Dynamic computer simulations of electrophoresis: three decades of active research.
Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A
2009-06-01
Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.
The simulation research for the dynamic performance of integrated PWR
International Nuclear Information System (INIS)
Yuan Jiandong; Xia Guoqing; Fu Mingyu
2005-01-01
The mathematical model of the reactor core of integrated PWR has been studied and simplified properly. With the lumped parameter method, authors have established the mathematical model of the reactor core, including the neutron dynamic equation, the feedback reactivities model and the thermo-hydraulic model of the reactor. Based on the above equations and models, the incremental transfer functions of the reactor core model have been built. By simulation experimentation, authors have compared the dynamic characteristics of the integrated PWR with the traditional dispersed PWR. The simulation results show that the mathematical models and equations are correct. (authors)
Research on hyperspectral dynamic scene and image sequence simulation
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.
Development of research reactor simulator and its application to dynamic test-bed
International Nuclear Information System (INIS)
Kwon, Kee-Choon; Baang, Dane; Park, Jae-Chang; Lee, Seung-Wook; Bae, Sung Won
2014-01-01
We developed a real-time simulator for 'High-flux Advanced Neutron Application ReactOr (HANARO), and the Jordan Research and Training Reactor (JRTR). The main purpose of this simulator is operator training, but we modified this simulator into a dynamic test-bed (DTB) to test the functions and dynamic control performance of reactor regulating system (RRS) in HANARO or JRTR before installation. The simulator hardware consists of a host computer, 6 operator stations, a network switch, and a large display panel. The software includes a mathematical model that implements plant dynamics in real-time, an instructor station module that manages user instructions, and a human machine interface module. The developed research reactor simulators are installed in the Korea Atomic Energy Research Institute nuclear training center for reactor operator training. To use the simulator as a dynamic test-bed, the reactor regulating system modeling software of the simulator was replaced by actual RRS cabinet, and was interfaced using a hard-wired and network-based interface. RRS cabinet generates control signals for reactor power control based on the various feedback signals from DTB, and the DTB runs plant dynamics based on the RRS control signals. Thus the Hardware-In-the-Loop Simulation between RRS and the emulated plant (DTB) has been implemented and tested in this configuration. The test result shows that the developed DTB and actual RRS cabinet works together simultaneously resulting in quite good dynamic control performances. (author)
Development of Research Reactor Simulator and Its Application to Dynamic Test-bed
International Nuclear Information System (INIS)
Kwon, Kee Choon; Park, Jae Chang; Lee, Seung Wook; Bang, Dane; Bae, Sung Won
2014-01-01
We developed HANARO and the Jordan Research and Training Reactor (JRTR) real-time simulator for operating staff training. The main purpose of this simulator is operator training, but we modified this simulator as a dynamic test-bed to test the reactor regulating system in HANARO or JRTR before installation. The simulator configuration is divided into hardware and software. The simulator hardware consists of a host computer, 6 operator stations, a network switch, and a large display panel. The simulator software is divided into three major parts: a mathematical modeling module, which executes the plant dynamic modeling program in real-time, an instructor station module that manages user instructions, and a human machine interface (HMI) module. The developed research reactors are installed in the Korea Atomic Energy Research Institute nuclear training center for reactor operator training. To use the simulator as a dynamic test-bed, the reactor regulating system modeling software of the simulator was replaced by a hardware controller and the simulator and target controller were interfaced with a hard-wired and network-based interface
Development of Research Reactor Simulator and Its Application to Dynamic Test-bed
Energy Technology Data Exchange (ETDEWEB)
Kwon, Kee Choon; Park, Jae Chang; Lee, Seung Wook; Bang, Dane; Bae, Sung Won [KAERI, Daejeon (Korea, Republic of)
2014-08-15
We developed HANARO and the Jordan Research and Training Reactor (JRTR) real-time simulator for operating staff training. The main purpose of this simulator is operator training, but we modified this simulator as a dynamic test-bed to test the reactor regulating system in HANARO or JRTR before installation. The simulator configuration is divided into hardware and software. The simulator hardware consists of a host computer, 6 operator stations, a network switch, and a large display panel. The simulator software is divided into three major parts: a mathematical modeling module, which executes the plant dynamic modeling program in real-time, an instructor station module that manages user instructions, and a human machine interface (HMI) module. The developed research reactors are installed in the Korea Atomic Energy Research Institute nuclear training center for reactor operator training. To use the simulator as a dynamic test-bed, the reactor regulating system modeling software of the simulator was replaced by a hardware controller and the simulator and target controller were interfaced with a hard-wired and network-based interface.
Energy Technology Data Exchange (ETDEWEB)
NONE
2015-07-01
Digital instrumentation and controls system technique is being introduced in new constructed research reactor or life extension of older research reactor. Digital systems are easy to change and optimize but the validated process for them is required. Also, to reduce project risk or cost, we have to make it sure that configuration and control functions is right before the commissioning phase on research reactor. For this purpose, simulators have been widely used in developing control systems in automotive and aerospace industries. In these literatures, however, very few of these can be found regarding test on the control system of research reactor with simulator. Therefore, this paper proposes a simulation platform to verify the performance of RRS (Reactor Regulating System) for research reactor. This simulation platform consists of the reactor simulation model and the interface module. This simulation platform is applied to I and C upgrade project of TRIGA reactor, and many problems of RRS configuration were found and solved. And it proved that the dynamic performance testing based on simulator enables significant time saving and improves economics and quality for RRS in the system test phase. (authors)
Marshall, Deborah A; Burgos-Liz, Lina; IJzerman, Maarten J; Crown, William; Padula, William V; Wong, Peter K; Pasupathy, Kalyan S; Higashi, Mitchell K; Osgood, Nathaniel D
2015-03-01
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 can be used more effectively than other modeling methods. The hierarchical relationship between the health care delivery system, providers, patients, and other stakeholders exhibits a level of complexity that ought to be captured using dynamic simulation modeling methods. As a tool to help researchers decide whether dynamic simulation modeling is an appropriate method for modeling the effects of an intervention on a health care system, we presented the System, Interactions, Multilevel, Understanding, Loops, Agents, Time, Emergence (SIMULATE) checklist consisting of eight elements. This report builds on the previous work, systematically comparing each of the three most commonly used dynamic simulation modeling methods-system dynamics, discrete-event simulation, and agent-based modeling. We review criteria for selecting the most suitable method depending on 1) the purpose-type of problem and research questions being investigated, 2) the object-scope of the model, and 3) the method to model the object to achieve the purpose. Finally, we provide guidance for emerging good practices for dynamic simulation modeling in the health sector, covering all aspects, from the engagement of decision makers in the model design through model maintenance and upkeep. We conclude by providing some recommendations about the application of these methods to add value to informed decision making, with an emphasis on stakeholder engagement, starting with the problem definition. Finally, we identify areas in which further methodological development will likely occur given the growing "volume, velocity and variety" and availability of "big data" to provide empirical evidence and techniques
2013-10-16
The Maryland State Highway Administration (SHA) uses dynamic message signs : (DMS) for traffic and incident management and for providing travel time information. : Previous research in Maryland has shown that a DMS can be an accurate, effective, and ...
Marshall, Deborah A.; Burgos-Liz, Lina; Pasupathy, Kalyan S.; Padula, William V.; IJzerman, Maarten Joost; 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
Conceptual Design of Korea Aerospace Research Institute Lunar Explorer Dynamic Simulator
Directory of Open Access Journals (Sweden)
Dong-Young Rew
2010-12-01
Full Text Available In lunar explorer development program, computer simulator is necessary to provide virtual environments that vehicle confronts in lunar transfer, orbit, and landing missions, and to analyze dynamic behavior of the spacecraft under these environments. Objective of simulation differs depending on its application in spacecraft development cycle. Scope of use cases considered in this paper includes simulation of software based, processor and/or hardware in the loop, and support of ground-based flight test of developed vehicle. These use cases represent early phase in development cycle but reusability of modeling results in the next design phase is considered in defining requirements. A simulator architecture in which simulator platform is located in the middle and modules for modeling, analyzing, and three dimensional visualizing are connected to that platform is suggested. Baseline concepts and requirements for simulator development are described. Result of trade study for selecting simulation platform and approaches of defining other simulator components are summarized. Finally, characters of lunar elevation map data which is necessary for lunar terrain generation is described.
The research of hourglass worm dynamic balancing simulation based on SolidWorks motion
Wang, Zhuangzhuang; Yang, Jie; Liu, Pingyi; Zhao, Junpeng
2018-02-01
Hourglass worm is extensively used in industry due to its characteristic of heavy-load and a large reduction ratio. Varying sizes of unbalanced mass distribution appeared in the design of a single head worm. With machines developing towards higher speed and precision, the vibration and shock caused by the unbalanced mass distribution of rotating parts must be considered. Therefore, the balance grade of these parts must meet higher requirements. A method based on theoretical analysis and SolidWorks motion software simulation is presented in this paper; the virtual dynamic balance simulation test of the hourglass worm was carried out during the design of the product, so as to ensure that the hourglass worm meet the requirements of dynamic balance in the design process. This can effectively support the structural design of the hourglass worm and provide a way of thinking and designing the same type of products.
Research on dynamic balancing simulation of rotary shaft based on ADAMS
Zheng, Weiqiang; Rui, Chengjie; Yang, Jie; Liu, Pingyi
2018-02-01
Due to the design and processing technology of rotary shaft, the mass center of it does not coincide with the rotating axis of the rotary shaft and there is an unbalanced mass. The unbalanced mass can have some disadvantages, such as the centrifugal force, the vibration and so on. Those disadvantages could reduce the accuracy and service life of the equipment.In this paper, the dynamic balance of the rotary shaft is analysed by the theory analysis combined with the dynamic simulation software. This method ensures that the rotary shaft meets the dynamic balancing requirements during the design stage. It effectively supports the structural design of the rotary shift, and provides a way of thinking and method for the design and development of the same type of products.
Dynamic Simulation Research on Chain Drive Mechanism of Corn Seeder Based on ADAMS
Wang, Y. B.; Jia, H. P.
2017-12-01
In order to reduce the damage to the chain and improve the seeding quality of the seeding machine, the corn seeder has the characteristics of the seeding quality and some technical indexes in the work of the corn seeding machine. The dynamic analysis of the chain drive mechanism is carried out by using the dynamic virtual prototype. In this paper, the speed of the corn planter is 5km/h, and the speed of the simulated knuckle is 0.1~0.9s. The velocity is 0.12m/s, which is equal to the chain speed when the seeder is running normally. Of the dynamic simulation of the movement and the actual situation is basically consistent with the apparent speed of the drive wheel has changed the acceleration and additional dynamic load, the chain drive has a very serious damage, and the maximum load value of 47.28N, in order to reduce the damage to the chain, As far as possible so that the sowing machine in the work to maintain a reasonable uniform speed, to avoid a greater acceleration, the corn sowing machine drive the design of a certain reference.
Using social simulation to explore the dynamics at stake in participatory research
Barreteau, Olivier; Le Page, Christophe
2011-01-01
This position paper contributes to the debate on perspectives for simulating the social processes of science through the specific angle of participatory research. This new way of producing science is still in its infancy and needs some step back and analysis, to understand what is taking place on the boundaries between academic, policy and lay worlds. We argue that social simulation of this practice of cooperation can help in understanding further this new way of doing science, building on ex...
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.
