modeling and control could be applied to other non-convention methods of energy generation such as solar energy and wave energy.A central feature of Dynamic Modeling, Simulation and Control of Energy Generation is that it brings together diverse topics in thermodynamics, fluid mechanics, heat transfer, electro-chemistry, electrical networks and electrical machines and focuses on their appli

  17. Neutron Scattering and Computer Simulation Studies of Ice Dynamics

    Institute of Scientific and Technical Information of China (English)

    DONG Shunle; YU Xinsheng

    2002-01-01

    In this article we describe a range of simulations (lattice dynamics and molecular dynamics) of the inelastic inco-herent neutron scattering spectra of ices (normal ice, ice Ⅱ and ice Ⅷ ). These simulations use a variety of different inter-molecular potentials from simple classic pair-wise (rigid and non-rigid molecule) potentials to sophisticated polarisable poten-tials. It was found that MCY makes stretching and bending interactions too weak while others do them well. We demon-strate that in order to reproduce the measured neutron spectrum, greater anisotropy (or orientational variation) is requiredthan these potentials presently provide.

  18. Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

    Science.gov (United States)

    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.

  19. Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

    Science.gov (United States)

    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.

  20. Molecular Dynamics Simulation on thermodynamic Properties and Transport Coefficients

    Institute of Scientific and Technical Information of China (English)

    D.X.Xiong

    1996-01-01

    Moecular dynamics simulation (MDS) is used to study the thermodynamic properties and transport coefficients of an argon system with Lennend-Jones potential.The results on the velocity distribution,mean free path,mean collison time,specific heat and self0diffusion coefficient agree well with the existing theoretical /experimental data,It shows that molecular dynamics method is another bridge to connect microworld and macreoworld.

  1. Molecular dynamics simulations of peptides on calcite surface

    OpenAIRE

    Yang, Mingjun; Rodger, Mark; Harding, John; Stipp, Susan S.L.

    2009-01-01

    Abstract A series of Molecular Dynamics (MD) simulations has been carried out to investigate the interaction between peptides and a calcite (1 0 -1 4) surface in water. A 16-amino acid and a 17-amino acid peptide have been built and three different configurations for each peptide are used as starting configurations. The dynamic behaviour of these peptides has been investigated by calculating their radii of gyration and distribution of dihedral angles. For comparison, the simulatio...

  2. Simulation of the Production Process Dynamics using Vensim and Stella

    Directory of Open Access Journals (Sweden)

    Corina SBUGHEA

    2016-04-01

    Full Text Available This paper aims to make a brief presentation of the principles of dynamic systems and to analyze two applications support for modeling and simulation of the evolution of these systems. For illustration, we chose a classic model of the dynamics of the production process, which we have implemented in Vensim and Stella, in order to obtain evolutionary trajectories of the endogenous variables and analyze the behavior of the system.

  3. Dynamic Garment Simulation based on Hybrid Bounding Volume Hierarchy

    Directory of Open Access Journals (Sweden)

    Zhu Dongyong

    2016-12-01

    Full Text Available In order to solve the computing speed and efficiency problem of existing dynamic clothing simulation, this paper presents a dynamic garment simulation based on a hybrid bounding volume hierarchy. It firstly uses MCASG graph theory to do the primary segmentation for a given three-dimensional human body model. And then it applies K-means cluster to do the secondary segmentation to collect the human body’s upper arms, lower arms, upper legs, lower legs, trunk, hip and woman’s chest as the elementary units of dynamic clothing simulation. According to different shapes of these elementary units, it chooses the closest and most efficient hybrid bounding box to specify these units, such as cylinder bounding box and elliptic cylinder bounding box. During the process of constructing these bounding boxes, it uses the least squares method and slices of the human body to get the related parameters. This approach makes it possible to use the least amount of bounding boxes to create close collision detection regions for the appearance of the human body. A spring-mass model based on a triangular mesh of the clothing model is finally constructed for dynamic simulation. The simulation result shows the feasibility and superiority of the method described.

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

    Science.gov (United States)

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

    2017-01-01

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

  5. Research of Steward Dynamic Platform Simulation Numerical Algorithm

    Institute of Scientific and Technical Information of China (English)

    Wang Mingwei; Hu Deji

    2015-01-01

    In order to achieve attitude control of the six degrees of freedom Steward dynamic platform, as well as the real time simulation cockpit attitude, Washout Filtering method was adopted in this paper as the simulation algorithm to derive Washout Filter high-pass, low-pass filter transfer function into a differential equation algorithm and longitudinal acceleration tilt strategy, pitching strategies etc. Experimental examples are used to verify correctness of the algorithm.

  6. Caloric Effects in Methylammonium Lead Iodide from Molecular Dynamics Simulations

    OpenAIRE

    Liu, Shi; Cohen, Ronald E.

    2016-01-01

    Organic-inorganic hybrid perovskite architecture could serve as a robust platform for materials design to realize functionalities beyond photovoltaic applications. We explore caloric effects in organometal halide perovskites, taking methylammonium lead iodide (MAPbI$_3$) as an example, using all-atom molecular dynamics simulations with a first-principles based interatomic potential. The adiabatic thermal change is estimated directly by introducing different driving fields in the simulations. ...

  7. Molecular Dynamics Simulation of Shear Moduli for Coulomb Crystals

    CERN Document Server

    Horowitz, C J

    2008-01-01

    Torsional (shear) oscillations of neutron stars may have been observed in quasiperiodic oscillations of Magnetar Giant Flares. The frequencies of these modes depend on the shear modulus of neutron star crust. We calculate the shear modulus of Coulomb crystals from molecular dynamics simulations. We find that electron screening reduces the shear modulus by about 10% compared to previous Ogata et al. results. Our MD simulations can be extended to calculate the effects of impurities and or polycrystalline structures on the shear modulus.

  8. Molecular Dynamics Simulations of DNA Translocation through a biological Nanopore

    OpenAIRE

    Barder, Simen Eidsmo

    2012-01-01

    Experimental and simulation studies of nucleic acid transport through nanosized channels, both biological and synthetic, has become a rapidly growing research area over the last decade. While the utilization of the alpha-hemolysin channel as a sequencing device is soon to be realized, other biological nanochannels may hold advantages that are yet unknown. Motivated by this, the first reported molecular dynamics simulations of DNA translocation through a connexon 26 channel were accomplished, ...

  9. A Dynamic Visual Simulation Environment for Internet of Things

    OpenAIRE

    Lavirotte, Stéphane; Tigli, Jean-Yves; Rocher, Gérald; El Beze, Léa; Palma, Adam

    2015-01-01

    Research report on works done on simulation framework for Internet and Web of Things; The development of living labs or smart spaces is a complex and challenging task. The choice of suitable sensors and actuators to deploy in these physical testbeds is difficult without experimentation. Moreover, several challenges still remain in improving and testing new fields of application based on Internet of Things (IoT). In this paper, we present UbiUnity, a dynamic visual simulator environment which ...

  10. Prototyping Bio-Nanorobots using Molecular Dynamics Simulation

    OpenAIRE

    Hamdi, Mustapha; Sharma, Gaurav; Ferreira, A.; Mavroidis, Constantinos

    2005-01-01

    Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920); International audience; This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The mai...

  11. Dynamic wind turbine models in power system simulation tool

    DEFF Research Database (Denmark)

    Hansen, A.; Jauch, Clemens; Soerensen, P.

    The present report describes the dynamic wind turbine models implemented in the power system simulation tool DIgSILENT. The developed models are a part of the results of a national research project, whose overall objective is to create a model database in different simulation tools. The report...... provides a description of the wind turbine modelling, both at a component level and at a system level....

  12. Prototyping Bio-Nanorobots using Molecular Dynamics Simulation

    OpenAIRE

    Hamdi, Mustapha; Sharma, Gaurav; Ferreira, A.; Mavroidis, Constantinos

    2005-01-01

    Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920); International audience; This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The mai...

  13. Combined molecular dynamics-spin dynamics simulations of bcc iron

    Energy Technology Data Exchange (ETDEWEB)

    Perera, Meewanage Dilina N [ORNL; Yin, Junqi [ORNL; Landau, David P [University of Georgia, Athens, GA; Nicholson, Don M [ORNL; Stocks, George Malcolm [ORNL; Eisenbach, Markus [ORNL; Brown, Greg [ORNL

    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.

  14. Response and Reliability Problems of Dynamic Systems

    DEFF Research Database (Denmark)

    Nielsen, Søren R. K.

    The present thesis consists of selected parts of the work performed by the author on stochastic dynamics and reliability theory of dynamically excited structures primarily during the period 1986-1996.......The present thesis consists of selected parts of the work performed by the author on stochastic dynamics and reliability theory of dynamically excited structures primarily during the period 1986-1996....

  15. Expansion Techniques for Collisionless Stellar Dynamical Simulations

    CERN Document Server

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

    2014-01-01

    We present GPU implementations of two fast force calculation methods, based on series expansions of the Poisson equation. One is the Self-Consistent Field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other is the Multipole Expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field method and optimized for collisionless galactic dynamics, but while SCF is a "pure" expansion, MEX is an expansion in just the angular part; it is thus capable of capturing radial structure easily, where 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...

  16. Molecular dynamics simulation of flow in pores

    Science.gov (United States)

    Blömer, Jan

    2001-08-01

    The gaseous flow in nano-scale pores is of wide interest for many today's industrial applications, e.g., in microelectronics, nano-mechanical devices (Knudsen compressor) and reaction and adsorption at porous surfaces. This can be seen from a variety of papers of recent RGD Symposia. Furthermore it is possible to separate gases by porous membranes. Although the fundamental problem of all these applications is same, namely the important role of the gas-surface interaction in such small structures, we will primarily concentrate on the separation of different gas species by porous membranes. These membranes are typically very robust (temperature, chemical resistance) because they are made from ceramics which offers new application fields. Porous flow can roughly be divided in several flow regimes by the Knudsen number: From viscous flow to Knudsen diffusion to surface diffusion and up to capillary condensation. A Molecular Dynamics (MD) model for the gas as well as the surface is formulated to investigate the interaction of gas atoms or molecules with internal degrees of freedom and the pore. The MD method seems to be well suited to study these phenomena because it can deal with the high density and the many-body-interactions, which occur during the multilayer adsorption and condensation at the surface, although it is clear that it is limited to a small physical space because of its high computational consumption.

  17. Dissipative Particle Dynamics simulation of colloidal suspensions

    Science.gov (United States)

    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.

  18. Achieving Reliable Communication in Dynamic Emergency Responses

    Science.gov (United States)

    Chipara, Octav; Plymoth, Anders N.; Liu, Fang; Huang, Ricky; Evans, Brian; Johansson, Per; Rao, Ramesh; Griswold, William G.

    2011-01-01

    Emergency responses require the coordination of first responders to assess the condition of victims, stabilize their condition, and transport them to hospitals based on the severity of their injuries. WIISARD is a system designed to facilitate the collection of medical information and its reliable dissemination during emergency responses. A key challenge in WIISARD is to deliver data with high reliability as first responders move and operate in a dynamic radio environment fraught with frequent network disconnections. The initial WIISARD system employed a client-server architecture and an ad-hoc routing protocol was used to exchange data. The system had low reliability when deployed during emergency drills. In this paper, we identify the underlying causes of unreliability and propose a novel peer-to-peer architecture that in combination with a gossip-based communication protocol achieves high reliability. Empirical studies show that compared to the initial WIISARD system, the redesigned system improves reliability by as much as 37% while reducing the number of transmitted packets by 23%. PMID:22195075

  19. Dynamic Hybrid Simulation of the Lunar Wake During ARTEMIS Crossing

    Science.gov (United States)

    Wiehle, S.; Plaschke, F.; Angelopoulos, V.; Auster, H.; Glassmeier, K.; Kriegel, H.; Motschmann, U. M.; Mueller, J.

    2010-12-01

    The interaction of the highly dynamic solar wind with the Moon is simulated with the A.I.K.E.F. (Adaptive Ion Kinetic Electron Fluid) code for the ARTEMIS P1 flyby on February 13, 2010. The A.I.K.E.F. hybrid plasma simulation code is the improved version of the Braunschweig code. It is able to automatically increase simulation grid resolution in areas of interest during runtime, which greatly increases resolution as well as performance. As the Moon has no intrinsic magnetic field and no ionosphere, the solar wind particles are absorbed at its surface, resulting in the formation of the lunar wake at the nightside. The solar wind magnetic field is basically convected through the Moon and the wake is slowly filled up with solar wind particles. However, this interaction is strongly influenced by the highly dynamic solar wind during the flyby. This is considered by a dynamic variation of the upstream conditions in the simulation using OMNI solar wind measurement data. By this method, a very good agreement between simulation and observations is achieved. The simulations show that the stationary structure of the lunar wake constitutes a tableau vivant in space representing the well-known Friedrichs diagram for MHD waves.

  20. Selecting a Dynamic Simulation Modeling Method for Health Care Delivery Research—Part 2: Report of the ISPOR Dynamic Simulation Modeling Emerging Good Practices Task Force

    NARCIS (Netherlands)

    Marshall, Deborah A.; Burgos-Liz, Lina; IJzerman, Maarten Joost; Crown, William; Padula, William V.; Wong, Peter K.; Pasupathy, Kalyan S.; Higashi, Mitchell K.; Osgood, Nathaniel D.

    2015-01-01

    In a previous report, the ISPOR Task Force on Dynamic Simulation Modeling Applications in Health Care Delivery Research Emerging Good Practices introduced the fundamentals of dynamic simulation modeling and identified the types of health care delivery problems for which dynamic simulation modeling

  1. Selecting a Dynamic Simulation Modeling Method for Health Care Delivery Research—Part 2: Report of the ISPOR Dynamic Simulation Modeling Emerging Good Practices Task Force

    NARCIS (Netherlands)

    Marshall, Deborah A.; Burgos-Liz, Lina; IJzerman, Maarten Joost; Crown, William; Padula, William V.; Wong, Peter K.; Pasupathy, Kalyan S.; Higashi, Mitchell K.; Osgood, Nathaniel D.

    2015-01-01

    In a previous report, the ISPOR Task Force on Dynamic Simulation Modeling Applications in Health Care Delivery Research Emerging Good Practices introduced the fundamentals of dynamic simulation modeling and identified the types of health care delivery problems for which dynamic simulation modeling c

  2. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

    Science.gov (United States)

    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.

  3. A method of moments for calculating dynamic responses beyond linear response theory

    Institute of Scientific and Technical Information of China (English)

    Kang Yan-Mei; Xu Jian-Xue; Xie Yong

    2005-01-01

    A method of moments for calculating the dynamic response of periodically driven overdamped nonlinear stochastic systems in the general response sense is proposed, which is a modification of the method of moments confined within linear response theory. The calculating experience suggests that the proposed technique is simple and efficient in implementation, and the comparison with stochastic simulation shows that the first three orders of susceptibilities calculated by the proposed technique have high accuracy. The dependence of the spectral amplification parameters at the first three harmonics on the noise intensity is also investigated, and another observed phenomenon of stochastic resonance in the systems induced by the location of a single periodic orbit is disclosed and explained.

  4. 地震动力作用触发的斜坡崩滑效应模拟%Numerical Simulation of Collapsing and Sliding Response of Slope Triggered by Seismic Dynamic Action

    Institute of Scientific and Technical Information of China (English)

    崔芳鹏; 许强; 谭儒蛟; 殷跃平

    2011-01-01

    A simulation was carried out on initial collapsingsliding and a subsequent running out process of Wangjiayan Landslide in Beichuan County during the Wenchuan Earthquake triggered by single and combined action with time difference, regionality and spatial heterogeneity of primary and secondary seismic waves based on discrete element method by taking into the consideration the fact that vertical ground motion was still evident in post-earthquake field geological investigation, and formation mechanism and key controlling factors of slope collapsing and sliding under seismic load were determined, which was different with the traditional dynamic response analysis based on a consideration of horizontal seismic load.The result shows that initial collapsing and sliding of the slope are triggered by combined action of vertical and horizontal tension, which plays a dominant role,of primary seismic wave, whereas a subsequent collision and debris flow of slope mass fractured are triggered by combined action of primary and secondary seismic wave.On the other hand, single action of primary seismic wave is the key controlling factor inducing the slope initial collapsing and sliding, and the topography near the slope is the key controlling factor leading to collision and debris flow of the slope mass fractured in later process.%依据震后实地调查中竖向地震力作用十分明显的现象,突破传统斜坡动力反应分析中仅考虑水平地震力作用的局限,运用离散元数值模拟技术,对北川王家岩斜坡体在具地域性和空间非均质性的地震纵横波时差耦合作用下产生崩滑破坏的动力全过程进行了模拟,确定了地震动力作用下该斜坡体崩滑破坏的形成机制及主控因素.研究表明:该斜坡体的初期崩滑破坏是受到纵波产生的水平和竖向拉裂耦合作用所致,且以水平拉裂作用占优,而后期的抛射及碎屑流动则是受到纵横波耦合作用所致;即纵波的个体作用是

  5. A framework for response surface methodology for simulation optimization

    NARCIS (Netherlands)

    H.G. Neddermeijer; G.J. van Oortmarssen (Gerrit); N. Piersma (Nanda); R. Dekker (Rommert)

    2000-01-01

    textabstractWe develop a framework for automated optimization of stochastic simulation models using Response Surface Methodology. The framework is especially intended for simulation models where the calculation of the corresponding stochastic response function is very expensive or time-consuming. Re

  6. Equilibrium and dynamic simulations of bidisperse suspensions

    Science.gov (United States)

    Jacobson, Charles Andrew

    Monte Carlo simulations are being used to investigate the structural behavior of bidisperse colloidal (silica) liquids. The solids volume fraction is 40%, and the bidispersity is characterized by two parameters: alpha, the particle size ratio, and beta, the relative volume fraction of small particles over the total volume fraction of solids. Four different size ratios are used (two, three, four, and five-to-one). The largest particle size is 0.6 mum, while the smallest is 0.12 mum. The variables (electrolyte concentration, surface potential, etc.) of the potential are set to ensure the system is stable and non-flocculating. The radial distribution function g(r) for all combinations (small-small, small-large, and large-large) of particles along with the osmotic compressibility is calculated for the various size ratios at different beta values. There are two interesting changes between the monodisperse and bidisperse suspensions. First, g(r) for the large-large particles shows an interesting structural change in that the HCP (hexagonal close packing) structure for the monodisperse large particles evolves to a BCC-like (body centered cubic) structure as beta is increased. There is also an indication of phase separation which may be a consequence of depletion flocculation. These changes appear to occur for all size ratios that have been investigated. Also, the HCP (hexagonal close packing) structure for the monodisperse small particles is completely broken up when added to the large particle system. Second, the structural change appears approximately at the beta value corresponding to the minimum in the osmotic compressibility. The structure factor is also calculated from the Fourier transform of the radial distribution function. It is suggested as future work to obtain an effective potential between large particle potentials, treating the small particle-laden fluid as a continuum. This effective potential, which can be obtained using an inversion scheme, may indicate

  7. Molecular dynamics simulations of radon accumulation in water and oil

    Energy Technology Data Exchange (ETDEWEB)

    Pafong, Elvira; Drossel, Barbara [Institut fuer Festkoerperphysik, Technische Universitaet Darmstadt (Germany)

    2016-07-01

    Radon is a radioactive gas that can enter the human body from air or from ground water. Radon can accumulate to levels that considerably rise the risk of lung cancer while it is also known as a a treatment of various ailments, most notably rheumatoid arthritis. The accumulation of radon differs between tissues, with particularly high concentrations in fatty cells. In order to understand the mechanisms responsible for the different solubility of radon in water and fat, we perform molecular dynamics simulations of radon gas at ambient conditions in contact with a bulk material consisting either of water or oil. We evaluate the diffusion coefficient of radon in both media as well as the equilibrium concentration. The crucial point here is to understand the hydrophobic interaction between water and radon as compared to the dispersive interaction between radon and oil. Therefore, we artificially vary the water charges (i.e., the hydrophobicity) as well as the parameters of the van-der-Waals interaction.

  8. Molecular dynamics simulations of ether- and ester-linked phospholipids.

    Science.gov (United States)

    Kruczek, James; Saunders, Matthew; Khosla, Meghna; Tu, Yicheng; Pandit, Sagar A

    2017-09-04

    Dissimilarities in the bulk structure of bilayers composed of ether- vs ester-linked lipids are well-established; however, the atomistic interactions responsible for these differences are not well known. These differences are important in understanding of why archaea have a different bilayer composition than the other domains of life and why humans have larger concentrations of plasmalogens in specialized membranes? In this paper, we simulate two lipid bilayers, the ester linked dipalmitoylphosphatidylcholine (DPPC) and the ether lined dihexadecylphosphatidylcholine (DHPC), to study these variations. The structural analysis of the bilayers reveals that DPPC is more compressible than DHPC. A closer examination of dipole potential shows DHPC, despite having a smaller dipole potential of the bilayer, has a higher potential barrier than DPPC at the surface. Analysis of water order and dynamics suggests DHPC has a more ordered, less mobile layer of water in the headgroup. These results seem to resolve the issue as to whether the decrease in permeability of DHPC is due to of differences in minimum area per lipid (A0) or diffusion coefficient of water in the headgroup region (Dhead) (Guler et al., 2009) since we have shown significant changes in the order and mobility of water in that region. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Thermal transport properties of uranium dioxide by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Taku; Sinnott, Susan B. [Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611 (United States); Tulenko, James S. [Department of Nuclear and Radiological Engineering, University of Florida, Gainesville, FL 32611 (United States); Grimes, Robin W. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Schelling, Patrick K. [AMPAC and Department of Physics, University of Central Florida, Orlando, FL 32816 (United States); Phillpot, Simon R. [Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611 (United States)], E-mail: sphil@mse.ufl.edu

    2008-04-30

    The thermal conductivities of single crystal and polycrystalline UO{sub 2} are calculated using molecular dynamics simulations, with interatomic interactions described by two different potential models. For single crystals, the calculated thermal conductivities are found to be strongly dependent on the size of the simulation cell. However, a scaling analysis shows that the two models predict essentially identical values for the thermal conductivity for infinite system sizes. By contrast, simulations with the two potentials for identical fine polycrystalline structures yield estimated thermal conductivities that differ by a factor of two. We analyze the origin of this difference.

  10. Acoustic Simulation with Dynamic Mechanisms in Virtual Reality

    Institute of Scientific and Technical Information of China (English)

    张琼; 石教英

    1998-01-01

    Although most investigators have realized the importance of acoustic simulation in sophisticated VR systems,large computational load involved in this process often contradicts the requirements of real-time interaction,which in return bring on applying the expensive hardware or VR-specific workstations to this area.In order to reduce the computational cost and try to realize the real-time acoustic simulation in software with (or even without)some low-cost hardware,this paper proposes some dynamic mechanisms which can be used as possible strategies embedded into acoustic simulation in VR.Preliminary implementation of those mechanisms has proved to be fairly effective.

  11. Dynamic simulator of helium refrigeration system; Hemiumu reitoki doteki shumyureta

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimura, H.; Mori, M.; Miyake, A. [Ishikawajima-Harima Heavy Industries Co., Ltd., Tokyo (Japan)

    1999-06-07

    The helium refrigerator has various operation modes. Therefore, it is insufficient for developing the refrigerating machine only by the static simulator, which simulates only one design point. It is necessary to carry out the design, which can deal with the change of the operation mode and construction of the appropriate controllability of the system. The construction of the dynamic simulator is required in the reason. This time, the heat exchanger in the helium refrigerator cool-down was unsteadily analyzed, and it was compared with the measured value. (NEDO)

  12. Development and verification of a dynamic underbalanced drilling simulator

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Z.; Vefring, E.H.; Rommetveit, R. [RF-Rogaland Research, Bergen (Norway); Bieseman, T. [Shell RTS, Rijswijk (Netherlands); Maglione, R. [Agip Spa, Milano (Italy); Lage, A.C.; Nakagawa, E. [Petrobras/CENPES, Rio de Janeiro (Brazil)

    1997-07-01

    A dynamic underbalanced drilling (UBD) simulator has been developed in a joint industry project. The simulator incorporates models for multiphase flow, well-reservoir interaction, gas/oil solubility and gas injection systems. The fluid components in the system include injected gases, mud, produced gas, produced oil and water and drilled cuttings. Both coiled tubing and conventional jointed pipe can be simulated. The primary use of the simulator is in the planning phase of an UBD operation. An UBD operation is very dynamic due to the changes in flow conditions and other operations. The importance of the dynamic effects is illustrated by a field example. The dynamic simulator allows for the analysis of various operations that cannot be analyzed with a steady state simulator. Some of these operations include starting/stopping circulation; various gas injection techniques, e.g.: parasitic string, parasitic casing, through completion, and drill string injection; drilling operations: drilling, tripping, pipe connections, and BHA deployment. To verify the simulator, two phase flow tests in near-horizontal annulus were performed in order to provide data for validation. Field data are actively collected for this purpose. In this paper, two field cases are presented. One is a coiled tubing drilling operation in Dalen field in the Netherlands where a Nitrogen lift test was performed in a through completion configuration. The second case is a UBD operation in Candeias field in Brazil. In this case, drillstring gas injection tests were performed in a cemented 9-5/8-in. casing at 1,800 m.

  13. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    Science.gov (United States)

    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.

  14. Dynamic System Simulation of the KRUSTY Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Steven Karl [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kimpland, Robert Herbert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-09

    The proposed KRUSTY experiment is a demonstration of a reactor operating at power. The planned experimental configuration includes a highly enriched uranium (HEU) reflected core, cooled by multiple heat pipes leading to Stirling engines for primary heat rejection. Operating power is expected to be approximately four (4) to five (5) kilowatts with a core temperature above 1,000 K. No data is available on any historical reactor employing HEU metal that operated over the temperature range required for the KRUSTY experiment. Further, no reactor has operated with heat pipes as the primary cooling mechanism. Historic power reactors have employed either natural or forced convection so data on their operation is not directly applicable to the KRUSTY experiment. The primary purpose of the system model once developed and refined by data from these component experiments, will be used to plan the KRUSTY experiment. This planning will include expected behavior of the reactor from start-up, through various transient conditions where cooling begins to become present and effective, and finally establishment of steady-state. In addition, the model can provide indicators of anticipated off-normal events and appropriate operator response to those conditions. This information can be used to develop specific experiment operating procedures and aids to guide the operators in conduct of the experiment.

  15. Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

    CERN Document Server

    Xu, Ji; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai

    2010-01-01

    Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further spee...