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
2016-02-01
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 modelling (DSM) and big data share characteristics, they present distinct and complementary value in healthcare. Big data and DSM are synergistic-big data offer support to enhance the application of dynamic models, but DSM also can greatly enhance the value conferred by big data. Big data can inform patient-centred care with its high velocity, volume, and variety (the three Vs) over traditional data analytics; however, big data are not sufficient to extract meaningful insights to inform approaches to improve healthcare delivery. DSM can serve as a natural bridge between the wealth of evidence offered by big data and informed decision making as a means of faster, deeper, more consistent learning from that evidence. We discuss the synergies between big data and DSM, practical considerations and challenges, and how integrating big data and DSM can be useful to decision makers to address complex, systemic health economics and outcomes questions and to transform healthcare delivery.
Computational fluid dynamics simulation of a single cylinder research engine working with biodiesel
Directory of Open Access Journals (Sweden)
Moldovanu Dan
2013-01-01
Full Text Available The main objective of the paper is to present the results of the CFD simulation of a DI single cylinder engine using diesel, biodiesel, or different mixture proportions of diesel and biodiesel and compare the results to a test bed measurement in the same functioning point. The engine used for verifying the results of the simulation is a single cylinder research engine from AVL with an open ECU, so that the injection timings and quantities can be controlled and analyzed. In Romania, until the year 2020 all the fuel stations are obliged to have mixtures of at least 10% biodiesel in diesel [14]. The main advantages using mixtures of biofuels in diesel are: the fact that biodiesel is not harmful to the environment; in order to use biodiesel in your engine no modifications are required; the price of biodiesel is smaller than diesel and also if we compare biodiesel production to the classic petroleum based diesel production, it is more energy efficient; biodiesel assures more lubrication to the engine so the life of the engine is increased; biodiesel is a sustainable fuel; using biodiesel helps maintain the environment and it keeps the people more healthy [1-3].
Interactive Dynamic-System Simulation
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
Molecular dynamics simulations
International Nuclear Information System (INIS)
Alder, B.J.
1985-07-01
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs
Dynamic simulation of a reboiler
International Nuclear Information System (INIS)
Moeck, E.O.; McMorran, P.D.
1977-07-01
A hybrid-computer simulation of reboiler dynamics was prepared, comprising models of steam condensation in tubes, heat conduction, steam generation, a surge tank, steam transmission line and flow-control valve. Time and frequency responses were obtained to illustrate the dynamics of this multivariable process. (author)
Visualizing Energy on Target: Molecular Dynamics Simulations
2017-12-01
ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target
International Nuclear Information System (INIS)
Trucco, A.; Corallo, C.; Pini Prato, A.; Porro, S.
1999-01-01
Among the innovative cycle recently proposed in literature, the Humid Air Turbine Cycle - Hat better seems to fulfil the main energy market requirements of today: High efficiency in a large power ranger, low pollution, low specific capital cost. The previous results of an analysis at partial load and transient conditions are here presented, where the Hat plant has been simulated using the original model implemented in LEGO environment [it
Fissile solution dynamics: Student research
Energy Technology Data Exchange (ETDEWEB)
Hetrick, D.L.
1994-09-01
There are two research projects in criticality safety at the University of Arizona: one in dynamic simulation of hypothetical criticality accidents in fissile solutions, and one in criticality benchmarks using transport theory. We have used the data from nuclear excursions in KEWB, CRAC, and SILENE to help in building models for solution excursions. An equation of state for liquids containing gas bubbles has been developed and coupled to point-reactor dynamics in an attempt to predict fission rate, yield, pressure, and kinetic energy. It appears that radiolytic gas is unimportant until after the first peak, but that it does strongly affect the shape of the subsequent power decrease and also the dynamic pressure.
DEFF Research Database (Denmark)
Markussen, Thomas; Bang, Anne Louise; Knutz, Eva
2012-01-01
that recognize the process of designing and making an artifact as a legitimate method of inquiry. However, even though this type of research is thus grounded in design practice there are many different ways in which the process of designing and making an artifact can be used as a method of inquiry in order...... to explore a research question. Occasionally, the lack of a systematic methodology for research through design being able to make clarifications and distinctions between various methods has been pointed out. Yet, only few attempts have been made to compensate for this lack. In this paper, the aim is to make...... a first step toward such a methodology. Initially, we set the scene by providing a critical examination of existing literature on the subject. Then, we demonstrate the explanatory strength of dynamic research sketching by applying it to three case examples. In so doing, we uncover three different methods...
Vehicle dynamics modeling and simulation
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.
Plasma theory and simulation research
International Nuclear Information System (INIS)
Birdsall, C.K.
1989-01-01
Our research group uses both theory and simulation as tools in order to increase the understanding of instabilities, heating, diffusion, transport and other phenomena in plasmas. We also work on the improvement of simulation, both theoretically and practically. Our focus has been more and more on the plasma edge (the ''sheath''), interactions with boundaries, leading to simulations of whole devices (someday a numerical tokamak)
International Nuclear Information System (INIS)
Serres, M.; Klein, E.; Besnard, D.
2002-01-01
The scientific activity of old used to practice following two modes: the theory and the experiment. The last ten years saw the emergence of a third approach: the simulation. In this evolution the CEA played a major part, in particular to answer the need of the nuclear park and the nuclear disarmament. In this framework, the document presents the simulation activities of the CEA in many domains: the climate, the radioactive wastes management, the particles Physics, the biological macromolecules, the interfaces and surfaces, the nuclear reactors, the welding, the non destructive testing, the fusion. (A.L.B.)
Simulation of a pool type research reactor
International Nuclear Information System (INIS)
Oliveira, Andre Felipe da Silva de; Moreira, Maria de Lourdes
2011-01-01
Computational fluid dynamic is used to simulate natural circulation condition after a research reactor shutdown. A benchmark problem was used to test the viability of usage such code to simulate the reactor model. A model which contains the core, the pool, the reflector tank, the circulation pipes and chimney was simulated. The reactor core contained in the full scale model was represented by a porous media. The parameters of porous media were obtained from a separate CFD analysis of the full core model. Results demonstrate that such studies can be carried out for research and test of reactors design. (author)
Dynamic simulation of LMFBR systems
International Nuclear Information System (INIS)
Agrawal, A.K.; Khatib-Rahbar, M.
1980-01-01
This review article focuses on the dynamic analysis of liquid-metal-cooled fast breeder reactor systems in the context of protected transients. Following a brief discussion on various design and simulation approaches, a critical review of various models for in-reactor components, intermediate heat exchangers, heat transport systems and the steam generating system is presented. A brief discussion on choice of fuels as well as core and blanket system designs is also included. Numerical considerations for obtaining system-wide steady-state and transient solutions are discussed, and examples of various system transients are presented. Another area of major interest is verification of phenomenological models. Various steps involved in the code and model verification are briefly outlined. The review concludes by posing some further areas of interest in fast reactor dynamics and safety. (author)
Parallelization of quantum molecular dynamics simulation code
International Nuclear Information System (INIS)
Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu
1998-02-01
A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)
Human motion simulation predictive dynamics
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...
Dynamic benchmarking of simulation codes
International Nuclear Information System (INIS)
Henry, R.E.; Paik, C.Y.; Hauser, G.M.
1996-01-01
Computer simulation of nuclear power plant response can be a full-scope control room simulator, an engineering simulator to represent the general behavior of the plant under normal and abnormal conditions, or the modeling of the plant response to conditions that would eventually lead to core damage. In any of these, the underlying foundation for their use in analysing situations, training of vendor/utility personnel, etc. is how well they represent what has been known from industrial experience, large integral experiments and separate effects tests. Typically, simulation codes are benchmarked with some of these; the level of agreement necessary being dependent upon the ultimate use of the simulation tool. However, these analytical models are computer codes, and as a result, the capabilities are continually enhanced, errors are corrected, new situations are imposed on the code that are outside of the original design basis, etc. Consequently, there is a continual need to assure that the benchmarks with important transients are preserved as the computer code evolves. Retention of this benchmarking capability is essential to develop trust in the computer code. Given the evolving world of computer codes, how is this retention of benchmarking capabilities accomplished? For the MAAP4 codes this capability is accomplished through a 'dynamic benchmarking' feature embedded in the source code. In particular, a set of dynamic benchmarks are included in the source code and these are exercised every time the archive codes are upgraded and distributed to the MAAP users. Three different types of dynamic benchmarks are used: plant transients; large integral experiments; and separate effects tests. Each of these is performed in a different manner. The first is accomplished by developing a parameter file for the plant modeled and an input deck to describe the sequence; i.e. the entire MAAP4 code is exercised. The pertinent plant data is included in the source code and the computer
Hoang, Tuan L.; Nazarov, Roman; Kang, Changwoo; Fan, Jiangyuan
2018-07-01
Under the multi-ion irradiation conditions present in accelerated material-testing facilities or fission/fusion nuclear reactors, the combined effects of atomic displacements with radiation products may induce complex synergies in the structural materials. However, limited access to multi-ion irradiation facilities and the lack of computational models capable of simulating the evolution of complex defects and their synergies make it difficult to understand the actual physical processes taking place in the materials under these extreme conditions. In this paper, we propose the application of pulsed single/dual-beam irradiation as replacements for the expensive steady triple-beam irradiation to study radiation damages in materials under multi-ion irradiation.
A eural etwork Model for Dynamics Simulation
African Journals Online (AJOL)
Nafiisah
Results 5 - 18 ... situations, such as a dynamic environment (e.g., a molecular dynamics (MD) simulation whereby an atom constantly changes its local environment and number ..... of systems including both small clusters and bulk structures. 7.
Development Of Dynamic Probabilistic Safety Assessment: The Accident Dynamic Simulator (ADS) Tool
International Nuclear Information System (INIS)
Chang, Y.H.; Mosleh, A.; Dang, V.N.
2003-01-01
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)
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)
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
Effects of dynamical quarks in UKQCD simulations
International Nuclear Information System (INIS)
Allton, Chris
2002-01-01
Recent results from the UKQCD Collaboration's dynamical simulations are presented. The main feature of these ensembles is that they have a fixed lattice spacing and volume, but varying sea quark mass from infinite (corresponding to the quenched simulation) down to roughly that of the strange quark mass. The main aim of this work is to uncover dynamical quark effects from these 'matched' ensembles. We obtain some evidence of dynamical quark effects in the static quark potential with less effects in the hadronic spectrum
Metrics for comparing dynamic earthquake rupture simulations
Barall, Michael; Harris, Ruth A.
2014-01-01
Earthquakes are complex events that involve a myriad of interactions among multiple geologic features and processes. One of the tools that is available to assist with their study is computer simulation, particularly dynamic rupture simulation. A dynamic rupture simulation is a numerical model of the physical processes that occur during an earthquake. Starting with the fault geometry, friction constitutive law, initial stress conditions, and assumptions about the condition and response of the near‐fault rocks, a dynamic earthquake rupture simulation calculates the evolution of fault slip and stress over time as part of the elastodynamic numerical solution (Ⓔ see the simulation description in the electronic supplement to this article). The complexity of the computations in a dynamic rupture simulation make it challenging to verify that the computer code is operating as intended, because there are no exact analytic solutions against which these codes’ results can be directly compared. One approach for checking if dynamic rupture computer codes are working satisfactorily is to compare each code’s results with the results of other dynamic rupture codes running the same earthquake simulation benchmark. To perform such a comparison consistently, it is necessary to have quantitative metrics. In this paper, we present a new method for quantitatively comparing the results of dynamic earthquake rupture computer simulation codes.