  16. Dynamic Multiaxial Response of a Hot-Pressed Aluminum Nitride

    Science.gov (United States)

    2012-01-05

    Dynamic Multiaxial Response of a Hot-Pressed Aluminum Nitride by Guangli Hu, C. Q. Chen, K. T. Ramesh, and J. W. McCauley ARL-RP-0487...Laboratory Aberdeen Proving Ground, MD 21005-5066 ARL-RP-0487 June 2014 Dynamic Multiaxial Response of a Hot-Pressed Aluminum Nitride...3. DATES COVERED (From - To) January 2010–January 2013 4. TITLE AND SUBTITLE Dynamic Multiaxial Response of a Hot-Pressed Aluminum Nitride 5a

  17. Molecular dynamics simulations on PGLa using NMR orientational constraints.

    Science.gov (United States)

    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.

  18. Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations

    NARCIS (Netherlands)

    Bulacu, Monica; Goga, Nicolae; Zhao, Wei; Rossi, Giulia; Monticelli, Luca; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.

    2013-01-01

    Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules.

  19. Molecular dynamics simulations on PGLa using NMR orientational constraints

    Energy Technology Data Exchange (ETDEWEB)

    Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

    2015-11-15

    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.

  20. Efficient dynamic simulation of flexible link manipulators with PID control

    NARCIS (Netherlands)

    Aarts, Ronald G.K.M.; Jonker, Jan B.; Mook, D.T.; Balachandran, B.

    2001-01-01

    For accurate simulations of the dynamic behavior of flexible manipulators the combination of a perturbation method and modal analysis is proposed. First, the vibrational motion is modeled as a first-order perturbation of a nominal rigid link motion. The vibrational motion is then described by a set

  1. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting tr

  2. Simulating Poverty and Inequality Dynamics in Developing Countries

    Science.gov (United States)

    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…

  3. Benchmark of Schemes for Multiscale Molecular Dynamics Simulations

    NARCIS (Netherlands)

    Goga, N.; Melo, M. N.; Rzepiela, A. J.; de Vries, Alex; Hadar, A.; Marrink, S. J.; Berendsen, Herman

    2015-01-01

    In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hy

  4. Brownian dynamics simulations of nanosheet solutions under shear.

    Science.gov (United States)

    Xu, Yueyi; Green, Micah J

    2014-07-14

    The flow-induced conformation dynamics of nanosheets are simulated using a Brownian Dynamics (BD) formulation applied to a bead-rod sheetlike molecular model. This is the first-ever use of BD to simulate flow-induced dynamics of two-dimensional structures. Using this framework, we simulate dilute suspensions of coarse-grained nanosheets and compute conformation dynamics for simple shear flow. The data show power law scaling relationships between nanosheet parameters (such as bending moduli and molecular weight) and the resulting intrinsic viscosity and conformation. For nonzero bending moduli, an effective dimension of 2.77 at equilibrium is calculated from the scaling relationship between radius of gyration and molecular weight. We also find that intrinsic viscosity varies with molecular weight with an exponent of 2.12 ± 0.23; this dependence is significantly larger than those found for linear polymers. Weak shear thinning is observed at high Weissenberg number (Wi). This simulation method provides a computational basis for developing manufacturing processes for nanosheet-derived materials by relating flow forces and nanosheet parameters to the resulting material morphology.

  5. Molecular dynamics simulations of barrier crossings in the condensed phase

    NARCIS (Netherlands)

    den Otter, Wouter K.

    1998-01-01

    The isomerisation rates of a calix[4]arene in vacuo and in two solvents have been computed by means of molecular dynamics simulations (MD). In MD the equations of classical mechanics are used to calculate the motion of the reacting molecule and the surrounding solvent molecules. Thus, the intricate

  6. A Dynamic Simulation Game (UNIGAME) for Strategic University Management.

    Science.gov (United States)

    Barlas, Yaman; Diker, Vedat Guclu

    2000-01-01

    Presents an interactive simulation model on which the academic aspects of university management can be analyzed and alternative management strategies tested. Focuses specifically on long-term, dynamic, strategic management problems and yields performance measures about the fundamental activities in a university that can support strategic…

  7. Computational Fluid Dynamics and Building Energy Performance Simulation

    DEFF Research Database (Denmark)

    Nielsen, Peter Vilhelm; Tryggvason, T.

    1998-01-01

    An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...

  8. Molecular dynamics simulations of lipid vesicle fusion in atomic detail

    NARCIS (Netherlands)

    Knecht, Volker; Marrink, Siewert-Jan

    The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic

  9. Molecular dynamics simulations of oscillatory flows in microfluidic channels

    DEFF Research Database (Denmark)

    Hansen, J.S.; Ottesen, Johnny T.

    2006-01-01

    In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...

  10. Using Simulation to Assess the Opportunities of Dynamic Waste Collection

    NARCIS (Netherlands)

    Mes, Martijn R.K.

    In this paper, we illustrate the use of discrete event simulation to evaluate how dynamic planning methodologies can be best applied for the collection of waste from underground containers. We present a case study that took place at the waste collection company Twente Milieu, located in The

  11. Using simulation to assess the opportunities of dynamic waste collection

    NARCIS (Netherlands)

    Mes, Martijn R.K.; Bangsow, S.

    2012-01-01

    In this chapter, we illustrate the use of discrete event simulation to evaluate how dynamic planning methodologies can be best applied for the collection of waste from underground containers. We present a case study that took place at the waste collection company Twente Milieu, located in The

  12. Simulation study of water and sugar dynamics in supercooled mixtures

    Science.gov (United States)

    Molinero, Valeria; Cagin, Tahir; Goddard, William A.

    2003-03-01

    Water dynamics in concentrated carbohydrate solutions is of utmost importance in food and pharmaceutical technology, where low water mobility is desirable to slow down chemical degradation and preserve biomolecules. We have studied the microscopic mechanism of water diffusion in binary and polydisperse malto-oligosaccharides and water mixtures by means of molecular dynamics simulations. The computations were performed with a coarse grain model (M3B), derived from atomistic simulations of water and malto-oligosaccharides. The use of the M3B model permits simulations of the order of 0.1 microsecond, thus allowing us to explore water dynamics from the liquid to the deep supercooled regime. The dynamics of water confined in the sugar matrix is slowed down with respect to bulk water. We found that at low moisture content and low temperature, ranslational diffusion of water and glucose rotation proceed through a hopping-diffusion mechanism. Moreover, we found water mobility to be heterogeneous: there is a broad distribution of time scales for different water molecules in the mixtures. We discuss whether there is a relationship between the heterogeneous structure of these mixtures in the sub-nanometer scale and the heterogeneous dynamics of water molecules.

  13. Dynamic simulation for effective workforce management in new product development

    Directory of Open Access Journals (Sweden)

    M. Mutingi

    2012-10-01

    Full Text Available Effective planning and management of workforce for new product development (NPD projects is a great challenge to many organisations, especially in the presence of engineering changes during the product development process. The management objective in effective workforce management is to recruit, develop and deploy the right people at the right place at the right time so as to fulfill organizational objectives. In this paper, we propose a dynamic simulation model to address the workforce management problem in a typical NPD project consisting of design, prototyping, and production phases. We assume that workforce demand is a function of project work remaining and the current available skill pool. System dynamics simulation concepts are used to capture the causality relationships and feedback loops in the workforce system from a systems thinking. The evaluation of system dynamics simulation reveals the dynamic behaviour in NPD workforce management systems and shows how adaptive dynamic recruitment and training decisions can effectively balance the workforce system during the NPD process.

  14. Dynamic simulation of sustainable farm development scenarios using cognitive modeling

    Directory of Open Access Journals (Sweden)

    Tuzhyk Kateryna

    2017-03-01

    Full Text Available Dynamic simulation of sustainable farm development scenarios using cognitive modeling. The paper presents a dynamic simulation system of sustainable development scenarios on farms using cognitive modeling. The system incorporates relevant variables which affect the sustainable development of farms. Its user provides answers to strategic issues connected with the level of farm sustainability over a long-term perspective of dynamic development. The work contains a description of the model structure as well as the results of simulations carried out on 16 farms in northern Ukraine. The results show that the process of sustainability is based mainly on the potential for innovation in agricultural production and biodiversity. The user is able to simulate various scenarios for the sustainable development of a farm and visualize the influence of factors on the economic and social situation, as well as on environmental aspects. Upon carrying out a series of simulations, it was determined that the development of farms characterized by sustainable development is based on additional profit, which serves as the main motivation for transforming a conventional farm into a sustainable one. Nevertheless, additional profit is not the only driving force in the system of sustainable development. The standard of living, market condition, and legal regulations as well as government support also play a significant motivational role.

  15. Acoustic properties in glycerol glass-former: Molecular dynamics simulation

    Science.gov (United States)

    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.

  16. Steered molecular dynamics simulations of protein-ligand interactions

    Institute of Scientific and Technical Information of China (English)

    XU; Yechun; SHEN; Jianhua; LUO; Xiaomin; SHEN; Xu; CHEN; Ka

    2004-01-01

    Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and kinetic processes of ligand-receptor binding and unbinding, which cannot be accessed by the experimental methods. In this article, the methodology of SMD is described, and the applications of SMD simulations for obtaining dynamic insights into protein-ligand interactions are illustrated through two of our own examples. One is associated with the simulations of binding and unbinding processes between huperzine A and acetylcholinesterase, and the other is concerned with the unbinding process of α-APA from HIV-1 reverse transcriptase.

  17. Quantum Dynamics Simulations for Modeling Experimental Pump-Probe Measurements

    Science.gov (United States)

    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).

  18. Understanding diabetes population dynamics through simulation modeling and experimentation.

    Science.gov (United States)

    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.

  19. DISCOS- DYNAMIC INTERACTION SIMULATION OF CONTROLS AND STRUCTURES (IBM VERSION)

    Science.gov (United States)

    Frisch, H. P.

    1994-01-01

    The Dynamic Interaction Simulation of Controls and Structure (DISCOS) program was developed for the dynamic simulation and stability analysis of passive and actively controlled spacecraft. In the use of DISCOS, the physical system undergoing analysis may be generally described as a cluster of contiguous flexible structures (bodies) that comprise a mechanical system, such as a spacecraft. The entire system (spacecraft) or portions thereof may be either spinning or nonspinning. Member bodies of the system may undergo large relative excursions, such as those of appendage deployment or rotor/ stator motion. The general system of bodies is, by its inherent nature, a feedback system in which inertial forces (such as those due to centrifugal and Coriolis acceleration) and the restoring and damping forces are motion-dependent. The system may possess a control system in which certain position and rate errors are actively controlled through the use of reaction control jets, servomotors, or momentum wheels. Bodies of the system may be interconnected by linear or nonlinear springs and dampers, by a gimbal and slider block mechanism, or by any combination of these. The DISCOS program can be used to obtain nonlinear and linearized time response of the system, interaction constant forces in the system, total system resonance properties, and frequency domain response and stability information for the system. DISCOS is probably the most powerful computational tool to date for the computer simulation of actively controlled coupled multi-flexible-body systems. The program is not easy to understand and effectively apply, but is not intended for simple problems. The DISCOS user is expected to have extensive working knowledge of rigid-body and flexible-body dynamics, finite-element techniques, numerical methods, and frequency-domain analysis. Various applications of DISCOS include simulation of the Shuttle payload deployment/retrieval mechanism, solar panel array deployment, antenna

  20. Parallel alternating direction preconditioner for isogeometric simulations of explicit dynamics

    KAUST Repository

    Łoś, Marcin

    2015-04-27

    In this paper we present a parallel implementation of the alternating direction preconditioner for isogeometric simulations of explicit dynamics. The Alternating Direction Implicit (ADI) algorithm, belongs to the category of matrix-splitting iterative methods, was proposed almost six decades ago for solving parabolic and elliptic partial differential equations, see [1–4]. The new version of this algorithm has been recently developed for isogeometric simulations of two dimensional explicit dynamics [5] and steady-state diffusion equations with orthotropic heterogenous coefficients [6]. In this paper we present a parallel version of the alternating direction implicit algorithm for three dimensional simulations. The algorithm has been incorporated as a part of PETIGA an isogeometric framework [7] build on top of PETSc [8]. We show the scalability of the parallel algorithm on STAMPEDE linux cluster up to 10,000 processors, as well as the convergence rate of the PCG solver with ADI algorithm as preconditioner.

  1. Simulation of stochastic network dynamics via entropic matching.

    Science.gov (United States)

    Ramalho, Tiago; Selig, Marco; Gerland, Ulrich; Ensslin, Torsten A

    2013-02-01

    The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a model's dynamics over a large parameter space renders full-fledged stochastic simulations impractical, motivating approximation schemes. Here we propose an approximation scheme which improves upon the standard linear noise approximation while retaining similar computational complexity. The underlying idea is to minimize, at each time step, the Kullback-Leibler divergence between the true time evolved probability distribution and a Gaussian approximation (entropic matching). This condition leads to ordinary differential equations for the mean and the covariance matrix of the Gaussian. For cases of weak nonlinearity, the method is more accurate than the linear method when both are compared to stochastic simulations.

  2. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

    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.

  3. Ultrascale simulations of non-smooth granular dynamics

    Science.gov (United States)

    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.

  4. Ultrascale Simulations of Non-smooth Granular Dynamics

    CERN Document Server

    Preclik, Tobias

    2015-01-01

    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 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 458752 processor cores. The simulations can reach unprecedented resolution of up to ten billion non-spherical particles and contacts.

  5. Ice Formation on Kaolinite: Insights from Molecular Dynamics Simulations

    CERN Document Server

    Sosso, Gabriele C; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

    2016-01-01

    The formation of ice affects many aspects of our everyday life as well as technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even via state-of-the-art experimental techniques. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long timescales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaol...

  6. A parameters optimization method for planar joint clearance model and its application for dynamics simulation of reciprocating compressor

    Science.gov (United States)

    Hai-yang, Zhao; Min-qiang, Xu; Jin-dong, Wang; Yong-bo, Li

    2015-05-01

    In order to improve the accuracy of dynamics response simulation for mechanism with joint clearance, a parameter optimization method for planar joint clearance contact force model was presented in this paper, and the optimized parameters were applied to the dynamics response simulation for mechanism with oversized joint clearance fault. By studying the effect of increased clearance on the parameters of joint clearance contact force model, the relation of model parameters between different clearances was concluded. Then the dynamic equation of a two-stage reciprocating compressor with four joint clearances was developed using Lagrange method, and a multi-body dynamic model built in ADAMS software was used to solve this equation. To obtain a simulated dynamic response much closer to that of experimental tests, the parameters of joint clearance model, instead of using the designed values, were optimized by genetic algorithms approach. Finally, the optimized parameters were applied to simulate the dynamics response of model with oversized joint clearance fault according to the concluded parameter relation. The dynamics response of experimental test verified the effectiveness of this application.

  7. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

    Science.gov (United States)

    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.

  8. Information diversity in structure and dynamics of simulated neuronal networks.

    Science.gov (United States)

    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.

  9. TRPM8-Dependent Dynamic Response in a Mathematical Model of Cold Thermoreceptor

    Science.gov (United States)

    Olivares, Erick; Salgado, Simón; Maidana, Jean Paul; Herrera, Gaspar; Campos, Matías; Madrid, Rodolfo; Orio, Patricio

    2015-01-01

    Cold-sensitive nerve terminals (CSNTs) encode steady temperatures with regular, rhythmic temperature-dependent firing patterns that range from irregular tonic firing to regular bursting (static response). During abrupt temperature changes, CSNTs show a dynamic response, transiently increasing their firing frequency as temperature decreases and silencing when the temperature increases (dynamic response). To date, mathematical models that simulate the static response are based on two depolarizing/repolarizing pairs of membrane ionic conductance (slow and fast kinetics). However, these models fail to reproduce the dynamic response of CSNTs to rapid changes in temperature and notoriously they lack a specific cold-activated conductance such as the TRPM8 channel. We developed a model that includes TRPM8 as a temperature-dependent conductance with a calcium-dependent desensitization. We show by computer simulations that it appropriately reproduces the dynamic response of CSNTs from mouse cornea, while preserving their static response behavior. In this model, the TRPM8 conductance is essential to display a dynamic response. In agreement with experimental results, TRPM8 is also needed for the ongoing activity in the absence of stimulus (i.e. neutral skin temperature). Free parameters of the model were adjusted by an evolutionary optimization algorithm, allowing us to find different solutions. We present a family of possible parameters that reproduce the behavior of CSNTs under different temperature protocols. The detection of temperature gradients is associated to a homeostatic mechanism supported by the calcium-dependent desensitization. PMID:26426259

  10. TRPM8-Dependent Dynamic Response in a Mathematical Model of Cold Thermoreceptor.

    Directory of Open Access Journals (Sweden)

    Erick Olivares

    Full Text Available Cold-sensitive nerve terminals (CSNTs encode steady temperatures with regular, rhythmic temperature-dependent firing patterns that range from irregular tonic firing to regular bursting (static response. During abrupt temperature changes, CSNTs show a dynamic response, transiently increasing their firing frequency as temperature decreases and silencing when the temperature increases (dynamic response. To date, mathematical models that simulate the static response are based on two depolarizing/repolarizing pairs of membrane ionic conductance (slow and fast kinetics. However, these models fail to reproduce the dynamic response of CSNTs to rapid changes in temperature and notoriously they lack a specific cold-activated conductance such as the TRPM8 channel. We developed a model that includes TRPM8 as a temperature-dependent conductance with a calcium-dependent desensitization. We show by computer simulations that it appropriately reproduces the dynamic response of CSNTs from mouse cornea, while preserving their static response behavior. In this model, the TRPM8 conductance is essential to display a dynamic response. In agreement with experimental results, TRPM8 is also needed for the ongoing activity in the absence of stimulus (i.e. neutral skin temperature. Free parameters of the model were adjusted by an evolutionary optimization algorithm, allowing us to find different solutions. We present a family of possible parameters that reproduce the behavior of CSNTs under different temperature protocols. The detection of temperature gradients is associated to a homeostatic mechanism supported by the calcium-dependent desensitization.

  11. TRPM8-Dependent Dynamic Response in a Mathematical Model of Cold Thermoreceptor.

    Science.gov (United States)

    Olivares, Erick; Salgado, Simón; Maidana, Jean Paul; Herrera, Gaspar; Campos, Matías; Madrid, Rodolfo; Orio, Patricio

    2015-01-01

    Cold-sensitive nerve terminals (CSNTs) encode steady temperatures with regular, rhythmic temperature-dependent firing patterns that range from irregular tonic firing to regular bursting (static response). During abrupt temperature changes, CSNTs show a dynamic response, transiently increasing their firing frequency as temperature decreases and silencing when the temperature increases (dynamic response). To date, mathematical models that simulate the static response are based on two depolarizing/repolarizing pairs of membrane ionic conductance (slow and fast kinetics). However, these models fail to reproduce the dynamic response of CSNTs to rapid changes in temperature and notoriously they lack a specific cold-activated conductance such as the TRPM8 channel. We developed a model that includes TRPM8 as a temperature-dependent conductance with a calcium-dependent desensitization. We show by computer simulations that it appropriately reproduces the dynamic response of CSNTs from mouse cornea, while preserving their static response behavior. In this model, the TRPM8 conductance is essential to display a dynamic response. In agreement with experimental results, TRPM8 is also needed for the ongoing activity in the absence of stimulus (i.e. neutral skin temperature). Free parameters of the model were adjusted by an evolutionary optimization algorithm, allowing us to find different solutions. We present a family of possible parameters that reproduce the behavior of CSNTs under different temperature protocols. The detection of temperature gradients is associated to a homeostatic mechanism supported by the calcium-dependent desensitization.

  12. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    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 pos......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...... 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....

  13. Research on hyperspectral dynamic scene and image sequence simulation

    Science.gov (United States)

    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.

  14. The Fermi-Pasta-Ulam problem: Simulation and modern dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Dynamic bioactive stimuli-responsive polymeric surfaces

    Science.gov (United States)

    Pearson, Heather Marie

    This dissertation focuses on the design, synthesis, and development of antimicrobial and anticoagulant surfaces of polyethylene (PE), polypropylene (PP), and poly(tetrafluoroethylene) (PTFE) polymers. Aliphatic polymeric surfaces of PE and PP polymers functionalized using click chemistry reactions by the attachment of --COOH groups via microwave plasma reactions followed by functionalization with alkyne moieties. Azide containing ampicillin (AMP) was synthesized and subsequently clicked into the alkyne prepared PE and PP surfaces. Compared to non-functionalized PP and PE surfaces, the AMP clicked surfaces exhibited substantially enhanced antimicrobial activity against Staphylococcus aureus bacteria. To expand the biocompatibility of polymeric surface anticoagulant attributes, PE and PTFE surfaces were functionalized with pH-responsive poly(2-vinyl pyridine) (P2VP) and poly(acrylic acid) (PAA) polyelectrolyte tethers terminated with NH2 and COOH groups. The goal of these studies was to develop switchable stimuli-responsive polymeric surfaces that interact with biological environments and display simultaneous antimicrobial and anticoagulant properties. Antimicrobial AMP was covalently attached to --COOH terminal ends of protected PAA, while anticoagulant heparin (HEP) was attached to terminal --NH2 groups of P2VP. When pH 5.5, they collapse while the PAA segments extend. Such surfaces, when exposed to Staphylococcus aureus, inhibit bacterial growth due to the presence of AMP, as well as are effective anticoagulants due to the presence of covalently attached HEP. Comparison of these "dynamic" pH responsive surfaces with "static" surfaces terminated with AMP entities show significant enhancement of longevity and surface activity against microbial film formation. The last portion of this dissertation focuses on the covalent attachment of living T1 and Φ11 bacteriophages (phages) on PE and PTFE surface. This was accomplished by carbodiimide coupling between --COOH

  16. Nonlinear dynamic response of stay cables under axial harmonic excitation

    Institute of Scientific and Technical Information of China (English)

    Xu XIE; He ZHAN; Zhi-cheng ZHANG

    2008-01-01

    This paper proposes a new numerical simulation method for analyzing the parametric vibration of stay cables based on the theory of nonlinear dynamic response of structures under the asynchronous support excitation.The effects of important parameters related to parametric vibration of cables,I.e., characteristics of structure,excitation frequency,excitation amplitude,damping effect of the air and the viscous damping coefficient of the cables,were investigated by using the proposed method for the cables with significant length difference as examples.The analysis results show that nonlinear finite element method is a powerful technique in analyzing the parametric vibration of cables,the behavior of parametric vibration of the two cables with different Irvine parameters has similar properties,the amplitudes of parametric vibration of cables are related to the frequency and amplitude of harmonic support excitations and the effect of distributed viscous damping on parametric vibration of the cables is very small.

  17. Adaptive workflow simulation of emergency response

    NARCIS (Netherlands)

    Bruinsma, Guido Wybe Jan

    2010-01-01

    Recent incidents and major training exercises in and outside the Netherlands have persistently shown that not having or not sharing information during emergency response are major sources of emergency response inefficiency and error, and affect incident mitigation outcomes through workflow planning

  18. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    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 parameterized 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.

  19. Nonlinear dynamic response of an electrically actuated imperfect microbeam resonator

    KAUST Repository

    Ruzziconi, Laura

    2013-08-04

    We present a study of the dynamic behavior of a MEMS device constituted of an imperfect clamped-clamped microbeam subjected to electrostatic and electrodynamic actuation. Our objective is to develop a theoretical analysis, which is able to describe and predict all the main relevant aspects of the experimental response. Extensive experimental investigation is conducted, where the main imperfections coming from microfabrication are detected and the nonlinear dynamics are explored at increasing values of electrodynamic excitation, in a neighborhood of the first symmetric resonance. The nonlinear behavior is highlighted, which includes ranges of multistability, where the non-resonant and the resonant branch coexist, and intervals where superharmonic resonances are clearly visible. Numerical simulations are performed. Initially, two single mode reduced-order models are considered. One is generated via the Galerkin technique, and the other one via the combined use of the Ritz method and the Padé approximation. Both of them are able to provide a satisfactory agreement with the experimental data. This occurs not only at low values of electrodynamic excitation, but also at higher ones. Their computational efficiency is discussed in detail, since this is an essential aspect for systematic local and global simulations. Finally, the theoretical analysis is further improved and a two-degree-of-freedom reduced-order model is developed, which is capable also to capture the measured second symmetric superharmonic resonance. Despite the apparent simplicity, it is shown that all the proposed reduced-order models are able to describe the experimental complex nonlinear dynamics of the device accurately and properly, which validates the proposed theoretical approach. Copyright © 2013 by ASME.

  20. Modeling ramp compression experiments using large-scale molecular dynamics simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

    2011-10-01

    Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

  1. Dynamic Response Analysis for Embedded Large-Cylinder Breakwaters Under Wave Excitation

    Institute of Scientific and Technical Information of China (English)

    王元战; 祝振宇; 周枝荣

    2004-01-01

    A numerical model is developed for dynamic analysis of large-cylinder breakwaters embedded in soft soil. In the model, the large cylinder is taken as a rigid body divided into elements and the soft soil is replaced by discrete 3D nonlinear spring-dashpot systems. The numerical model is used to simulate the dynamic response of a large-cylinder breakwater to breaking wave excitation. The effects of the dynamic stress-strain relationship models of the soil, the radius and embedded depth of the cylinder, the nonlinear behaviors of the soil, and the limit strength condition of the soil on the dynamic responses of the large-cylinder structure are investigated with an example given. It is indicated that the above-mentioned factors have significant effects on the dynamic responses of an embedded large cylinder breakwater under breaking wave excitation.

  2. Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control

    Directory of Open Access Journals (Sweden)

    Bing Li

    2012-04-01

    Full Text Available In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results.

  3. The fractional-nonlinear robotic manipulator: Modeling and dynamic simulations

    Science.gov (United States)

    David, S. A.; Balthazar, J. M.; Julio, B. H. S.; Oliveira, C.

    2012-11-01

    In this paper, we applied the Riemann-Liouville approach and the fractional Euler-Lagrange equations in order to obtain the fractional-order nonlinear dynamics equations of a two link robotic manipulator. The aformentioned equations have been simulated for several cases involving: integer and non-integer order analysis, with and without external forcing acting and some different initial conditions. The fractional nonlinear governing equations of motion are coupled and the time evolution of the angular positions and the phase diagrams have been plotted to visualize the effect of fractional order approach. The new contribution of this work arises from the fact that the dynamics equations of a two link robotic manipulator have been modeled with the fractional Euler-Lagrange dynamics approach. The results reveal that the fractional-nonlinear robotic manipulator can exhibit different and curious behavior from those obtained with the standard dynamical system and can be useful for a better understanding and control of such nonlinear systems.

  4. Generic solar photovoltaic system dynamic simulation model specification

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, Abraham [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Behnke, Michael Robert [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Elliott, Ryan Thomas [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2013-10-01

    This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intended to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.