Molecular dynamics simulation of a phospholipid membrane
Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.
We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in
Dynamics of Research through Design
DEFF Research Database (Denmark)
Basballe, Ditte Amund; Halskov, Kim
2012-01-01
In this paper, we investigate Research through Design at a micro-level, by addressing the dynamic interplay of research and design as they unfold throughout a design process. As our principal case, we consider the design of a three-dimensional projection installation, a process that unfolded over...... a one-year period. We analyse material collected from 18 key events during the process, in order to identify the ongoing dynamics. Based on the analysis, we establish how the interplay evolves in a complex structure, where the design and research interests continuously couple, interweave, and decouple...
Dynamics of Research through Design
DEFF Research Database (Denmark)
Basballe, Ditte Amund; Halskov, Kim
2012-01-01
a one-year period. We analyse material collected from 18 key events during the process, in order to identify the ongoing dynamics. Based on the analysis, we establish how the interplay evolves in a complex structure, where the design and research interests continuously couple, interweave, and decouple......In this paper, we investigate Research through Design at a micro-level, by addressing the dynamic interplay of research and design as they unfold throughout a design process. As our principal case, we consider the design of a three-dimensional projection installation, a process that unfolded over...
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...
Institute of Scientific and Technical Information of China (English)
张雅彬; 李伯虎; 柴旭东; 杨晨
2012-01-01
为使得云仿真平台能够支持仿真用户快速、高效、灵活地获得个性化仿真服务,基于虚拟化技术研究了云仿真运行环境动态构建技术,设计了基于虚拟化技术的云仿真运行环境动态构建模型,研究了面向多用户的、以仿真模型需求为依据的云仿真运行环境动态构建的三层映射算法.最后通过一个应用示例说明了基于虚拟化技术的云仿真运行环境动态构建技术的可行性和有效性.%In order to enable a cloud simulation platform (CSP) to support users obtaining individual simulation services quickly, effectively and neatly, the cloud simulation running environment dynamic building technology is researched based on virtualization technology. A virtualization-based cloud simulation running environment dynamic building model is designed and the multi-user oriented three-layer algorithm built dynamically by the cloud simulation running environment is researched according to the demand of simulation resources. Finally, an example is given to show the feasibility and effectiveness.
Simulation tools for robotics research and assessment
Fields, MaryAnne; Brewer, Ralph; Edge, Harris L.; Pusey, Jason L.; Weller, Ed; Patel, Dilip G.; DiBerardino, Charles A.
2016-05-01
The Robotics Collaborative Technology Alliance (RCTA) program focuses on four overlapping technology areas: Perception, Intelligence, Human-Robot Interaction (HRI), and Dexterous Manipulation and Unique Mobility (DMUM). In addition, the RCTA program has a requirement to assess progress of this research in standalone as well as integrated form. Since the research is evolving and the robotic platforms with unique mobility and dexterous manipulation are in the early development stage and very expensive, an alternate approach is needed for efficient assessment. Simulation of robotic systems, platforms, sensors, and algorithms, is an attractive alternative to expensive field-based testing. Simulation can provide insight during development and debugging unavailable by many other means. This paper explores the maturity of robotic simulation systems for applications to real-world problems in robotic systems research. Open source (such as Gazebo and Moby), commercial (Simulink, Actin, LMS), government (ANVEL/VANE), and the RCTA-developed RIVET simulation environments are examined with respect to their application in the robotic research domains of Perception, Intelligence, HRI, and DMUM. Tradeoffs for applications to representative problems from each domain are presented, along with known deficiencies and disadvantages. In particular, no single robotic simulation environment adequately covers the needs of the robotic researcher in all of the domains. Simulation for DMUM poses unique constraints on the development of physics-based computational models of the robot, the environment and objects within the environment, and the interactions between them. Most current robot simulations focus on quasi-static systems, but dynamic robotic motion places an increased emphasis on the accuracy of the computational models. In order to understand the interaction of dynamic multi-body systems, such as limbed robots, with the environment, it may be necessary to build component
Dynamic simulation of hydrogen isotope distillation unit
International Nuclear Information System (INIS)
Le Lann, J.M.; Latge, C.; Joulia, X.; Sere-Peyrigain, P.
1995-01-01
Dynamic simulation of hydrogen isotope distillation unit involved in the complex environment of a fusion power plant can be a powerful technique in view to analyze the tritium hazard potential. In this paper, issues related to the development of such a dynamic simulator with model formulation and the numerical treatment of the resulting Differential-Algebraic equation (DAE) system are properly adressed. The typical dynamic characteristics of such columns are quantitatively and qualitatively enlighted on case study with very large disturbances. The developed system has proven to be beneficial for understanding the dynamic behaviour and further for developing control schemes. (orig.)
Dynamic simulation of hydrogen isotope distillation unit
International Nuclear Information System (INIS)
Le Lann, J.M.; Joulia, X.; Sere-Peyrigain, P.
1994-01-01
Dynamic simulation of hydrogen isotope distillation unit involved in the complex environment of a fusion power plant can be a powerful technique in view to analyze the tritium hazard potential. Issues related to the development of such a dynamic simulator with model formulation and the numerical treatment of the resulting Differential-Algebraic equation (DAE) system are properly addressed. The typical dynamic characteristics of such columns are quantitatively and qualitatively enlightened on case study with very large disturbances. The developed system has proven to be beneficial for understanding the dynamic behaviour and further for developing control schemes. (author) 12 refs.; 4 figs
A Process for Comparing Dynamics of Distributed Space Systems Simulations
Cures, Edwin Z.; Jackson, Albert A.; Morris, Jeffery C.
2009-01-01
The paper describes a process that was developed for comparing the primary orbital dynamics behavior between space systems distributed simulations. This process is used to characterize and understand the fundamental fidelities and compatibilities of the modeling of orbital dynamics between spacecraft simulations. This is required for high-latency distributed simulations such as NASA s Integrated Mission Simulation and must be understood when reporting results from simulation executions. This paper presents 10 principal comparison tests along with their rationale and examples of the results. The Integrated Mission Simulation (IMSim) (formerly know as the Distributed Space Exploration Simulation (DSES)) is a NASA research and development project focusing on the technologies and processes that are related to the collaborative simulation of complex space systems involved in the exploration of our solar system. Currently, the NASA centers that are actively participating in the IMSim project are the Ames Research Center, the Jet Propulsion Laboratory (JPL), the Johnson Space Center (JSC), the Kennedy Space Center, the Langley Research Center and the Marshall Space Flight Center. In concept, each center participating in IMSim has its own set of simulation models and environment(s). These simulation tools are used to build the various simulation products that are used for scientific investigation, engineering analysis, system design, training, planning, operations and more. Working individually, these production simulations provide important data to various NASA projects.
molecular dynamics simulations and quantum chemical calculations
African Journals Online (AJOL)
ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.
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...
Simbody: multibody dynamics for biomedical research.
Sherman, Michael A; Seth, Ajay; Delp, Scott L
Multibody software designed for mechanical engineering has been successfully employed in biomedical research for many years. For real time operation some biomedical researchers have also adapted game physics engines. However, these tools were built for other purposes and do not fully address the needs of biomedical researchers using them to analyze the dynamics of biological structures and make clinically meaningful recommendations. We are addressing this problem through the development of an open source, extensible, high performance toolkit including a multibody mechanics library aimed at the needs of biomedical researchers. The resulting code, Simbody, supports research in a variety of fields including neuromuscular, prosthetic, and biomolecular simulation, and related research such as biologically-inspired design and control of humanoid robots and avatars. Simbody is the dynamics engine behind OpenSim, a widely used biomechanics simulation application. This article reviews issues that arise uniquely in biomedical research, and reports on the architecture, theory, and computational methods Simbody uses to address them. By addressing these needs explicitly Simbody provides a better match to the needs of researchers than can be obtained by adaptation of mechanical engineering or gaming codes. Simbody is a community resource, free for any purpose. We encourage wide adoption and invite contributions to the code base at https://simtk.org/home/simbody.
Scalable Atomistic Simulation Algorithms for Materials Research
Directory of Open Access Journals (Sweden)
Aiichiro Nakano
2002-01-01
Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.
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.
Molecular dynamics simulation of impact test
International Nuclear Information System (INIS)
Akahoshi, Y.; Schmauder, S.; Ludwig, M.
1998-01-01
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.)
Modular simulation of reefer container dynamics
DEFF Research Database (Denmark)
Sørensen, Kresten Kjær; Nielsen, Jens Frederik Dalsgaard; Stoustrup, Jakob
2014-01-01
for faults enabling preventive maintenance. In this paper the feasibility of using different simulation methods is assessed with the goal of identifying a fast but accurate method that works well in a multi-rate environment. A modular multi-rate simulation environment for a dynamical system consisting...
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.)
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.
Dynamic Simulation of AN Helium Refrigerator
Deschildre, C.; Barraud, A.; Bonnay, P.; Briend, P.; Girard, A.; Poncet, J. M.; Roussel, P.; Sequeira, S. E.
2008-03-01
A dynamic simulation of a large scale existing refrigerator has been performed using the software Aspen Hysys®. The model comprises the typical equipments of a cryogenic system: heat exchangers, expanders, helium phase separators and cold compressors. It represents the 400 W @ 1.8 K Test Facility located at CEA—Grenoble. This paper describes the model development and shows the possibilities and limitations of the dynamic module of Aspen Hysys®. Then, comparison between simulation results and experimental data are presented; the simulation of cooldown process was also performed.
Selection of Activities in Dynamic Business Process Simulation
Directory of Open Access Journals (Sweden)
Toma Rusinaitė
2016-06-01
Full Text Available Maintaining dynamicity of business processes is one of the core issues of today's business as it enables businesses to adapt to constantly changing environment. Upon changing the processes, it is vital to assess possible impact, which is achieved by using simulation of dynamic processes. In order to implement dynamicity in business processes, it is necessary to have an ability to change components of the process (a set of activities, a content of activity, a set of activity sequences, a set of rules, performers and resources or dynamically select them during execution. This problem attracted attention of researches over the past few years; however, there is no proposed solution, which ensures the business process (BP dynamicity. This paper proposes and specifies dynamic business process (DBP simulation model, which satisfies all of the formulated DBP requirements.
Computational plasticity algorithm for particle dynamics simulations
Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.
2018-01-01
The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.
Lattice dynamics and molecular dynamics simulation of complex materials
International Nuclear Information System (INIS)
Chaplot, S.L.
1997-01-01
In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)
IMPROVING MEDICAL EDUCATION: SIMULATING CHANGES IN PATIENT ANATOMY USING DYNAMIC HAPTIC FEEDBACK
Yovanoff, Mary; Pepley, David; Mirkin, Katelin; Moore, Jason; Han, David; Miller, Scarlett
2016-01-01
Virtual simulation is an emerging field in medical education. Research suggests that simulation reduces complication rates and improves learning gains for medical residents. One benefit of simulators is their allowance for more realistic and dynamic patient anatomies. While potentially useful throughout medical education, few studies have explored the impact of dynamic haptic simulators on medical training. In light of this research void, this study was developed to examine how a Dynamic-Hapt...
Simulation of quantum dynamics with integrated photonics
Sansoni, Linda; Sciarrino, Fabio; Mataloni, Paolo; Crespi, Andrea; Ramponi, Roberta; Osellame, Roberto
2012-12-01
In recent years, quantum walks have been proposed as promising resources for the simulation of physical quantum systems. In fact it is widely adopted to simulate quantum dynamics. Up to now single particle quantum walks have been experimentally demonstrated by different approaches, while only few experiments involving many-particle quantum walks have been realized. Here we simulate the 2-particle dynamics on a discrete time quantum walk, built on an array of integrated waveguide beam splitters. The polarization independence of the quantum walk circuit allowed us to exploit the polarization entanglement to encode the symmetry of the two-photon wavefunction, thus the bunching-antibunching behavior of non interacting bosons and fermions has been simulated. We have also characterized the possible distinguishability and decoherence effects arising in such a structure. This study is necessary in view of the realization of a quantum simulator based on an integrated optical array built on a large number of beam splitters.
A model for nuclear research reactor dynamics
Energy Technology Data Exchange (ETDEWEB)
Barati, Ramin, E-mail: Barati.ramin@aut.ac.ir; Setayeshi, Saeed, E-mail: setayesh@aut.ac.ir
2013-09-15
Highlights: • A thirty-fourth order model is used to simulate the dynamics of a research reactor. • We consider delayed neutrons fraction as a function of time. • Variable fuel and temperature reactivity coefficients are used. • WIMS, BORGES and CITVAP codes are used for initial condition calculations. • Results are in agreement with experimental data rather than common codes. -- Abstract: In this paper, a useful thirty-fourth order model is presented to simulate the kinetics and dynamics of a research reactor core. The model considers relevant physical phenomena that govern the core such as reactor kinetics, reactivity feedbacks due to coolant and fuel temperatures (Doppler effects) with variable reactivity coefficients, xenon, samarium, boron concentration, fuel burn up and thermal hydraulics. WIMS and CITVAP codes are used to extract neutron cross sections and calculate the initial neuron flux respectively. The purpose is to present a model with results similar to reality as much as possible with reducing common simplifications in reactor modeling to be used in different analyses such as reactor control, functional reliability and safety. The model predictions are qualified by comparing with experimental data, detailed simulations of reactivity insertion transients, and steady state for Tehran research reactor reported in the literature and satisfactory results have been obtained.
Dynamic large eddy simulation: Stability via realizability
Mokhtarpoor, Reza; Heinz, Stefan
2017-10-01
The concept of dynamic large eddy simulation (LES) is highly attractive: such methods can dynamically adjust to changing flow conditions, which is known to be highly beneficial. For example, this avoids the use of empirical, case dependent approximations (like damping functions). Ideally, dynamic LES should be local in physical space (without involving artificial clipping parameters), and it should be stable for a wide range of simulation time steps, Reynolds numbers, and numerical schemes. These properties are not trivial, but dynamic LES suffers from such problems over decades. We address these questions by performing dynamic LES of periodic hill flow including separation at a high Reynolds number Re = 37 000. For the case considered, the main result of our studies is that it is possible to design LES that has the desired properties. It requires physical consistency: a PDF-realizable and stress-realizable LES model, which requires the inclusion of the turbulent kinetic energy in the LES calculation. LES models that do not honor such physical consistency can become unstable. We do not find support for the previous assumption that long-term correlations of negative dynamic model parameters are responsible for instability. Instead, we concluded that instability is caused by the stable spatial organization of significant unphysical states, which are represented by wall-type gradient streaks of the standard deviation of the dynamic model parameter. The applicability of our realizability stabilization to other dynamic models (including the dynamic Smagorinsky model) is discussed.
Dynamics of Laboratory Simulated Microbursts
Alahyari, Abbas Alexander
1995-01-01
A downburst (or microburst) is an intense, localized downdraft of cold air which reaches the Earth and spreads radially outward after it impinges on the ground. Downdrafts are typically induced by rapid evaporation of moisture or melting of hail. The divergent outflow created by a microburst produces strong winds in opposite directions. The sudden changes in the speed and direction of both horizontal and vertical winds within a microburst can create hazardous conditions for aircraft within 1000 ft of the ground, particularly during takeoff and landing. The objective of this investigation was to obtain detailed measurements within a laboratory -simulated version of this flow. The flow was modeled experimentally by releasing a small volume of heavier fluid into a less dense ambient surrounding. The heavier fluid impinged on a horizontal plate which represented the ground. Indices of refraction of the light and heavy fluid were matched to yield clear photographic images. Particle image velocimetry (PIV) was used to obtain detailed maps of the instantaneous velocity fields within horizontal and vertical cross sections through the flow. Laser-induced fluorescence (LIF) was used to determine the local concentration of heavy fluid within the downburst flow at different times. PIV measurements showed that the leading edge of the falling fluid rolled up into a vortex ring which then impacted on the ground and expanded radially outward. After touchdown, the largest horizontal velocities occurred beneath the vortex ring but also extended over some distance upstream of the vortex core. PIV results showed small vertical velocity gradients in the region below the core of the vortex ring. The effects of parameters such as initial release height and release volume shape were investigated. Using appropriate length and time scales, the measured velocities were scaled to and compared with previously studied atmospheric microbursts. The experimental data generally agree well with
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.
Cyclotron beam dynamic simulations in MATLAB
International Nuclear Information System (INIS)
Karamysheva, G.A.; Karamyshev, O.V.; Lepkina, O.E.
2008-01-01
MATLAB is useful for beam dynamic simulations in cyclotrons. Programming in an easy-to-use environment permits creation of models in a short space of time. Advanced graphical tools of MATLAB give good visualization features to created models. The beam dynamic modeling results with an example of two different cyclotron designs are presented. Programming with MATLAB opens wide possibilities of the development of the complex program, able to perform complete block of calculations for the design of the accelerators
Development of HTGR plant dynamics simulation code
International Nuclear Information System (INIS)
Ohashi, Kazutaka; Tazawa, Yujiro; Mitake, Susumu; Suzuki, Katsuo.
1987-01-01
Plant dynamics simulation analysis plays an important role in the design work of nuclear power plant especially in the plant safety analysis, control system analysis, and transient condition analysis. The authors have developed the plant dynamics simulation code named VESPER, which is applicable to the design work of High Temperature Engineering Test Reactor, and have been improving the code corresponding to the design changes made in the subsequent design works. This paper describes the outline of VESPER code and shows its sample calculation results selected from the recent design work. (author)
Dynamic Simulations of Advanced Fuel Cycles
International Nuclear Information System (INIS)
Piet, Steven J.; Dixon, Brent W.; Jacobson, Jacob J.; Matthern, Gretchen E.; Shropshire, David E.
2011-01-01
Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the U.S. Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe 'lessons learned' from dynamic simulations but attempt to answer the 'so what' question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
International Nuclear Information System (INIS)
Vashishta, Priya; Kalia, Rajiv
2005-01-01
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report
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.)
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.
Intelligent Flight Control Simulation Research Program
National Research Council Canada - National Science Library
Stolarik, Brian
2007-01-01
...). Under the program, entitled "Intelligent Flight Control Simulation Research Laboratory," a variety of technologies were investigated or developed during the course of the research for AFRL/VAC...
Fluid dynamics theory, computation, and numerical simulation
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...
Fluid Dynamics Theory, Computation, and Numerical Simulation
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 ...
Monte carlo simulation for soot dynamics
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.
Dynamic modeling and simulation of wind turbines
International Nuclear Information System (INIS)
Ghafari Seadat, M.H.; Kheradmand Keysami, M.; Lari, H.R.
2002-01-01
Using wind energy for generating electricity in wind turbines is a good way for using renewable energies. It can also help to protect the environment. The main objective of this paper is dynamic modeling by energy method and simulation of a wind turbine aided by computer. In this paper, the equations of motion are extracted for simulating the system of wind turbine and then the behavior of the system become obvious by solving the equations. The turbine is considered with three blade rotor in wind direction, induced generator that is connected to the network and constant revolution for simulation of wind turbine. Every part of the wind turbine should be simulated for simulation of wind turbine. The main parts are blades, gearbox, shafts and generator
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...
Molecular dynamics simulations and quantum chemical calculations ...
African Journals Online (AJOL)
Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...
Generator dynamics in aeroelastic analysis and simulations
Energy Technology Data Exchange (ETDEWEB)
Larsen, T.J.; Hansen, M.H.; Iov, F.
2003-05-01
This report contains a description of a dynamic model for a doubly-fed induction generator implemented in the aeroelastic code HAWC. The model has physical input parameters (resistance, reactance etc.) and input variables (stator and rotor voltage and rotor speed). The model can be used to simulate the generator torque as well as the rotor and stator currents, active and reactive power. 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 model from the slow variations and deduce a reduced order expression for the slow part. Dynamic effects of the first order terms in the model as well as the influence on drive train eigenfrequencies and damping has been investigated. Load response during time simulation of wind turbine response have been compared to simulations with a linear static generator model originally implemented i HAWC. A 2 MW turbine has been modelled in the aeroelastic code HAWC. When using the new dynamic generator model there is an interesting coupling between the generator dynamics and a global turbine vibration mode at 4.5 Hz, which only occurs when a dynamic formulation of the generator equations is applied. This frequency can especially be seen in the electrical power of the generator and the rotational speed of the generator, but also as torque variations in the drive train. (au)
Developments of multibody system dynamics: computer simulations and experiments
International Nuclear Information System (INIS)
Yoo, Wan-Suk; Kim, Kee-Nam; Kim, Hyun-Woo; Sohn, Jeong-Hyun
2007-01-01
It is an exceptional success when multibody dynamics researchers Multibody System Dynamics journal one of the most highly ranked journals in the last 10 years. In the inaugural issue, Professor Schiehlen wrote an interesting article explaining the roots and perspectives of multibody system dynamics. Professor Shabana also wrote an interesting article to review developments in flexible multibody dynamics. The application possibilities of multibody system dynamics have grown wider and deeper, with many application examples being introduced with multibody techniques in the past 10 years. In this paper, the development of multibody dynamics is briefly reviewed and several applications of multibody dynamics are described according to the author's research results. Simulation examples are compared to physical experiments, which show reasonableness and accuracy of the multibody formulation applied to real problems. Computer simulations using the absolute nodal coordinate formulation (ANCF) were also compared to physical experiments; therefore, the validity of ANCF for large-displacement and large-deformation problems was shown. Physical experiments for large deformation problems include beam, plate, chain, and strip. Other research topics currently being carried out in the author's laboratory are also briefly explained
Dynamic aspects of dislocation motion: atomistic simulations
International Nuclear Information System (INIS)
Bitzek, Erik; Gumbsch, Peter
2005-01-01
Atomistic simulations of accelerating edge and screw dislocations were carried out to study the dynamics of dislocations in a face centered cubic metal. Using two different embedded atom potentials for nickel and a simple slab geometry, the Peierls stress, the effective mass, the line tension and the drag coefficient were determined. A dislocation intersecting an array of voids is used to study dynamic effects in dislocation-obstacle interactions. A pronounced effect caused by inertial overshooting is found. A dynamic line tension model is developed which reproduces the simulation results. The model can be used to easily estimate the magnitude of inertial effects in the interaction of dislocations with localized obstacles for different obstacle strengths, -spacings and temperatures
Kinetics from Replica Exchange Molecular Dynamics Simulations.
Stelzl, Lukas S; Hummer, Gerhard
2017-08-08
Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.