  5. Dynamic simulation on rubber spring supporting equipment of vibrating screen

    Institute of Scientific and Technical Information of China (English)

    SU Rong-hua; PENG Chen-yu

    2011-01-01

    By ANSYS, dynamic simulation analysis of rubber spring supporting equipment used in vibrating screen was made. The modal frequency, mode, and harmonic displacement under working frequency were obtained. Variation of rubber spring supporting equipment's dynamic performance was discussed first, which is under the condition of existing spring stiffness difference and exciting force bias. Also, the quantitative calculation formulas were given. The results indicate that the performance of vibrating screen is closely related with rubber spring supporting equipment's dynamic performance. Differences of springs' stiffness coefficients reduce the modal frequency reduced, decrease the dynamic stiffness, and increase vibration displacement. Exciting force bias induces a larger lateral displacement. When rubber springs' stiffness coefficients exist, differences and lateral force accounts for 5% in total exciting force; rubber spring supporting equipment's side swing is larger than 1 mm, exceeding the side swing limit.

  6. Synthesis of recurrent neural networks for dynamical system simulation.

    Science.gov (United States)

    Trischler, Adam P; D'Eleuterio, Gabriele M T

    2016-08-01

    We review several of the most widely used techniques for training recurrent neural networks to approximate dynamical systems, then describe a novel algorithm for this task. The algorithm is based on an earlier theoretical result that guarantees the quality of the network approximation. We show that a feedforward neural network can be trained on the vector-field representation of a given dynamical system using backpropagation, then recast it as a recurrent network that replicates the original system's dynamics. After detailing this algorithm and its relation to earlier approaches, we present numerical examples that demonstrate its capabilities. One of the distinguishing features of our approach is that both the original dynamical systems and the recurrent networks that simulate them operate in continuous time.

  7. NETIMIS: Dynamic Simulation of Health Economics Outcomes Using Big Data.

    Science.gov (United States)

    Johnson, Owen A; Hall, Peter S; Hulme, Claire

    2016-02-01

    Many healthcare organizations are now making good use of electronic health record (EHR) systems to record clinical information about their patients and the details of their healthcare. Electronic data in EHRs is generated by people engaged in complex processes within complex environments, and their human input, albeit shaped by computer systems, is compromised by many human factors. These data are potentially valuable to health economists and outcomes researchers but are sufficiently large and complex enough to be considered part of the new frontier of 'big data'. This paper describes emerging methods that draw together data mining, process modelling, activity-based costing and dynamic simulation models. Our research infrastructure includes safe links to Leeds hospital's EHRs with 3 million secondary and tertiary care patients. We created a multidisciplinary team of health economists, clinical specialists, and data and computer scientists, and developed a dynamic simulation tool called NETIMIS (Network Tools for Intervention Modelling with Intelligent Simulation; http://www.netimis.com ) suitable for visualization of both human-designed and data-mined processes which can then be used for 'what-if' analysis by stakeholders interested in costing, designing and evaluating healthcare interventions. We present two examples of model development to illustrate how dynamic simulation can be informed by big data from an EHR. We found the tool provided a focal point for multidisciplinary team work to help them iteratively and collaboratively 'deep dive' into big data.

  8. Molecular-dynamics simulation of a ceramide bilayer

    Science.gov (United States)

    Pandit, Sagar A.; Scott, H. Larry

    2006-01-01

    Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368K (5° above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall "dipole potential," when ceramide is compared to sphingomyelin.

  9. Determination of Reference Chemical Potential Using Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Krishnadeo Jatkar

    2010-01-01

    Full Text Available A new method implementing molecular dynamics (MD simulations for calculating the reference properties of simple gas hydrates has been proposed. The guest molecules affect interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed simulations to validate the experimental data for determining Δ0, the chemical potential difference between water and theoretical empty cavity at the reference state, for structure II type gas hydrates. Simulations have also been used to observe the variation of the hydrate unit cell volume with temperature. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. The values were close to the experimental values obtained by the Lee-Holder model, considering lattice distortion.

  10. Computational Fluid Dynamics and Building Energy Performance Simulation

    DEFF Research Database (Denmark)

    Nielsen, Peter V.; Tryggvason, Tryggvi

    An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...... simulation program requires a detailed description of the energy flow in the air movement which can be obtained by a CFD program. The paper describes an energy consumption calculation in a large building, where the building energy simulation program is modified by CFD predictions of the flow between three...... program and a building energy performance simulation program will improve both the energy consumption data and the prediction of thermal comfort and air quality in a selected area of the building....

  11. Molecular Dynamics Simulations of Helium Behaviour in Titanium Crystals

    Institute of Scientific and Technical Information of China (English)

    SUN Tie-Ying; LONG Xing-Gui; WANG Jun; HOU Qing; WU Zhong-Cheng; PENG Shu-Ming; LUO Shun-Zhong

    2008-01-01

    Molecular dynamics simulations are performed to investigate the behaviour of helium atoms in titanium at a temperature of 300 K.The nucleation and growth of helium bubble has been simulated up to 50 helium atoms.The approach to simulate the bubble growth is to add helium atoms one by one to the bubble and let the system evolve.The titanium cohesion is based on the tight binding scheme derived from the embedded atom method,and the helium-titanium interaction is characterized by fitted potential in the form of a Lennard-Jones function.The pressure in small helium bubbles is approximately calculated.The simulation results show that the pressure will decrease with the increasing bubble size,while increase with the increasing helium atoms.An analytic function about the quantitative relationship of the pressure with the bubble size and number of helium atoms is also fitted.

  12. Molecular dynamics simulation of amplitude modulation atomic force microscopy.

    Science.gov (United States)

    Hu, Xiaoli; Egberts, Philip; Dong, Yalin; Martini, Ashlie

    2015-06-12

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip-substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip-sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement.

  13. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  14. Prototyping Bio-Nanorobots using Molecular Dynamics Simulation

    CERN Document Server

    Hamdi, Mustapha; Ferreira, A; Mavroidis, Constantinos

    2007-01-01

    This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The main novelty of the proposed simulations is based on the characterization of stiffness performances of passive joints-based deca-alanine protein molecule and active joints-based viral protein motor (VPL) in their native environment. Their use as elementary Bio-NanoRobotic components (1 dof platform) are also simulated and the results discussed.

  15. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  16. Spontaneous Facial Mimicry in Response to Dynamic Facial Expressions

    Science.gov (United States)

    Sato, Wataru; Yoshikawa, Sakiko

    2007-01-01

    Based on previous neuroscientific evidence indicating activation of the mirror neuron system in response to dynamic facial actions, we hypothesized that facial mimicry would occur while subjects viewed dynamic facial expressions. To test this hypothesis, dynamic/static facial expressions of anger/happiness were presented using computer-morphing…

  17. Lattice Boltzmann simulations of multiple-droplet interaction dynamics

    Science.gov (United States)

    Zhou, Wenchao; Loney, Drew; Fedorov, Andrei G.; Degertekin, F. Levent; Rosen, David W.

    2014-03-01

    A lattice Boltzmann (LB) formulation, which is consistent with the phase-field model for two-phase incompressible fluid, is proposed to model the interface dynamics of droplet impingement. The interparticle force is derived by comparing the macroscopic transport equations recovered from LB equations with the governing equations of the continuous phase-field model. The inconsistency between the existing LB implementations and the phase-field model in calculating the relaxation time at the phase interface is identified and an approximation is proposed to ensure the consistency with the phase-field model. It is also shown that the commonly used equilibrium velocity boundary for the binary fluid LB scheme does not conserve momentum at the wall boundary and a modified scheme is developed to ensure the momentum conservation at the boundary. In addition, a geometric formulation of the wetting boundary condition is proposed to replace the popular surface energy formulation and results show that the geometric approach enforces the prescribed contact angle better than the surface energy formulation in both static and dynamic wetting. The proposed LB formulation is applied to simulating droplet impingement dynamics in three dimensions and results are compared to those obtained with the continuous phase-field model, the LB simulations reported in the literature, and experimental data from the literature. The results show that the proposed LB simulation approach yields not only a significant speed improvement over the phase-field model in simulating droplet impingement dynamics on a submillimeter length scale, but also better accuracy than both the phase-field model and the previously reported LB techniques when compared to experimental data. Upon validation, the proposed LB modeling methodology is applied to the study of multiple-droplet impingement and interactions in three dimensions, which demonstrates its powerful capability of simulating extremely complex interface

  18. Simulation of liquid dynamics in a cryogenic mobile vessels

    Directory of Open Access Journals (Sweden)

    E. Lisowski

    2010-07-01

    Full Text Available Technical gases becomes liquid in extremely low temperature ranging minus 200 °C and very high pressure what makes that transportationdevices have to perform very strict requirement. Presented paper shows selected aspect of simulation of liquefied gas sloshing in aspect of requirements that mobile vessels have to fulfill. Mobile vessel which is the object of simulation is a two shell tank with vacuum and layer insulation between shells adapted to 20 ft container. It is assigned for see, railway and road transport and have to follow all of requirements for such transportation systems. Requirements for such tank are enclosed in standard ISO 1496-3 which deals with freight containers and standard EN13530-2 that describes vacuum, cryogenic vessels. The standards EN13530-2 defines that vessels which are to be filled equal or less than 80% should be fitted with surge plates to provide vessel stability and limit dynamic loads. Additionally surge plates area has tobe at least 70% of cross section of the vessel and volume between surge plates shall be not higher than 7.5 m3. Structure of the vessel as well as the surge plate should resist of longitudinal acceleration of 2g. Additionally surge plates shall resists stresses caused by pressure distributed across the area of surge plate and the pressure shall be calculated as mass of liquid between plates and acceleration 2g. In this paper is presented way of simulation of dynamic behavior of liquefied Argon on vessel structure. A numerical methods likeComputational Fluid Dynamics (CFD and Finite Element Analysis (FEA were used for this purpose. Combination of both tools allowedto get pick value of dynamic pressure that arising during acceleration of 2g, which was assumed is 0.2 s and investigate resistance of vessel and container structure. Presented approach is called Fluid – Structure Interaction simulation. In CFD simulation was used Ansys CFX code, while for FEA calculations Pro/Mechanica package.

  19. Simulating structural response to water impact

    OpenAIRE

    Campbell, James C; Vignjevic, Rade

    2012-01-01

    Structural response to water impact is important for several areas, including the aerospace and marine industries. Aircraft must be designed to cope with ditching and offshore structures are subject to extreme wave impact and green water loading. The goal is a reliable technique for predicting the structural response to extreme water loading. This is a complex problem involving the interaction of non-linear fluid behaviour (breaking waves, fluid impact) with non-linear structural behaviour (l...

  20. Dynamic modeling and simulation for nonholonomic welding mobile robot

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Based on the Newton-Euler method, the dynamic behaviors of the left and right driving wheels and the robot body for the welding mobile robot were derived. In order to realize the combination control of body turning and slider adjustment, the dynamic behaviors of sliders were also investigated. As a result, a systematic and complete dynamic model for the welding mobile robot was constructed. In order to verify the effectiveness of the above model, a sliding mode tracking control method was proposed and simulated, the lateral error stabilizes between -0.2 mm and +0.2 mm, and the total distance of travel for the slider is consistently within ±2 mm. The simulation results verify the effectiveness of the established dynamic model and also show that the seam tracking controller based on the dynamic model has excellent performance in terms of stability and robustness. Furthermore, the model is found to be very suitable for practical applications of the welding mobile robot.

  1. Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

    Science.gov (United States)

    Lu, Yan; Salsbury, Freddie R.

    2015-01-01

    ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.

  2. Nonlinear response and dynamical transitions in a phase-field crystal model for adsorbed overlayers

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, J A P [Departamento de Ciencias Exatas, Universidade Estadual do Sudoeste da Bahia, 45000-000 Vitoria da Conquista, BA (Brazil); Granato, E [Laboratorio Associado de Sensores e Materiais, Instituto Nacional de Pesquisas Espaciais, 12245-970 Sao Jose dos Campos, SP (Brazil); Ying, S C; Ala-Nissila, T [Department of Physics, PO Box 1843, Brown University, Providence, RI 02912-1843 (United States); Achim, C V [Department of Applied Physics, Aalto University School of Science and Technology, PO Box 11000, FI-00076 Aalto, Espoo (Finland); Elder, K R, E-mail: Jorge@las.inpe.b [Department of Physics, Oakland University, Rochester, Michigan 48309-4487 (United States)

    2010-09-01

    The nonlinear response and sliding friction behavior of a phase-field crystal model for driven adsorbed atomic layers is determined numerically. The model describes the layer as a continuous density field coupled to the pinning potential of the substrate and under an external driving force. Dynamical equations which take into account both thermal fluctuations and inertial effects are used for numerical simulations of commensurate and incommensurate layers. At low temperatures, the velocity response of an initially commensurate layer shows hysteresis with dynamical melting and freezing transitions at different critical forces. The main features of the sliding friction behavior are similar to the results obtained previously from molecular dynamics simulations of particle models. However, the dynamical transitions correspond to nucleations of stripes rather than closed domains.