GRODY - GAMMA RAY OBSERVATORY DYNAMICS SIMULATOR IN ADA
Stark, M.
1994-01-01
Analysts use a dynamics simulator to test the attitude control system algorithms used by a satellite. The simulator must simulate the hardware, dynamics, and environment of the particular spacecraft and provide user services which enable the analyst to conduct experiments. Researchers at Goddard's Flight Dynamics Division developed GRODY alongside GROSS (GSC-13147), a FORTRAN simulator which performs the same functions, in a case study to assess the feasibility and effectiveness of the Ada programming language for flight dynamics software development. They used popular object-oriented design techniques to link the simulator's design with its function. GRODY is designed for analysts familiar with spacecraft attitude analysis. The program supports maneuver planning as well as analytical testing and evaluation of the attitude determination and control system used on board the Gamma Ray Observatory (GRO) satellite. GRODY simulates the GRO on-board computer and Control Processor Electronics. The analyst/user sets up and controls the simulation. GRODY allows the analyst to check and update parameter values and ground commands, obtain simulation status displays, interrupt the simulation, analyze previous runs, and obtain printed output of simulation runs. The video terminal screen display allows visibility of command sequences, full-screen display and modification of parameters using input fields, and verification of all input data. Data input available for modification includes alignment and performance parameters for all attitude hardware, simulation control parameters which determine simulation scheduling and simulator output, initial conditions, and on-board computer commands. GRODY generates eight types of output: simulation results data set, analysis report, parameter report, simulation report, status display, plots, diagnostic output (which helps the user trace any problems that have occurred during a simulation), and a permanent log of all runs and errors. The
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...
GROSS- GAMMA RAY OBSERVATORY ATTITUDE DYNAMICS SIMULATOR
Garrick, J.
1994-01-01
The Gamma Ray Observatory (GRO) spacecraft will constitute a major advance in gamma ray astronomy by offering the first opportunity for comprehensive observations in the range of 0.1 to 30,000 megaelectronvolts (MeV). The Gamma Ray Observatory Attitude Dynamics Simulator, GROSS, is designed to simulate this mission. The GRO Dynamics Simulator consists of three separate programs: the Standalone Profile Program; the Simulator Program, which contains the Simulation Control Input/Output (SCIO) Subsystem, the Truth Model (TM) Subsystem, and the Onboard Computer (OBC) Subsystem; and the Postprocessor Program. The Standalone Profile Program models the environment of the spacecraft and generates a profile data set for use by the simulator. This data set contains items such as individual external torques; GRO spacecraft, Tracking and Data Relay Satellite (TDRS), and solar and lunar ephemerides; and star data. The Standalone Profile Program is run before a simulation. The SCIO subsystem is the executive driver for the simulator. It accepts user input, initializes parameters, controls simulation, and generates output data files and simulation status display. The TM subsystem models the spacecraft dynamics, sensors, and actuators. It accepts ephemerides, star data, and environmental torques from the Standalone Profile Program. With these and actuator commands from the OBC subsystem, the TM subsystem propagates the current state of the spacecraft and generates sensor data for use by the OBC and SCIO subsystems. The OBC subsystem uses sensor data from the TM subsystem, a Kalman filter (for attitude determination), and control laws to compute actuator commands to the TM subsystem. The OBC subsystem also provides output data to the SCIO subsystem for output to the analysts. The Postprocessor Program is run after simulation is completed. It generates printer and CRT plots and tabular reports of the simulated data at the direction of the user. GROSS is written in FORTRAN 77 and
Exploring travelers' behavior in response to dynamic message signs (DMS) using a driving simulator.
2013-10-01
This research studies the effectiveness of a dynamic message sign (DMS) using a driving : simulator. Over 100 subjects from different socio-economic and age groups were recruited to : drive the simulator under different traffic and driving conditions...
2013-10-01
This research studies the effectiveness of a dynamic message sign (DMS) using a driving : simulator. Over 100 subjects from different socio-economic and age groups were recruited to : drive the simulator under different traffic and driving conditions...
Modelling, simulation and applications of longitudinal train dynamics
Cole, Colin; Spiryagin, Maksym; Wu, Qing; Sun, Yan Quan
2017-10-01
Significant developments in longitudinal train simulation and an overview of the approaches to train models and modelling vehicle force inputs are firstly presented. The most important modelling task, that of the wagon connection, consisting of energy absorption devices such as draft gears and buffers, draw gear stiffness, coupler slack and structural stiffness is then presented. Detailed attention is given to the modelling approaches for friction wedge damped and polymer draft gears. A significant issue in longitudinal train dynamics is the modelling and calculation of the input forces - the co-dimensional problem. The need to push traction performances higher has led to research and improvement in the accuracy of traction modelling which is discussed. A co-simulation method that combines longitudinal train simulation, locomotive traction control and locomotive vehicle dynamics is presented. The modelling of other forces, braking propulsion resistance, curve drag and grade forces are also discussed. As extensions to conventional longitudinal train dynamics, lateral forces and coupler impacts are examined in regards to interaction with wagon lateral and vertical dynamics. Various applications of longitudinal train dynamics are then presented. As an alternative to the tradition single wagon mass approach to longitudinal train dynamics, an example incorporating fully detailed wagon dynamics is presented for a crash analysis problem. Further applications of starting traction, air braking, distributed power, energy analysis and tippler operation are also presented.
Engineering dynamics from the Lagrangian to simulation
Gans, Roger F
2013-01-01
This engineering dynamics textbook is aimed at beginning graduate students in mechanical engineering and other related engineering disciplines who need training in dynamics as applied to engineering mechanisms. It introduces the formal mathematical development of Lagrangian mechanics (and its corollaries), while solving numerous engineering applications. The author’s goal is to instill an understanding of the basic physics required for engineering dynamics, while providing a recipe (algorithm) for the simulation of engineering mechanisms such as robots. The book is reasonably self-contained so that the practicing engineer interested in this area can also make use of it. This book is made accessible to the widest possible audience by numerous, solved examples and diagrams that apply the principles to real engineering applications. • Provides an applied textbook for intermediate/advanced engineering dynamics courses; • Discusses Lagrangian mechanics in the context of numerous engineering applications...
Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Cedrix J. Dongmo Foumthuim
2018-01-01
Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
Dynamic Simulator for Nuclear Power Plants (DSNP)
International Nuclear Information System (INIS)
Saphier, D.
1976-01-01
A new simulation language DSNP (Dynamic Simulator for Nuclear Power Plants) is being developed. It is a simple block oriented simulation language with an extensive library of component and auxiliary modules. Each module is a self-contained unit of a part of a physical component to be found in nuclear power plants. Each module will be available in four levels of sophistication, the fourth being a user supplied model. A module can be included in the simulation by a single statement. The precompiler translates DSNP statements into FORTRAN statements, takes care of the module parameters and the intermodular communication blocks, prepares proper data files and I/0 statements and searches the various libraries for the appropriate component modules. The documentation is computerized and all the necessary information for a particular module can be retrieved by a special document generator. The DSNP will be a flexible tool which will allow dynamic simulations to be performed on a large variety of nuclear power plants or specific components of these plants
Dynamic bounds coupled with Monte Carlo simulations
Energy Technology Data Exchange (ETDEWEB)
Rajabalinejad, M., E-mail: M.Rajabalinejad@tudelft.n [Faculty of Civil Engineering, Delft University of Technology, Delft (Netherlands); Meester, L.E. [Delft Institute of Applied Mathematics, Delft University of Technology, Delft (Netherlands); Gelder, P.H.A.J.M. van; Vrijling, J.K. [Faculty of Civil Engineering, Delft University of Technology, Delft (Netherlands)
2011-02-15
For the reliability analysis of engineering structures a variety of methods is known, of which Monte Carlo (MC) simulation is widely considered to be among the most robust and most generally applicable. To reduce simulation cost of the MC method, variance reduction methods are applied. This paper describes a method to reduce the simulation cost even further, while retaining the accuracy of Monte Carlo, by taking into account widely present monotonicity. For models exhibiting monotonic (decreasing or increasing) behavior, dynamic bounds (DB) are defined, which in a coupled Monte Carlo simulation are updated dynamically, resulting in a failure probability estimate, as well as a strict (non-probabilistic) upper and lower bounds. Accurate results are obtained at a much lower cost than an equivalent ordinary Monte Carlo simulation. In a two-dimensional and a four-dimensional numerical example, the cost reduction factors are 130 and 9, respectively, where the relative error is smaller than 5%. At higher accuracy levels, this factor increases, though this effect is expected to be smaller with increasing dimension. To show the application of DB method to real world problems, it is applied to a complex finite element model of a flood wall in New Orleans.
Lipid Configurations from Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek
2018-01-01
of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...
Description of the grout system dynamic simulation
International Nuclear Information System (INIS)
Zimmerman, B.D.
1993-07-01
The grout system dynamic computer simulation was created to allow investigation of the ability of the grouting system to meet established milestones, for various assumed system configurations and parameters. The simulation simulates the movement of tank waste through the system versus time, from initial storage tanks, through feed tanks and the grout plant, then finally to a grout vault. The simulation properly accounts for the following (1) time required to perform various actions or processes, (2) delays involved in gaining regulatory approval, (3) random system component failures, (4) limitations on equipment capacities, (5) available parallel components, and (6) different possible strategies for vault filling. The user is allowed to set a variety of system parameters for each simulation run. Currently, the output of a run primarily consists of a plot of projected grouting campaigns completed versus time, for comparison with milestones. Other outputs involving any model component can also be quickly created or deleted as desired. In particular, sensitivity runs where the effect of varying a model parameter (flow rates, delay times, number of feed tanks available, etc.) on the ability of the system to meet milestones can be made easily. The grout system simulation was implemented using the ITHINK* simulation language for Macintosh** computers
Hydration dynamics in water clusters via quantum molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of
Dislocation dynamics simulations in a cylinder
International Nuclear Information System (INIS)
Weinberger, Christopher R; Aubry, Sylvie; Cai, Wei; Lee, Seok-Woo
2009-01-01
In this work we describe how to perform dislocation dynamics simulations in a cylindrical geometry. An algorithm for computing the image stress is given in detail including methods for handling the singularity. Additional remesh rules address the problems of the cylindrical geometry and the required self consistency with mobility laws. Numerical studies benchmark the accuracy of the algorithms and the importance of handling the singularity correctly.
Electronic Concepts Simulation Research Facility
Federal Laboratory Consortium — The laboratory utilizes state-of-the-art digital models and simulations of both friendly and enemy airborne and ground-based weapon and command and control systems....
A molecular dynamics simulation code ISIS
International Nuclear Information System (INIS)
Kambayashi, Shaw
1992-06-01
Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)
A molecular dynamics simulation study of chloroform
Tironi, Ilario G.; van Gunsteren, Wilfred F.
Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.
Simulating coronal condensation dynamics in 3D
Moschou, S. P.; Keppens, R.; Xia, C.; Fang, X.
2015-12-01
We present numerical simulations in 3D settings where coronal rain phenomena take place in a magnetic configuration of a quadrupolar arcade system. Our simulation is a magnetohydrodynamic simulation including anisotropic thermal conduction, optically thin radiative losses, and parametrised heating as main thermodynamical features to construct a realistic arcade configuration from chromospheric to coronal heights. The plasma evaporation from chromospheric and transition region heights eventually causes localised runaway condensation events and we witness the formation of plasma blobs due to thermal instability, that evolve dynamically in the heated arcade part and move gradually downwards due to interchange type dynamics. Unlike earlier 2.5D simulations, in this case there is no large scale prominence formation observed, but a continuous coronal rain develops which shows clear indications of Rayleigh-Taylor or interchange instability, that causes the denser plasma located above the transition region to fall down, as the system moves towards a more stable state. Linear stability analysis is used in the non-linear regime for gaining insight and giving a prediction of the system's evolution. After the plasma blobs descend through interchange, they follow the magnetic field topology more closely in the lower coronal regions, where they are guided by the magnetic dips.
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.
Rarefield gas dynamics fundamentals, simulations and micro flows
Shen, Ching
2006-01-01
This book elucidates the methods of molecular gas dynamics or rarefied gas dynamics which treat the problems of gas flows when the discrete molecular effects of the gas prevail under the circumstances of low density, the emphasis being on the basis of the methods, the direct simulation Monte Carlo method applied to the simulation of non-equilibrium effects and the frontier subjects related to low speed microscale rarefied gas flows. It provides a solid basis for the study of molecular gas dynamics for senior students and graduates in the aerospace and mechanical engineering departments of universities and colleges. It gives a general acquaintance of modern developments of rarefied gas dynamics in various regimes and leads to the frontier topics of non-equilibrium rarefied gas dynamics and low speed microscale gas dynamics. It will be also of benefit to the scientific and technical researchers engaged in aerospace high altitude aerodynamic force and heating design and in the research on gas flow in MEMS.
Czech Academy of Sciences Publication Activity Database
Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.
2004-01-01
Roč. 70, č. 6 (2004), 0611031-0611034 ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant - others:NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004
Dynamic simulation of an electrorheological fluid
International Nuclear Information System (INIS)
Bonnecaze, R.T.; Brady, J.F.
1992-01-01
A molecular-dynamics-like method is presented for the simulation of a suspension of dielectric particles in a nonconductive solvent forming an electrorheological fluid. The method accurately accounts for both hydrodynamic and electrostatic interparticle interactions from dilute volume fractions to closest packing for simultaneous shear and electric fields. The hydrodynamic interactions and rheology are determined with the Stokesian dynamics methodology, while the electrostatic interactions, in particular, the conservative electrostatic interparticle forces, are determined from the electrostatic energy of the suspension. The energy of the suspension is computed from the induced particle dipoles by a method previously developed [R. T. Bonnecaze and J. F. Brady, Proc. R. Soc. London, Ser. A 430, 285 (1990)]. Using the simulation, the dynamics can be directly correlated to the observed macroscopic rheology of the suspension for a range of the so-called Mason number, Ma, the ratio of viscous to electrostatic forces. The simulation is specifically applied to a monolayer of spherical particles of areal fraction 0.4 with a particle-to-fluid dielectric constant ratio of 4 for Ma=10 -4 to ∞. The effective viscosity of the suspension increases as Ma -1 or with the square of the electric field for small Ma and has a plateau value at large Ma, as is observed experimentally. This rheological behavior can be interpreted as Bingham plastic-like with a dynamic yield stress. The first normal stress difference is negative, and its magnitude increases as Ma -1 at small Ma with a large Ma plateau value of zero. In addition to the time averages of the rheology, the time traces of the viscosities are presented along with selected ''snapshots'' of the suspension microstructure
Molecular dynamics simulations of RNA motifs
Czech Academy of Sciences Publication Activity Database
Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.
2002-01-01
Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics
Computer simulation of confined liquid crystal dynamics
International Nuclear Information System (INIS)
Webster, R.E.
2001-11-01
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 show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations 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. (author)
Computer simulation of confined liquid crystal dynamics
Energy Technology Data Exchange (ETDEWEB)
Webster, R.E
2001-11-01
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 show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations 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. (author)
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....... The systems dynamics model essentially provides other researchers with a clear demonstration of inputs, outputs and assumptions used in the calculations. I propose, that EROI studies are supplemented with such models for clarity....... along with publications where inputs and outputs from energy systems are shown, but that is seldom or ever the case. Doing so would allow other researchers to see if energy systems or studies are actually comparable and if inputs, outputs and assumptions are the same. In this study, I demonstrate how...
First Principles Modelling of Shape Memory Alloys Molecular Dynamics Simulations
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...
HTTR plant dynamic simulation using a hybrid computer
International Nuclear Information System (INIS)
Shimazaki, Junya; Suzuki, Katsuo; Nabeshima, Kunihiko; Watanabe, Koichi; Shinohara, Yoshikuni; Nakagawa, Shigeaki.
1990-01-01
A plant dynamic simulation of High-Temperature Engineering Test Reactor has been made using a new-type hybrid computer. This report describes a dynamic simulation model of HTTR, a hybrid simulation method for SIMSTAR and some results obtained from dynamics analysis of HTTR simulation. It concludes that the hybrid plant simulation is useful for on-line simulation on account of its capability of computation at high speed, compared with that of all digital computer simulation. With sufficient accuracy, 40 times faster computation than real time was reached only by changing an analog time scale for HTTR simulation. (author)
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...... of the first order terms in the model as well as the influence on drive train eigenfrequencies and damping has been investigated. Load response during timesimulation of wind turbine response have been compared to simulations with a traditional static generator model based entirely on the slip angle. A 2 MW...
Traffic flow dynamics data, models and simulation
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 ...
Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package
Dizkirici, Ayten; Tekpinar, Mustafa
2015-03-01
GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.
Parallel beam dynamics simulation of linear accelerators
International Nuclear Information System (INIS)
Qiang, Ji; Ryne, Robert D.
2002-01-01
In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity beams and to the study of beam transport in a proposed accelerator for the development of accelerator-driven waste transmutation technologies
Viscosity calculations at molecular dynamics simulations
International Nuclear Information System (INIS)
Kirova, E M; Norman, G E
2015-01-01
Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)
dynamic performance of research reactors
International Nuclear Information System (INIS)
Abo elnor, A.G.M.
2007-01-01
this work studies the dynamic performance of material testing reactor (MTR), where the dynamic performance of any reactor reflects its safety behavior and it should enhance its intrinsic characteristics s ystem corrects itself internally without introducing external corrective action . the present work analyzes and studies the dynamic performance of mtr through the transfer function. the servo system parameters can be changed to fit the system demand. the servo system is an excellent approximation to some of the practical servo system currently use in reactor control system, and a quadratic form of this sort should closely approximate the behavior of almost any type of physical equipment which might be chosen to drive a control rod. proposed changes in servo system parameters could enhance the dynamic performance of the system , but the suitable parameters can be evaluated by using the automatic reactor power control system model
Parallel Monte Carlo simulation of aerosol dynamics
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.
Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.
Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao
2018-02-01
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.
[Use of driving simulators in psychological research].
Andysz, Aleksandra; Waszkowska, Małgorzata; Merecz, Dorota; Drabek, Marcin
2010-01-01
The history of simulators dates back to the first decades of the twentieth century. At the beginning they were used to train pilots, and eventually they were used in the automotive industry for testing the strength of new vehicles and ergonomic solutions. With time research institutions and technical universities from outside the automotive industry have become more and more interested in simulators. Attractiveness of simulators for researchers is based on a number of important factors: they create the possibility of modeling, control and repeatability of different experimental situations, reducing at the same time the impact of confounding factors. Simulators have a great potential for data collection and processing. What's more, they are safe and ecologic. These values make them almost an ideal research tool. The article presents a review of psychological studies with use of vehicle driving simulators. It also points to advantages and disadvantages of these devices and outlines the future prospects for experimental research.
Fluid dynamics theory, computation, and numerical simulation
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 ...
Dynamic characteristics of nanoindentation using atomistic simulation
International Nuclear Information System (INIS)
Fang, Te-Hua; Chang, Wen-Yang; Huang, Jian-Jin
2009-01-01
Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0 o , is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.
Dynamic characteristics of nanoindentation using atomistic simulation
Energy Technology Data Exchange (ETDEWEB)
Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China); Chang, Wen-Yang [Microsystems Technology Center, Industrial Technology Research Institute, Tainan 709, Taiwan (China); Huang, Jian-Jin [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China)
2009-06-15
Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0{sup o}, is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.
Choosing the speed of dynamic mental simulations.
Makin, Alexis D J
2017-01-01
The brain continuously maintains a current representation of its immediate surroundings. Perceptual representations are often updated when the world changes, e.g., when we notice an object move. However, we can also update representations internally, without incoming signals from the senses. In other words, we can run internal simulations of dynamic events. This ability is evident during mental object rotation. These uncontroversial observations lead to an obvious question that nevertheless remains to be answered: How does the brain control the speed of dynamic mental simulations? Is there a central rate controller or pacemaker module in the brain that can be temporarily coupled to sensory maps? We can refer to this as the common rate control theory. Alternatively, the primitive intelligence within each map could tune into the speed of recent changes and use this information to keep going after stimuli disappear. We can call this the separate rate control theory. Preliminary evidence from prediction motion experiments supports common rate control, although local predictive mechanisms may cover short gaps of cognitive timing literature. Indirect neuroimaging evidence suggests rate control is a function of the core timing system in the dorsal striatum. © 2017 Elsevier B.V. All rights reserved.
IMPROVING MEDICAL EDUCATION: SIMULATING CHANGES IN PATIENT ANATOMY USING DYNAMIC HAPTIC FEEDBACK.
Yovanoff, Mary; Pepley, David; Mirkin, Katelin; Moore, Jason; Han, David; Miller, Scarlett
2016-09-01
Virtual simulation is an emerging field in medical education. Research suggests that simulation reduces complication rates and improves learning gains for medical residents. One benefit of simulators is their allowance for more realistic and dynamic patient anatomies. While potentially useful throughout medical education, few studies have explored the impact of dynamic haptic simulators on medical training. In light of this research void, this study was developed to examine how a Dynamic-Haptic Robotic Trainer (DHRT) impacts medical student self-efficacy and skill gains compared to traditional simulators developed to train students in Internal Jugular Central Venous Catheter (IJ CVC) placement. The study was conducted with 18 third year medical students with no prior CVC insertion experience who underwent a pre-test, simulator training (manikin, robotic, or mixed) and post-test. The results revealed the DHRT as a useful method for training CVC skills and supports further research on dynamic haptic trainers in medical education.
Simulation and experimental research on line throwing rocket with flight
Directory of Open Access Journals (Sweden)
Wen-bin Gu
2014-06-01
Full Text Available The finite segment method is used to model the line throwing rocket system. A dynamic model of line throwing rocket with flight motion based on Kane's method is presented by the kinematics description of the system and the consideration of the forces acting on the system. The experiment designed according to the parameters of the dynamic model is made. The simulation and experiment results, such as range, velocity and flight time, are compared and analyzed. The simulation results are basically agreed with the test data, which shows that the flight motion of the line throwing rocket can be predicted by the dynamic model. A theoretical model and guide for the further research on the disturbance of rope and the guidance, flight control of line throwing rocket are provided by the dynamic modeling.
Modeling initial contact dynamics during ambulation with dynamic simulation.