  3. A phenomenological model for the dynamic response of wind turbines to turbulent wind

    Energy Technology Data Exchange (ETDEWEB)

    Rauh, Alexander; Peinke, Joachim [Institut fur Physik, Universitat Oldenburg, D-26111 Oldenburg (Germany)

    2004-02-01

    To predict the average power output of a wind turbine, a response model is proposed which takes into account: (1) the delayed response to the longitudinal wind speed fluctuations; (2) a response function of the turbine with arbitrary frequency dependence; and (3) wind fields of arbitrary turbulence intensity. In the limit of low turbulence intensity, the dynamical ansatz as proposed in 1992 by Rosen and Sheinman is reproduced. It is shown, how the response function of the turbine can be obtained from simulation experiments of a specific wind turbine. For two idealized situations the dynamic effect of fluctuating wind is estimated at turbulence intensities 0{<=}I{sub u}{<=}0.5. At the special mean wind speed V=8m/s, the turbine response function is determined from simulation data published by Sheinman and Rosen in 1992 and 1994.

  4. Molecular dynamical simulations of melting behaviors of metal clusters

    Directory of Open Access Journals (Sweden)

    Ilyar Hamid

    2015-04-01

    Full Text Available The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002] for the statically stable structures.

  5. Multi-Scale Dynamics, Control, and Simulation of Granular Spacecraft

    Science.gov (United States)

    Quadrelli, Marco B.; Basinger, Scott; Swartzlander, Grover

    2013-01-01

    In this paper, we present some ideas regarding the modeling, dynamics and control aspects of granular spacecraft. Granular spacecraft are complex multibody systems composed of a spatially disordered distribution of a large number of elements, for instance a cloud of grains in orbit. An example of application is a spaceborne observatory for exoplanet imaging, where the primary aperture is a cloud instead of a monolithic aperture. A model is proposed of a multi-scale dynamics of the grains and cloud in orbit, as well as a control approach for cloud shape maintenance and alignment, and preliminary simulation studies are carried out for the representative imaging system.

  6. Dynamic Modeling and Simulation of a Real World Billiard

    CERN Document Server

    Hartl, Alexandre E; Mazzoleni, Andre P

    2011-01-01

    Gravitational billiards provide an experimentally accessible arena for testing formulations of nonlinear dynamics. We present a mathematical model that captures the essential dynamics required for describing the motion of a realistic billiard for arbitrary boundaries. Simulations of the model are applied to parabolic, wedge and hyperbolic billiards that are driven sinusoidally. Direct comparisons are made between the model's predictions and previously published experimental data. It is shown that the data can be successfully modeled with a simple set of parameters without an assumption of exotic energy dependence.

  7. 3D vesicle dynamics simulations with a linearly triangulated surface

    Science.gov (United States)

    Boedec, G.; Leonetti, M.; Jaeger, M.

    2011-02-01

    Simulations of biomembranes have gained an increasing interest in the past years. Specificities of these membranes propose new challenges for the numerics. In particular, vesicle dynamics are governed by bending forces as well as a surface incompressibility constraint. A method to compute the bending force density resultant onto piecewise linearly triangulated surface meshes is described. This method is coupled with a boundary element method solver for inner and outer fluids, to compute vesicle dynamics under external flows. The surface incompressibility constraint is satisfied by the construction of a projection operator.

  8. Dynamical electron backscatter diffraction patterns. Part I: pattern simulations.

    Science.gov (United States)

    Callahan, Patrick G; De Graef, Marc

    2013-10-01

    A new approach for the simulation of dynamic electron backscatter diffraction (EBSD) patterns is introduced. The computational approach merges deterministic dynamic electron-scattering computations based on Bloch waves with a stochastic Monte Carlo (MC) simulation of the energy, depth, and directional distributions of the backscattered electrons (BSEs). An efficient numerical scheme is introduced, based on a modified Lambert projection, for the computation of the scintillator electron count as a function of the position and orientation of the EBSD detector; the approach allows for the rapid computation of an individual EBSD pattern by bi-linear interpolation of a master EBSD pattern. The master pattern stores the BSE yield as a function of the electron exit direction and exit energy and is used along with weight factors extracted from the MC simulation to obtain energy-weighted simulated EBSD patterns. Example simulations for nickel yield realistic patterns and energy-dependent trends in pattern blurring versus filter window energies are in agreement with experimental energy-filtered EBSD observations reported in the literature.

  9. Petascale Molecular Dynamics Simulations of Polymers and Liquid Crystals

    Science.gov (United States)

    Nguyen, Trung Dac; Carrillo, Jan-Michael; Brown, W. Michael

    2014-03-01

    The availability of faster and larger supercomputers and more efficient parallel algorithms now enable us to perform unprecedented simulations approaching experimental scales. Here we present two examples of our latest large-scale molecular dynamics simulations using the Titan supercomputer in the Oak Ridge Leadership Computing Facility (OLCF). In the first study, we address the rupture origin of liquid crystal thin films wetting a solid substrate. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation. Importantly, we found evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. In the second study, we used coarse-grained molecular dynamics to simulate the thermal annealing of poly(3-hexylthiophene) (P3HT) and Phenyl-C61-butyric acid methyl ester (PCBM) blends in the presence of a silicon substrate found in organic solar cells. Our simulations show different phase segregated morphologies dependent on the P3HT chain length and PCBM volume fraction in the blend. Furthermore, the ternary blend of short and long P3HT chains with PCBM affects the vertical phase segregation of PCBM decreasing its concentration in the vicinity of the substrate. U.S. DOE Contract No. DE-AC05-00OR22725.

  10. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.

    Science.gov (United States)

    Petsev, Nikolai D; Leal, L Gary; Shell, M Scott

    2015-01-28

    We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

  11. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott [Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080 (United States)

    2015-01-28

    We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

  12. Flight Dynamic Simulation with Nonlinear Aeroelastic Interaction using the ROM-ROM Procedure Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology, Inc. proposes to develop an integrated flight dynamics simulation capability with nonlinear aeroelastic interactions by combining a flight dynamics...

  13. Responsive supply chain: modeling and simulation

    Directory of Open Access Journals (Sweden)

    Amit Kumar Sinha

    2015-06-01

    Full Text Available Unexpected occurrence like natural calamity, abruptly change in customer demands, upgradation of technologies, necessity of compatible suppliers etc. is the most challenging issues even for efficient global supply chain management. Therefore, modeling of responsive supply chain is an emerging technology for sustaining any firm/industry in future competitive environment. In this paper, an attempt has been made to not only analyze the performance of efficient supply chain management but also how to improve the performance of existing supply chain with the objective of developing a modeling of responsive supply chain management. The complexity of the model is also highlighted with the help of numerical example. This paper also explores the possibility to mathematical modeling of the responsive supply chain which will be an emerging topic for researchers and practitioners. The modeling of responsive supply chain can be employed as a competitive strategy for e-commerce, green supply chain, and compatible supplier selection problem. The another salient feature of this paper is that a distinct comparative literature review of the lean, agile, efficient, and responsive supply chain management has been presented.

  14. Molecular dynamics simulation of liquid-vapor surface tension

    Institute of Scientific and Technical Information of China (English)

    王德; ZENG; Danling; 等

    2002-01-01

    A molecular dynamics simulation model is established based on the well-known Lennard-Jones 12-6 potential function to determine the surface tension of a Lennard-Jones liquid-vapor interface.The simulation is carried out with argon as the working fluid of a given molecular number at different temperature and different truncated radius.It is found that the surface tension of a Lennard-Jones fluid is likely to be bigger for a bigger truncated radius,and tends to be constant after the truncated radius increased to a certain value.It is also found that the surface tension becomes smaller as the temperature increases.

  15. Structural considerations for a software life cycle dynamic simulation model

    Science.gov (United States)

    Tausworthe, R. C.; Mckenzie, M.; Lin, C. Y.

    1983-01-01

    This paper presents the results of a preliminary study into the prospects for simulating the software implementation and maintenance life cycle process, with the aim of producing a computerized tool for use by management and software engineering personnel in project planning, tradeoff studies involving product, environmental, situational, and technological factors, and training. The approach taken is the modular application of a 'flow of resource' concept to the systems dynamics simulation modeling technique. The software life cycle process is represented as a number of stochastic, time-varying, interacting work tasks that each achieves one of the project milestones. Each task is characterized by the item produced, the personnel applied, and the budgetary profile.

  16. Molecular dynamics simulation of peeling a DNA molecule on substrate

    Institute of Scientific and Technical Information of China (English)

    Xinghua Shi; Yong Kong; Yapu Zhao; Huajian Gao

    2005-01-01

    Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

  17. Molecular dynamics simulation of thermodynamical properties of copper clusters

    Institute of Scientific and Technical Information of China (English)

    Wu Zhi-Min; Wang Xin-Qiang; Yang Yuan-Yuan

    2007-01-01

    The melting and freezing processes of CuN (N = 180, 256, 360, 408, 500, 628 and 736) nanoclusters are simulated by using micro-canonical molecular dynamics simulation technique. The potential energies and the heat capacities as a function of temperature are obtained. The results reveal that the melting and freezing points increase almost linearly with the atom number in the cluster increasing. All copper nanoclusters have negative heat capacity around the melting and freezing points, and hysteresis effect in the melting/freezing transition is derived in CuN nanoclusters for the first time.

  18. Dynamics simulation of electrorheological suspensions in poiseuille flow field

    Institute of Scientific and Technical Information of China (English)

    朱石沙; 罗成; 周杰; 陈娜

    2008-01-01

    Based on a modified Maxwell-Wagner model,molecular dynamics is carried out to simulate the structural changes of ER(electrorheological) suspensions in a poiseuille flow field.The simulation results show that the flow assists in the collection of particles at the electrodes under a low pressure gradient,and the negative ER effect will show under a high pressure gradient.By analyzing the relationship curves of the shear stress and the pressure gradient in different relaxation time,it is found that for the same kind of ER suspensions materials,there is an optimal dielectric relaxation frequency.

  19. Dynamic focusing approach to mixed-level simulation

    Science.gov (United States)

    Fall, Thomas C.

    1997-06-01

    The dynamic focusing approach (DFA) has been under development for several years. Its intent is to address several of the issues of mixed level simulations, particularly the aggregational issues. Though the approach requires that the system be able to be modeled within certain constraints, many systems of interest fit well within them. This approach combines a hierarchical representation of knowledge with a stochastic propagation mechanism; this provides capability to gracefully move from coarse granularity to fine granularity under user guidance. Prototype tools have been developed for engineering analysis, combat simulation and TQM process implementation. This paper gives an overview of the approach and its current status.

  20. Molecular Dynamics Simulations of Field Emission From a Planar Nanodiode

    CERN Document Server

    Torfason, Kristinn; Manolescu, Andrei

    2014-01-01

    High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.

  1. The very local Hubble flow: computer simulations of dynamical history

    CERN Document Server

    Chernin, A D; Valtonen, M J; Dolgachev, V P; Domozhilova, L M; Makarov, D I

    2003-01-01

    The phenomenon of the very local ($\\le3$ Mpc) Hubble flow is studied on the basis of the data of recent precision observations. A set of computer simulations is performed to trace the trajectories of the flow galaxies back in time to the epoch of the formation of the Local Group. It is found that the `initial conditions' of the flow are drastically different from the linear velocity-distance relation. The simulations enable also to recognize the major trends of the flow evolution and identify the dynamical role of universal antigravity produced by cosmic vacuum.

  2. Molecular dynamics simulations of diffusion mechanisms in NiAl

    Energy Technology Data Exchange (ETDEWEB)

    Soule De Bas, B.; Farkas, D

    2003-03-14

    Molecular dynamics simulations of the diffusion process in ordered B2 NiAl at high temperature were performed using an embedded atom interatomic potential. Diffusion occurs through a variety of cyclic mechanisms that accomplish the motion of the vacancy through nearest neighbor jumps restoring order to the alloy at the end of the cycle. The traditionally postulated six-jump cycle is only one of the various cycles observed and some of these are quite complex. A detailed sequential analysis of the observed six-jump cycles was performed and the results are analyzed in terms of the activation energies for individual jumps calculated using molecular statics simulations.

  3. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable...

  4. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp

    2012-06-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.

  5. Molecular dynamics simulation of the viscocapillary leveling of polymer films

    CERN Document Server

    Tanis, Ioannis; Salez, Thomas; Raphaël, Elie; Maggs, Anthony C; Baschnagel, Jörg

    2016-01-01

    Surface tension-driven flow techniques have recently emerged as an efficient means of shedding light into the rheology of thin polymer films. Motivated by experimental and theoretical approaches in films bearing a varying surface topography, we present results on the viscocapillary relaxation of a square pattern at the free surface of a polymer film, using molecular dynamics simulations of a coarse-grained polymer model. Height profiles are monitored as a function of time after heating the system above its glass-transition temperature. The associated relaxation rates are in agreement with the low-Reynolds-number hydrodynamic model, thus confirming the utility of the simulation method.

  6. Fast Quantum Molecular Dynamics Simulations of Simple Organic Liquids under Shock Compression

    Science.gov (United States)

    Cawkwell, Marc; Niklasson, Anders; Manner, Virginia; McGrane, Shawn; Dattelbaum, Dana

    2013-06-01

    The responses of liquid formic acid, acrylonitrile, and nitromethane to shock compression have been studied using quantum-based molecular dynamics simulations with the self-consistent tight-binding code LATTE. Microcanonical Born-Oppenheimer trajectories with precise energy conservation were computed without relying on an iterative self-consistent field optimization of the electronic degrees of freedom at each time step via the Fast Quantum Mechanical Molecular Dynamics formalism. The input shock pressures required to initiate chemistry in our simulations agree very well with recent laser- and flyer-plate-driven shock compression experiments. On-the-fly analysis of the electronic structure of the liquids over hundreds of picoseconds after dynamic compression revealed that their reactivity is strongly correlated with the temperature and pressure dependence of their HOMO-LUMO gap.