Meyer, Andrew R; Wang, Mei; Smith, Peter A; Harris, Gerald F
2007-04-01
Ankle-foot orthoses are frequently used interventions to correct pathological gait. Their effects on the kinematics and kinetics of the proximal joints are of great interest when prescribing ankle-foot orthoses to specific patient groups. Mathematical Dynamic Model (MADYMO) is developed to simulate motor vehicle crash situations and analyze tissue injuries of the occupants based multibody dynamic theories. Joint kinetics output from an inverse model were perturbed and input to the forward model to examine the effects of changes in the internal sagittal ankle moment on knee and hip kinematics following heel strike. Increasing the internal ankle moment (augmentation, equivalent to gastroc-soleus contraction) produced less pronounced changes in kinematic results at the hip, knee and ankle than decreasing the moment (attenuation, equivalent to gastroc-soleus relaxation). Altering the internal ankle moment produced two distinctly different kinematic curve morphologies at the hip. Decreased internal ankle moments increased hip flexion, peaking at roughly 8% of the gait cycle. Increasing internal ankle moments decreased hip flexion to a lesser degree, and approached normal at the same point in the gait cycle. Increasing the internal ankle moment produced relatively small, well-behaved extension-biased kinematic results at the knee. Decreasing the internal ankle moment produced more substantial changes in knee kinematics towards flexion that increased with perturbation magnitude. Curve morphologies were similar to those at the hip. Immediately following heel strike, kinematic results at the ankle showed movement in the direction of the internal moment perturbation. Increased internal moments resulted in kinematic patterns that rapidly approach normal after initial differences. When the internal ankle moment was decreased, differences from normal were much greater and did not rapidly decrease. This study shows that MADYMO can be successfully applied to accomplish forward
Dynamics and Chemistry in Jovian Atmospheres: 2D Hydrodynamical Simulations
Bordwell, B. R.; Brown, B. P.; Oishi, J.
2016-12-01
A key component of our understanding of the formation and evolution of planetary systems is chemical composition. Problematically, however, in the atmospheres of cooler gas giants, dynamics on the same timescale as chemical reactions pull molecular abundances out of thermochemical equilibrium. These disequilibrium abundances are treated using what is known as the "quench" approximation, based upon the mixing length theory of convection. The validity of this approximation is questionable, though, as the atmospheres of gas giants encompass two distinct dynamic regimes: convective and radiative. To resolve this issue, we conduct 2D hydrodynamical simulations using the state-of-the-art pseudospectral simulation framework Dedalus. In these simulations, we solve the fully compressible equations of fluid motion in a local slab geometry that mimics the structure of a planetary atmosphere (convective zone underlying a radiative zone). Through the inclusion of passive tracers, we explore the transport properties of both regimes, and assess the validity of the classical eddy diffusion parameterization. With the addition of active tracers, we examine the interactions between dynamical and chemical processes, and generate prescriptions for the observational community. By providing insight into mixing and feedback mechanisms in Jovian atmospheres, this research lays a solid foundation for future global simulations and the construction of physically-sound models for current and future observations.
Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong, E-mail: ganglong.cui@bnu.edu.cn [Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China)
2016-08-21
Herein we have used combined static electronic structure calculations and “on-the-fly” global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the {sup 1}ππ{sup ∗}, {sup 1}nπ{sup ∗}, and S{sub 0} states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated {sup 1}ππ{sup ∗} system. The first is the diabatic ESIPT process along the {sup 1}ππ{sup ∗} potential energy profile. The generated {sup 1}ππ{sup ∗} keto species then decays to the S{sub 0} state via the keto {sup 1}ππ{sup ∗}/gs conical intersection. The second is internal conversion to the dark {sup 1}nπ{sup ∗} state near the {sup 1}ππ{sup ∗} /{sup 1}nπ{sup ∗} crossing point in the course of the diabatic {sup 1}ππ{sup ∗} ESIPT process. Our following dynamics simulations have shown that the ESIPT and {sup 1}ππ{sup ∗} → S{sub 0} internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the {sup 1}ππ{sup ∗} → S{sub 0} internal conversion in the keto region, the {sup 1}ππ{sup ∗} → {sup 1}nπ{sup ∗} internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.
Simulation of Molten Salt Reactor dynamics
International Nuclear Information System (INIS)
Krepel, J.; Rohde, U.; Grundmann, U.
2005-01-01
Dynamics of the Molten Salt Reactor - one of the 'Generation IV' concepts - was studied in this paper. The graphite-moderated channel type MSR was selected for the numerical simulation of the reactor with liquid fuel. The MSR dynamics is very specific because of two physical peculiarities of the liquid fueled reactor: the delayed neutrons precursors are drifted by the fuel flow and the fission energy is immediately released directly into the coolant. Presently, there are not many accessible numerical codes appropriate for the MSR simulation, therefore the DYN3D-MSR code was developed based on the FZR in-house code DYN3D. It allows calculating of full 3D transient neutronics in combination with parallel channel type thermal-hydraulics. By means of DYN3D-MSR, several transients typical for the liquid fuel system were analyzed. Those transients were initiated by reactivity insertion, by overcooling of fuel at the core inlet, by the fuel pump start-up or coast-down, or by the blockage of selected fuel channels. In these considered transients, the response of the MSR is characterized by the immediate change of the fuel temperature with changing power and fast negative temperature feedback to the power. The response through the graphite temperature is slower. Furthermore, for big MSR cores fueled with U233 the graphite feedback coefficient can be positive. In this case the addition of erbium to the graphite can ensure the inherent safety features. The DYN3D-MSR code has been shown to be an effective tool for MSR dynamics studies. (author)
Virtual environments simulation in research reactor
Muhamad, Shalina Bt. Sheik; Bahrin, Muhammad Hannan Bin
2017-01-01
Virtual reality based simulations are interactive and engaging. It has the useful potential in improving safety training. Virtual reality technology can be used to train workers who are unfamiliar with the physical layout of an area. In this study, a simulation program based on the virtual environment at research reactor was developed. The platform used for virtual simulation is 3DVia software for which it's rendering capabilities, physics for movement and collision and interactive navigation features have been taken advantage of. A real research reactor was virtually modelled and simulated with the model of avatars adopted to simulate walking. Collision detection algorithms were developed for various parts of the 3D building and avatars to restrain the avatars to certain regions of the virtual environment. A user can control the avatar to move around inside the virtual environment. Thus, this work can assist in the training of personnel, as in evaluating the radiological safety of the research reactor facility.
Nonlinear mirror mode dynamics: Simulations and modeling
Czech Academy of Sciences Publication Activity Database
Califano, F.; Hellinger, Petr; Kuznetsov, E.; Passot, T.; Sulem, P. L.; Trávníček, Pavel
2008-01-01
Roč. 113, - (2008), A08219/1-A08219/20 ISSN 0148-0227 R&D Projects: GA AV ČR IAA300420702; GA AV ČR IAA300420602 Grant - others:PECS(CZ) 98024 Institutional research plan: CEZ:AV0Z30420517 Keywords : mirror instability * nonlinear evolution * numerical simulations * magnetic holes * mirror structures * kinetic plasma instabilities Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 3.147, year: 2008
Dynamics simulations for engineering macromolecular interactions
Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey
2013-01-01
The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could
Molecular dynamic simulation study of molten cesium
Directory of Open Access Journals (Sweden)
Yeganegi Saeid
2017-01-01
Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.
Dynamics of International Business Research
DEFF Research Database (Denmark)
Kunz, Werner; Manning, Stephan; Pedersen, Torben
2013-01-01
This study examines the evolution of the field of international business (IB) research based on a relational cluster analysis of co-citations in the Journal of International Business Studies (JIBS) from 1982 to 2011. Particularly, we examine the changing role of theory in relation to empirical IB...... research. Based on a factor and network analysis, we identify distinct clusters of IB research and their relations over time. We show that the initial focus of IB research on issues of international expansion has shifted towards issues of governance and implementation. In this process, debates on foreign...... entry mode and culture have served as important integrating themes. At the same time, theory debates in IB have expanded from a narrow focus on explaining international expansion, to a rather heterogeneous conglomerate of approaches which have assisted increasingly differentiated empirical research. Our...
Simulation of Tailrace Hydrodynamics Using Computational Fluid Dynamics Models
Energy Technology Data Exchange (ETDEWEB)
Cook, Christopher B.; Richmond, Marshall C.
2001-05-01
This report investigates the feasibility of using computational fluid dynamics (CFD) tools to investigate hydrodynamic flow fields surrounding the tailrace zone below large hydraulic structures. Previous and ongoing studies using CFD tools to simulate gradually varied flow with multiple constituents and forebay/intake hydrodynamics have shown that CFD tools can provide valuable information for hydraulic and biological evaluation of fish passage near hydraulic structures. These studies however are incapable of simulating the rapidly varying flow fields that involving breakup of the free-surface, such as those through and below high flow outfalls and spillways. Although the use of CFD tools for these types of flow are still an active area of research, initial applications discussed in this report show that these tools are capable of simulating the primary features of these highly transient flow fields.
Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation
Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting
2017-07-01
To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project
Traffic flow dynamics. Data, models and simulation
Energy Technology Data Exchange (ETDEWEB)
Treiber, Martin [Technische Univ. Dresden (Germany). Inst. fuer Wirtschaft und Verkehr; Kesting, Arne [TomTom Development Germany GmbH, Berlin (Germany)
2013-07-01
First comprehensive textbook of this fascinating interdisciplinary topic which explains advances in a way that it is easily accessible to engineering, physics and math students. Presents practical applications of traffic theory such as driving behavior, stability analysis, stop-and-go waves, and travel time estimation. Presents the topic in a novel and systematic way by addressing both microscopic and macroscopic models with a focus on traffic instabilities. Revised and extended edition of the German textbook ''Verkehrsdynamik und -simulation''. 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 traffic instabilities and model calibration/validation present these topics in a novel and systematic way. Finally, the theoretical framework is shown at work in selected applications such as traffic-state and travel-time estimation, intelligent transportation systems, traffic operations management, and a detailed physics-based model for fuel consumption and emissions.
Classical molecular dynamics simulation of nuclear fuels
International Nuclear Information System (INIS)
Devanathan, R.; Krack, M.; Bertolus, M.
2015-01-01
Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)
An Evaluative Review of Simulated Dynamic Smart 3d Objects
Romeijn, H.; Sheth, F.; Pettit, C. J.
2012-07-01
Three-dimensional (3D) modelling of plants can be an asset for creating agricultural based visualisation products. The continuum of 3D plants models ranges from static to dynamic objects, also known as smart 3D objects. There is an increasing requirement for smarter simulated 3D objects that are attributed mathematically and/or from biological inputs. A systematic approach to plant simulation offers significant advantages to applications in agricultural research, particularly in simulating plant behaviour and the influences of external environmental factors. This approach of 3D plant object visualisation is primarily evident from the visualisation of plants using photographed billboarded images, to more advanced procedural models that come closer to simulating realistic virtual plants. However, few programs model physical reactions of plants to external factors and even fewer are able to grow plants based on mathematical and/or biological parameters. In this paper, we undertake an evaluation of plant-based object simulation programs currently available, with a focus upon the components and techniques involved in producing these objects. Through an analytical review process we consider the strengths and weaknesses of several program packages, the features and use of these programs and the possible opportunities in deploying these for creating smart 3D plant-based objects to support agricultural research and natural resource management. In creating smart 3D objects the model needs to be informed by both plant physiology and phenology. Expert knowledge will frame the parameters and procedures that will attribute the object and allow the simulation of dynamic virtual plants. Ultimately, biologically smart 3D virtual plants that react to changes within an environment could be an effective medium to visually represent landscapes and communicate land management scenarios and practices to planners and decision-makers.