  7. Dynamic Simulation of Carbonate Fuel Cell-Gas Turbine Hybrid Systems

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, R.A. (U. of California, Irvine, CA); Brouwer, J. (U. of California, Irvine, CA); Liese, E.A.; Gemmen, R.S.

    2006-04-01

    Hybrid fuel cell/gas turbine systems provide an efficient means of producing electricity from fossil fuels with ultra low emissions. However, there are many significant challenges involved in integrating the fuel cell with the gas turbine and other components of this type of system. The fuel cell and the gas turbine must maintain efficient operation and electricity production while protecting equipment during perturbations that may occur when the system is connected to the utility grid or in stand-alone mode. This paper presents recent dynamic simulation results from two laboratories focused on developing tools to aid in the design and dynamic analyses of hybrid fuel cell systems. The simulation results present the response of a carbonate fuel cell/gas turbine, or molten carbonate fuel cell/gas turbine, (MCFC/GT) hybrid system to a load demand perturbation. Initial results suggest that creative control strategies will be needed to ensure a flexible system with wide turndown and robust dynamic operation.

  8. Design and Dynamics Simulation of a Novel Double-Ring-Plate Gear Reducer

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A patented double-ring-plate gear reducer was designed and its dynamic performance was simulated. One unique characteristic of this novel drive is that the phase angle difference between two parallelogram mechanisms is a little less than 180 degree and four counterweights on two crankshafts are designed to balance inertia forces and inertia moments of the mechanisms. lts oper ating principle, advantages, and design issues were discussed. An elasto-dynamics model was presented to acquire its dynamic response by considering the elastic deformations of ring-plates,gears, bearings, etc. The simulation results reveal that compared with housing bearings, planetary bearings work in more severe conditions. The fluctuation of loads on gears and bearings indicates that the main reason for reducer vibration is elastic deformations of the system rather than inertia forces and inertia moments of the mechanisms.

  9. Modeling of Protection in Dynamic Simulation Using Generic Relay Models and Settings

    Energy Technology Data Exchange (ETDEWEB)

    Samaan, Nader A.; Dagle, Jeffery E.; Makarov, Yuri V.; Diao, Ruisheng; Vallem, Mallikarjuna R.; Nguyen, Tony B.; Miller, Laurie E.; Vyakaranam, Bharat; Tuffner, Francis K.; Pai, M. A.; Conto, Jose; Kang, Sun Wook

    2016-07-19

    This paper shows how generic protection relay models available in planning tools can be augmented with settings that are based on NERC standards or best engineering practice. Selected generic relay models in Siemens PSS®E have been used in dynamic simulations in the proposed approach. Undervoltage, overvoltage, underfrequency, and overfrequency relays have been modeled for each generating unit. Distance-relay protection was modeled for transmission system protection. Two types of load-shedding schemes were modeled: underfrequency (frequency-responsive non-firm load shedding) and underfrequency and undervoltage firm load shedding. Several case studies are given to show the impact of protection devices on dynamic simulations. This is useful for simulating cascading outages.

  10. A Modal Model to Simulate Typical Structural Dynamic Nonlinearity [PowerPoint

    Energy Technology Data Exchange (ETDEWEB)

    Mayes, Randall L.; Pacini, Benjamin Robert; Roettgen, Dan

    2016-01-01

    Some initial investigations have been published which simulate nonlinear response with almost traditional modal models: instead of connecting the modal mass to ground through the traditional spring and damper, a nonlinear Iwan element was added. This assumes that the mode shapes do not change with amplitude and there are no interactions between modal degrees of freedom. This work expands on these previous studies. An impact experiment is performed on a structure which exhibits typical structural dynamic nonlinear response, i.e. weak frequency dependence and strong damping dependence on the amplitude of vibration. Use of low level modal test results in combination with high level impacts are processed using various combinations of modal filtering, the Hilbert Transform and band-pass filtering to develop response data that are then fit with various nonlinear elements to create a nonlinear pseudo-modal model. Simulations of forced response are compared with high level experimental data for various nonlinear element assumptions.

  11. A comparison of the lattice discrete particle method to the finite-element method and the K&C material model for simulating the static and dynamic response of concrete.

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Jovanca J.; Bishop, Joseph E.

    2013-11-01

    This report summarizes the work performed by the graduate student Jovanca Smith during a summer internship in the summer of 2012 with the aid of mentor Joe Bishop. The projects were a two-part endeavor that focused on the use of the numerical model called the Lattice Discrete Particle Model (LDPM). The LDPM is a discrete meso-scale model currently used at Northwestern University and the ERDC to model the heterogeneous quasi-brittle material, concrete. In the first part of the project, LDPM was compared to the Karagozian and Case Concrete Model (K&C) used in Presto, an explicit dynamics finite-element code, developed at Sandia National Laboratories. In order to make this comparison, a series of quasi-static numerical experiments were performed, namely unconfined uniaxial compression tests on four varied cube specimen sizes, three-point bending notched experiments on three proportional specimen sizes, and six triaxial compression tests on a cylindrical specimen. The second part of this project focused on the application of LDPM to simulate projectile perforation on an ultra high performance concrete called CORTUF. This application illustrates the strengths of LDPM over traditional continuum models.

  12. Dynamic simulation of urban hybrid electric vehicles; Dynamische Simulation von Stadthybridfahrzeugen

    Energy Technology Data Exchange (ETDEWEB)

    Winke, Florian; Bargende, Michael [Stuttgart Univ. (Germany). Inst. fuer Verbrennungsmotoren und Kraftfahrwesen (IVK)

    2013-09-15

    As a result of the rising requirements on the development process of modern vehicles, simulation models for the prediction of fuel efficiency have become an irreplaceable tool in the automotive industry. Especially for the design of hybrid electric drivetrains, the increasingly short development cycles can only be met by the use of efficient simulation models. At the IVK of the University of Stuttgart, different approaches to simulating the longitudinal dynamics of hybrid electric vehicles were analysed and compared within the presented project. The focus of the investigations was on urban operation. The objective was to develop a hybrid vehicle concept that allows an equitable comparison with pure battery electric vehicles. (orig.)

  13. Quantum Trajectory Approach to Molecular Dynamics Simulation with Surface Hopping

    CERN Document Server

    Feng, Wei; Li, Xin-Qi; Fang, Weihai

    2012-01-01

    The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic state. In this work we propose a quantum trajectory approach to the MD simulation with surface hopping, from an insight that an effective "observation" is actually implied in theMDsimulation through tracking the forces experienced, just like checking the meter's result in the quantum measurement process. This treatment can build the nonadiabatic surface hopping on a dynamical foundation, instead of the usual artificial and conceptually inconsistent hopping algorithms. The effects and advantages of the proposed scheme are preliminarily illustrated by a two-surface model system.

  14. DYNSYL: a general-purpose dynamic simulator for chemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Patterson, G.K.; Rozsa, R.B.

    1978-09-05

    Lawrence Livermore Laboratory is conducting a safeguards program for the Nuclear Regulatory Commission. The goal of the Material Control Project of this program is to evaluate material control and accounting (MCA) methods in plants that handle special nuclear material (SNM). To this end we designed and implemented the dynamic chemical plant simulation program DYNSYL. This program can be used to generate process data or to provide estimates of process performance; it simulates both steady-state and dynamic behavior. The MCA methods that may have to be evaluated range from sophisticated on-line material trackers such as Kalman filter estimators, to relatively simple material balance procedures. This report describes the overall structure of DYNSYL and includes some example problems. The code is still in the experimental stage and revision is continuing.

  15. Numerical simulations of dynamics and emission from relativistic astrophysical jets

    CERN Document Server

    Mimica, Petar; Rueda-Becerril, Jesus Misrayim; Tabik, Siham; Aloy, Carmen

    2012-01-01

    Broadband emission from relativistic outflows (jets) of active galactic nuclei (AGN) and gamma-ray bursts (GRBs) contains valuable information about the nature of the jet itself, and about the central engine which launches it. Using special relativistic hydrodynamics and magnetohydronamics simulations we study the dynamics of the jet and its interaction with the surrounding medium. The observational signature of the simulated jets is computed using a radiative transfer code developed specifically for the purpose of computing multi-wavelength, time-dependent, non-thermal emission from astrophysical plasmas. We present results of a series of long-term projects devoted to understanding the dynamics and emission of jets in parsec-scale AGN jets, blazars and the afterglow phase of the GRBs.

  16. Dislocation dynamics: simulation of plastic flow of bcc metals

    Energy Technology Data Exchange (ETDEWEB)

    Lassila, D H

    2001-02-20

    This is the final report for the LDRD strategic initiative entitled ''Dislocation Dynamic: Simulation of Plastic Flow of bcc Metals'' (tracking code: 00-SI-011). This report is comprised of 6 individual sections. The first is an executive summary of the project and describes the overall project goal, which is to establish an experimentally validated 3D dislocation dynamics simulation. This first section also gives some information of LLNL's multi-scale modeling efforts associated with the plasticity of bcc metals, and the role of this LDRD project in the multiscale modeling program. The last five sections of this report are journal articles that were produced during the course of the FY-2000 efforts.

  17. Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Alekseeva, Uliana, E-mail: Alekseeva@itc.rwth-aachen.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); German Research School for Simulation Sciences (GRS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Winkler, Roland G., E-mail: r.winkler@fz-juelich.de [Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Sutmann, Godehard, E-mail: g.sutmann@fz-juelich.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); ICAMS, Ruhr-University Bochum, D-44801 Bochum (Germany)

    2016-06-01

    A new adaptive resolution technique for particle-based multi-level simulations of fluids is presented. In the approach, the representation of fluid and solvent particles is changed on the fly between an atomistic and a coarse-grained description. The present approach is based on a hybrid coupling of the multiparticle collision dynamics (MPC) method and molecular dynamics (MD), thereby coupling stochastic and deterministic particle-based methods. Hydrodynamics is examined by calculating velocity and current correlation functions for various mixed and coupled systems. We demonstrate that hydrodynamic properties of the mixed fluid are conserved by a suitable coupling of the two particle methods, and that the simulation results agree well with theoretical expectations.

  18. Molecular dynamics simulation of radiation damage cascades in diamond

    Energy Technology Data Exchange (ETDEWEB)

    Buchan, J. T. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Robinson, M. [Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia); Christie, H. J.; Roach, D. L.; Ross, D. K. [Physics and Materials Research Centre, School of Computing, Science and Engineering, University of Salford, Salford, Greater Manchester M5 4WT (United Kingdom); Marks, N. A. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia)

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  19. Molecular dynamics simulations of nanoscale metal tips under electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Parviainen, S., E-mail: stefan.parviainen@helsinki.fi [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, FIN-00014 Helsinki (Finland); Djurabekova, F.; Pohjonen, A.; Nordlund, K. [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, FIN-00014 Helsinki (Finland)

    2011-07-15

    Vacuum arcing is a plasma discharge over a metal surface under high electric fields. Plasma formation requires the supply of neutral atoms, which under high vacuum condition can only come from the surface itself. Nevertheless, the mechanisms by which the atoms are supplied are not known. In the present work, we propose a model for the onset of surface roughness and field-enhanced atom evaporation. Specifically, we describe a dislocation mechanism of tip growth from near-surface voids. We also simulate surface charging and resistive heating using a hybrid electrodynamics and molecular dynamics (ED and MD) code for dynamic simulations of electronic effects. We study the morphological evolution of the nanoscale protrusion under the electronic effects, such as the stretching of the tip by the stress induced by the electric field.

  20. First Principles Modelling of Shape Memory Alloys Molecular Dynamics Simulations

    CERN Document Server

    Kastner, Oliver

    2012-01-01

    Materials sciences relate the macroscopic properties of materials to their microscopic structure and postulate the need for holistic multiscale research. The investigation of shape memory alloys is a prime example in this regard. This particular class of materials exhibits strong coupling of temperature, strain and stress, determined by solid state phase transformations of their metallic lattices. The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and  covers  thermodynamical, micro-mechanical  and crystallographical aspects. It addresses scientists in these research fields and thei...

  1. A dynamical formulation for multiflexible controlled spacecraft simulation

    Science.gov (United States)

    Corrado, G.; Ravazzotti, M. T.

    1981-09-01

    The dynamic behavior of highly flexible, rotating spacecraft is described by a method which does not require any particular approximation and is not limited to any particular arrangement of the bodies constituting the system. The analytical technique is based on the formalism of the DISCOS computer program (Bodley, 1978), a powerful tool for the dynamic simulation of complex spacecraft. The state equations, described in a general format, are applicable to any complex spacecraft under any environmental load. The approach takes into account the distributed flexibility, the relative motion of the bodies, the automatic coupling of the momentum wheels, the system control laws, and their interaction with the structure. Synthesis and analysis of the linearized system are used to solve time and frequency equations. The required computing times for different program options are listed, along with the number of equations and the integration step size. A block diagram of the DISCOS package structure is given, showing the development from problem definition to simulation results.

  2. Simulation of Spin-orbit Dynamics in Storage Rings

    Science.gov (United States)

    Ivanov, A.; Andrianov, S.; Senichev, Yu.

    2016-09-01

    In the article a mapping approach based on nonlinear matrix integration for longterm spin-orbit dynamics simulation is briefly described. Using this technique the nonlinear effects of spin dynamics in an electrostatics storage ring are investigated. Namely, the fringe fields, the energy conservation law and the random field errors are considered. The necessity of examination of such effects arises, for example, in the storage ring design for search the Electrical Dipole Moment of proton and deuteron. The EDM ring is proposed to measure EDM using the spin transformation of polarized particle in the magneto-electrostatic elements of the ring. The article consists of short description of the spin-orbit simulation results based on the nonlinear model.

  3. Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics

    Science.gov (United States)

    Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

    2016-02-01

    Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales.

  4. Dynamic simulation of flash drums using rigorous physical property calculations

    Directory of Open Access Journals (Sweden)

    F. M. Gonçalves

    2007-06-01

    Full Text Available The dynamics of flash drums is simulated using a formulation adequate for phase modeling with equations of state (EOS. The energy and mass balances are written as differential equations for the internal energy and the number of moles of each species. The algebraic equations of the model, solved at each time step, are those of a flash with specified internal energy, volume and mole numbers (UVN flash. A new aspect of our dynamic simulations is the use of direct iterations in phase volumes (instead of pressure for solving the algebraic equations. It was also found that an iterative procedure previously suggested in the literature for UVN flashes becomes unreliable close to phase boundaries and a new alternative is proposed. Another unusual aspect of this work is that the model expressions, including the physical properties and their analytical derivatives, were quickly implemented using computer algebra.

  5. Simulation of the dynamics in the magnetotail current sheet

    CERN Document Server

    Ojeda, Arian; Calzadilla, Alexander; Savio, Siomel; Alazo, Katy

    2013-01-01

    The dynamics in the magnetosphere current sheet was simulated following transformations to the rectangular NxM array of cells (cellular automaton) originally proposed by Koselov and Koselova (2002). The magnetosphere part of the modeling system was organized as a rectangular arrangement of cells with a stored energy, a local redistribution of the energy will exist when a value threshold is exceeded in one of the cells. We assume that the threshold value in each cell depends on external control parameter which influences the long boundaries of the rectangular array (40x80). The model dynamics controlled by the z-component of the interplanetary magnetic field (Bz) as well as analogies between the model transient processes and the observed substorm auroral activations are discussed. The Bz correspond to temporary windows of the solar wind for a group of magnetic clouds and plasmoids. The model simulates organized patterns in the energy distribution. The function of distribution of probability (or PDF) of the siz...

  6. Dynamic model of the vergence eye movement system: simulations using MATLAB/SIMULINK.

    Science.gov (United States)

    Hung, G K

    1998-01-01

    A dynamic model of the vergence eye movement system was developed and simulated using MATLAB/SIMULINK. The model was based on a dual-mode dynamic model previously written in FORTRAN. It consisted of a fast open-loop component and a slow closed-loop component. The new model contained several important modifications. For example, in the fast component, a zero-order hold element replaced the sampler and the target trajectory estimator in the earlier model to provide more stable and accurate responses. Also, a periodicity detector was added to automatically detect periodicity in the stimulus waveform. The stored periodic stimulus, with a reduction in latency, was used to drive the fast component output. Moreover, a connection representing the efference copy signal was added from the fast component output to the disparity input to provide an accurate estimate of the stimulus waveform. Further, Robinson's model of the extraocular muscles replaced the earlier 2nd-order plant to provide more realistic muscle dynamics. The entire model, containing the fast and slow components, was simulated using a variety of stimuli such as pulses, positive and negative ramps, square-wave, and sine-wave. The responses showed dynamic characteristics similar to experimental results. Thus, this new MATLAB/SIMULINK program provides a relatively easy-to-use, versatile, and powerful simulation environment for investigating the basic as well as clinical aspects of vergence dynamics. Moreover, the simulation program has general characteristics that can be modified to represent other oculomotor systems such as the versional and accommodation systems. This provides a framework for future investigation of dynamic interactions between oculomotor systems.

  7. Dynamic information architecture system (DIAS) : multiple model simulation management.

    Energy Technology Data Exchange (ETDEWEB)

    Simunich, K. L.; Sydelko, P.; Dolph, J.; Christiansen, J.

    2002-05-13

    Dynamic Information Architecture System (DIAS) is a flexible, extensible, object-based framework for developing and maintaining complex multidisciplinary simulations of a wide variety of application contexts. The modeling domain of a specific DIAS-based simulation is determined by (1) software Entity (domain-specific) objects that represent the real-world entities that comprise the problem space (atmosphere, watershed, human), and (2) simulation models and other data processing applications that express the dynamic behaviors of the domain entities. In DIAS, models communicate only with Entity objects, never with each other. Each Entity object has a number of Parameter and Aspect (of behavior) objects associated with it. The Parameter objects contain the state properties of the Entity object. The Aspect objects represent the behaviors of the Entity object and how it interacts with other objects. DIAS extends the ''Object'' paradigm by abstraction of the object's dynamic behaviors, separating the ''WHAT'' from the ''HOW.'' DIAS object class definitions contain an abstract description of the various aspects of the object's behavior (the WHAT), but no implementation details (the HOW). Separate DIAS models/applications carry the implementation of object behaviors (the HOW). Any model deemed appropriate, including existing legacy-type models written in other languages, can drive entity object behavior. The DIAS design promotes plug-and-play of alternative models, with minimal recoding of existing applications. The DIAS Context Builder object builds a constructs or scenario for the simulation, based on developer specification and user inputs. Because DIAS is a discrete event simulation system, there is a Simulation Manager object with which all events are processed. Any class that registers to receive events must implement an event handler (method) to process the event during execution. Event handlers

  8. Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Ronak Y. Patel

    2011-01-01

    Full Text Available Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.

  9. Static and dynamic properties of curved vapour-liquid interfaces by massively parallel molecular dynamics simulation

    CERN Document Server

    Horsch, Martin T; Vrabec, Jadran; Glass, Colin W; Niethammer, Christoph; Bernreuther, Martin F; Müller, Erich A; Jackson, George

    2011-01-01

    Curved fluid interfaces are investigated on the nanometre length scale by molecular dynamics simulation. Thereby, droplets surrounded by a metastable vapour phase are stabilized in the canonical ensemble. Analogous simulations are conducted for cylindrical menisci separating vapour and liquid phases under confinement in planar nanopores. Regarding the emergence of nanodroplets during nucleation, a non-equilibrium phenomenon, both the non-steady dynamics of condensation processes and stationary quantities related to supersaturated vapours are considered. Results for the truncated and shifted Lennard-Jones fluid and for mixtures of quadrupolar fluids confirm the applicability of the capillarity approximation and the classical nucleation theory.

  10. Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations

    OpenAIRE

    Olkhova, Elena; Hutter, Michael C; Lill, Markus A.; Helms, Volkhard; Michel, Hartmut

    2004-01-01

    We present a molecular dynamics study of cytochrome c oxidase from Paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. Parallel simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water ...

  11. The Fermi-Pasta Problem: Simulation and Modern Dynamics.

    Science.gov (United States)

    Weissert, Thomas P.

    In 1952, as a first approach to computational nonlinear problems, 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 the three-body problem, they expected to see the diffusion of energy from its single-mode initial condition to all other modes of the string (thermalization). 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 ergodicity follows from the lack of a complete set of integrals of the motion in a Hamiltonian model. I trace the history of this problem from the FPU simulation up to the point that a consensus was reached about its solution twenty years later. During this period, the simulation of nonlinearly-perturbed integrable models became the methodology for a new era in dynamics. Through the use of simulation, dynamicists discovered both 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. Historically, I map the set of conceptually-related journal articles into a chronological inference topology that tracks the emergent understanding of this so-called "fundamental problem of dynamics." Simulating non-integrable models on a digital computer requires the discretization of time and space. In turn, these approximations affect what the simulation can reveal about the model, and the model about reality. As the central feature of this new methodology, simulations play the role of experiments on mathematical models. Although similar in function to physical experiments, simulations differ significantly because they explore a mathematical

  12. Modeling human response errors in synthetic flight simulator domain

    Science.gov (United States)

    Ntuen, Celestine A.

    1992-01-01

    This paper presents a control theoretic approach to modeling human response errors (HRE) in the flight simulation domain. The human pilot is modeled as a supervisor of a highly automated system. The synthesis uses the theory of optimal control pilot modeling for integrating the pilot's observation error and the error due to the simulation model (experimental error). Methods for solving the HRE problem are suggested. Experimental verification of the models will be tested in a flight quality handling simulation.

  13. Simulation of a flowing snow avalanche using molecular dynamics

    OpenAIRE

    2010-01-01

    Ankara : The Department of Computer Engineering and the Institute of Engineering and Science of Bilkent University, 2010. Thesis (Master's) -- Bilkent University, 2010. Includes bibliographical references leaves 45-50. This thesis presents an approach for modeling and simulation of a flowing snow avalanche, which is formed of dry and liquefied snow that slides down a slope, by using molecular dynamics and discrete element method. A particle system is utilized as a base method for th...

  14. Dynamic Simulation for Hysteresis in Shape Memory Alloy under Tension

    Institute of Scientific and Technical Information of China (English)

    WANG Ping; ZHAO Jian-Bo; TANG Shao-Qiang

    2008-01-01

    We demonstrate that the Suliciu model is capable to model the hysteresis phenomenon observed experimentally in NiTi shape memory alloy micro-tubes.This model allows a class of stationary phase interfaces.By a series of fully dynamic numerical simulations that mimic quasi-static loading and unloading,the nominal stress-strain curve exhibits a big hysteresis loop,which quantitatively agrees with the experimental results.

  15. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

    Science.gov (United States)

    Rapaport, D. C.

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  16. Using Soft Computing Technologies for the Simulation of LCAC Dynamics

    Science.gov (United States)

    2011-09-01

    real-time, time-domain predictions of the vehicle’s dynamics as a function of the control signals given by the driver. Results are presented...free- running LCAC model, faster-than-real-time simulation, soft computing technology 1.0 INTRODUCTION The Maneuvering and Control Division (MCD...like all hovercraft , rides on a cushion of air. The air is supplied to the cushion by four centrifugal fans driven by the craft’s gas turbine

  17. Improved Pyrolysis Micro reactor Design via Computational Fluid Dynamics Simulations

    Science.gov (United States)

    2017-05-23

    NUMBER (Include area code) 23 May 2017 Briefing Charts 25 April 2017 - 23 May 2017 Improved Pyrolysis Micro-reactor Design via Computational Fluid... PYROLYSIS MICRO-REACTOR DESIGN VIA COMPUTATIONAL FLUID DYNAMICS SIMULATIONS Ghanshyam L. Vaghjiani* DISTRIBUTION A: Approved for public release...Approved for public release, distribution unlimited. PA Clearance 17247 Chen-Source (>240 references from SciFinder as of 5/1/17): Flash pyrolysis

  18. Simulation of dynamic systems with Matlab and Simulink

    CERN Document Server

    Klee, Harold

    2011-01-01

    Mathematical ModelingDerivation of a Mathematical ModelDifference EquationsFirst Look at Discrete-Time SystemsCase Study: Population Dynamics (Single Species)Continuous-Time SystemsFirst-Order SystemsSecond-Order SystemsSimulation DiagramsHigher-Order SystemsState VariablesNonlinear SystemsCase Study: Submarine Depth Control SystemElementary Numerical IntegrationDiscrete-Time System Approximation of a Continuous-

  19. Microscopic molecular superfluid response: theory and simulations

    Science.gov (United States)

    Zeng, Tao; Roy, Pierre-Nicholas

    2014-04-01

    Since its discovery in 1938, superfluidity has been the subject of much investigation because it provides a unique example of a macroscopic manifestation of quantum mechanics. About 60 years later, scientists successfully observed this phenomenon in the microscopic world though the spectroscopic Andronikashvili experiment in helium nano-droplets. This reduction of scale suggests that not only helium but also para-H2 (pH2) can be a candidate for superfluidity. This expectation is based on the fact that the smaller number of neighbours and surface effects of a finite-size cluster may hinder solidification and promote a liquid-like phase. The first prediction of superfluidity in pH2 clusters was reported in 1991 based on quantum Monte Carlo simulations. The possible superfluidity of pH2 was later indirectly observed in a spectroscopic Andronikashvili experiment in 2000. Since then, a growing number of studies have appeared, and theoretical simulations have been playing a special role because they help guide and interpret experiments. In this review, we go over the theoretical studies of pH2 superfluid clusters since the experiment of 2000. We provide a historical perspective and introduce the basic theoretical formalism along with key experimental advances. We then present illustrative results of the theoretical studies and comment on the possible future developments in the field. We include sufficient theoretical details such that the review can serve as a guide for newcomers to the field.

  20. EMMD-Prony approach for dynamic validation of simulation models

    Institute of Scientific and Technical Information of China (English)

    Ruiyang Bai

    2015-01-01

    Model validation and updating is critical to model credi-bility growth. In order to assess model credibility quantitatively and locate model error precisely, a new dynamic validation method based on extremum field mean mode decomposition (EMMD) and the Prony method is proposed in this paper. Firstly, complex dy-namic responses from models and real systems are processed into stationary components by EMMD. These components always have definite physical meanings which can be the evidence about rough model error location. Secondly, the Prony method is applied to identify the features of each EMMD component. Amplitude si-milarity, frequency similarity, damping similarity and phase simi-larity are defined to describe the similarity of dynamic responses. Then quantitative validation metrics are obtained based on the improved entropy weight and energy proportion. Precise model error location is realized based on the physical meanings of these features. The application of this method in aircraft control er design provides evidence about its feasibility and usability.