Simulating market dynamics: interactions between consumer psychology and social networks.
Janssen, Marco A; Jager, Wander
2003-01-01
Markets can show different types of dynamics, from quiet markets dominated by one or a few products, to markets with continual penetration of new and reintroduced products. In a previous article we explored the dynamics of markets from a psychological perspective using a multi-agent simulation model. The main results indicated that the behavioral rules dominating the artificial consumer's decision making determine the resulting market dynamics, such as fashions, lock-in, and unstable renewal. Results also show the importance of psychological variables like social networks, preferences, and the need for identity to explain the dynamics of markets. In this article we extend this work in two directions. First, we will focus on a more systematic investigation of the effects of different network structures. The previous article was based on Watts and Strogatz's approach, which describes the small-world and clustering characteristics in networks. More recent research demonstrated that many large networks display a scale-free power-law distribution for node connectivity. In terms of market dynamics this may imply that a small proportion of consumers may have an exceptional influence on the consumptive behavior of others (hubs, or early adapters). We show that market dynamics is a self-organized property depending on the interaction between the agents' decision-making process (heuristics), the product characteristics (degree of satisfaction of unit of consumption, visibility), and the structure of interactions between agents (size of network and hubs in a social network).
Brownian dynamics simulations of insulin microspheres formation
Li, Wei; Chakrabarti, Amit; Gunton, James
2010-03-01
Recent experiments have indicated a novel, aqueous process of microsphere insulin fabrication based on controlled phase separation of protein from water-soluble polymers. We investigate the insulin microsphere crystal formation from insulin-PEG-water systems via 3D Brownian Dynamics simulations. We use the two component Asakura-Oosawa model to simulate the kinetics of this colloid polymer mixture. We first perform a deep quench below the liquid-crystal boundary that leads to fractal formation. We next heat the system to obtain a break-up of the fractal clusters and subsequently cool the system to obtain a spherical aggregation of droplets with a relatively narrow size distribution. We analyze the structure factor S(q) to identify the cluster dimension. S(q) crosses over from a power law q dependence of 1.8 (in agreement with DLCA) to 4 as q increases, which shows the evolution from fractal to spherical clusters. By studying the bond-order parameters, we find the phase transition from liquid-like droplets to crystals which exhibit local HCP and FCC order. This work is supported by grants from the NSF and Mathers Foundation.
Dynamic Simulation and Optimization of Nuclear Hydrogen Production Systems
Energy Technology Data Exchange (ETDEWEB)
Paul I. Barton; Mujid S. Kaximi; Georgios Bollas; Patricio Ramirez Munoz
2009-07-31
This project is part of a research effort to design a hydrogen plant and its interface with a nuclear reactor. This project developed a dynamic modeling, simulation and optimization environment for nuclear hydrogen production systems. A hybrid discrete/continuous model captures both the continuous dynamics of the nuclear plant, the hydrogen plant, and their interface, along with discrete events such as major upsets. This hybrid model makes us of accurate thermodynamic sub-models for the description of phase and reaction equilibria in the thermochemical reactor. Use of the detailed thermodynamic models will allow researchers to examine the process in detail and have confidence in the accurary of the property package they use.
Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations
International Nuclear Information System (INIS)
Kim, Woongkee; Kaviany, Massoud; Shim, J. H.
2014-01-01
It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments
Application of subset simulation methods to dynamic fault tree analysis
International Nuclear Information System (INIS)
Liu Mengyun; Liu Jingquan; She Ding
2015-01-01
Although fault tree analysis has been implemented in the nuclear safety field over the past few decades, it was recently criticized for the inability to model the time-dependent behaviors. Several methods are proposed to overcome this disadvantage, and dynamic fault tree (DFT) has become one of the research highlights. By introducing additional dynamic gates, DFT is able to describe the dynamic behaviors like the replacement of spare components or the priority of failure events. Using Monte Carlo simulation (MCS) approach to solve DFT has obtained rising attention, because it can model the authentic behaviors of systems and avoid the limitations in the analytical method. In this paper, it provides an overview and MCS information for DFT analysis, including the sampling of basic events and the propagation rule for logic gates. When calculating rare-event probability, large amount of simulations in standard MCS are required. To improve the weakness, subset simulation (SS) approach is applied. Using the concept of conditional probability and Markov Chain Monte Carlo (MCMC) technique, the SS method is able to accelerate the efficiency of exploring the failure region. Two cases are tested to illustrate the performance of SS approach, and the numerical results suggest that it gives high efficiency when calculating complicated systems with small failure probabilities. (author)
Micellar polymerization: Computer simulations by dissipative particle dynamics.
Shupanov, Ruslan; Chertovich, Alexander; Kos, Pavel
2018-07-15
Nowadays, micellar polymerization is widely used in different fields of industry and research, including modern living polymerization technique. However, this process has many variables and there is no comprehensive model to describe all features. This research presents simulation methodology which describes key properties of such reactions to take a guide through a variety of their modifications. Dissipative particle dynamics is used in addition to Monte Carlo scheme to simulate initiation, propagation, and termination events. Influence of initiation probability and different termination processes on final conversion and molecular-weight distribution are presented. We demonstrate that prolonged initiation leads to increasing in polymer average molecular weight, and surface termination events play major role in conversion limitation, in comparison with recombination. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Computational fluid dynamics for sport simulation
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.
Dynamic Response and Simulations of Nanoparticle-Enhanced Composites
National Research Council Canada - National Science Library
Mantena, P. R; Al-Ostaz, Ahmed; Cheng, Alexander H
2007-01-01
...) molecular dynamics simulations of nanoparticle-enhanced composites and fly- ash based foams that are being considered for the future generation naval structures or retrofitting of existing ones...
Simulating CubeSat Structure Deployment Dynamics, Phase I
National Aeronautics and Space Administration — There is high value in simulating the nonlinear dynamics of stowing, deploying, and performance of deployable space structures, especially given the profound...
Parallel Stochastic discrete event simulation of calcium dynamics in neuron.
Ishlam Patoary, Mohammad Nazrul; Tropper, Carl; McDougal, Robert A; Zhongwei, Lin; Lytton, William W
2017-09-26
The intra-cellular calcium signaling pathways of a neuron depends on both biochemical reactions and diffusions. Some quasi-isolated compartments (e.g. spines) are so small and calcium concentrations are so low that one extra molecule diffusing in by chance can make a nontrivial difference in its concentration (percentage-wise). These rare events can affect dynamics discretely in such way that they cannot be evaluated by a deterministic simulation. Stochastic models of such a system provide a more detailed understanding of these systems than existing deterministic models because they capture their behavior at a molecular level. Our research focuses on the development of a high performance parallel discrete event simulation environment, Neuron Time Warp (NTW), which is intended for use in the parallel simulation of stochastic reaction-diffusion systems such as intra-calcium signaling. NTW is integrated with NEURON, a simulator which is widely used within the neuroscience community. We simulate two models, a calcium buffer and a calcium wave model. The calcium buffer model is employed in order to verify the correctness and performance of NTW by comparing it to a serial deterministic simulation in NEURON. We also derived a discrete event calcium wave model from a deterministic model using the stochastic IP3R structure.
Nuclear Research Center IRT reactor dynamics calculation
International Nuclear Information System (INIS)
Aleman Fernandez, J.R.
1990-01-01
The main features of the code DIRT, for dynamical calculations are described in the paper. With the results obtained by the program, an analysis of the dynamic behaviour of the Research Reactor IRT of the Nuclear Research Center (CIN) is performed. Different transitories were considered such as variation of the system reactivity, coolant inlet temperature variation and also variations of the coolant velocity through the reactor core. 3 refs
MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
cellGPU: Massively parallel simulations of dynamic vertex models
Sussman, Daniel M.
2017-10-01
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cells interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. This article discusses its implementation for a pair of two-dimensional models, and compares the typical performance that can be expected between running cellGPU entirely on the CPU versus its performance when running on a range of commercial and server-grade graphics cards. By implementing the calculation of topological changes and forces on cells in a highly parallelizable fashion, cellGPU enables researchers to simulate time- and length-scales previously inaccessible via existing single-threaded CPU implementations. Program Files doi:http://dx.doi.org/10.17632/6j2cj29t3r.1 Licensing provisions: MIT Programming language: CUDA/C++ Nature of problem: Simulations of off-lattice "vertex models" of cells, in which the interaction forces depend on both the geometry and the topology of the cellular aggregate. Solution method: Highly parallelized GPU-accelerated dynamical simulations in which the force calculations and the topological features can be handled on either the CPU or GPU. Additional comments: The code is hosted at https://gitlab.com/dmsussman/cellGPU, with documentation additionally maintained at http://dmsussman.gitlab.io/cellGPUdocumentation
Simulation of burning plasma dynamics in ITER
International Nuclear Information System (INIS)
Wang, J.F.; Amano, T.; Ogawa, Y.; Inoue, N.
1996-02-01
Dynamics of burning plasma for various transient situations in ITER plasma has been simulated with a 1.5-dimensional up-down asymmetry Tokamak Transport Simulation Code (TTSC). We have mainly paid attention to intrinsic plasma transport processes such as the confinement improvement and the change of plasma profiles. It is shown that a large excursion of the fusion power takes place with a small improvement of the plasma confinement; e.g., an increase of the global energy confinement by a factor of 1.22 yields the fusion power excursion of ∼ 30% within a few seconds. Any feedback control of fueling D-T gas is difficult to respond to this short time scale of fusion power transient. The effect of the plasma profile on the fusion power excursion has been studied, by changing the particle transport denoted by the inward pinch parameter C V . It is found that the fusion power excursion is mild and slow, and the feedback control is quite effective in suppressing the fusion power excursion and in shortening the duration time of power transient in this case. The change in the pumping efficiency has also been studied and a large excursion of the fusion power has not been observed, because of the decrease in the fuel density itself in the case of the increase in the pumping efficiency, and the helium ash accumulation in the case of the decrease in the pumping efficiency. Finally it is shown that the MHD sawteeth activity leads to the fusion power fluctuation of ± 20%, although it is helpful for the helium ash exhaust. (author)
Computer simulation of dynamic processes on accelerators
International Nuclear Information System (INIS)
Kol'ga, V.V.
1979-01-01
The problems of computer numerical investigation of motion of accelerated particles in accelerators and storages, an effect of different accelerator systems on the motion, determination of optimal characteristics of accelerated charged particle beams are considered. Various simulation representations are discussed which describe the accelerated particle dynamics, such as the enlarged particle method, the representation where a great number of discrete particle is substituted for a field of continuously distributed space charge, the method based on determination of averaged beam characteristics. The procedure is described of numerical studies involving the basic problems, viz. calculation of closed orbits, establishment of stability regions, investigation of resonance propagation determination of the phase stability region, evaluation of the space charge effect the problem of beam extraction. It is shown that most of such problems are reduced to solution of the Cauchy problem using a computer. The ballistic method which is applied to solution of the boundary value problem of beam extraction is considered. It is shown that introduction into the equation under study of additional members with the small positive regularization parameter is a general idea of the methods for regularization of noncorrect problems [ru
Parachute-Payload System Flight Dynamics and Trajectory Simulation
Directory of Open Access Journals (Sweden)
Giorgio Guglieri
2012-01-01
Full Text Available The work traces a general procedure for the design of a flight simulation tool still representative of the major flight physics of a parachute-payload system along decelerated trajectories. An example of limited complexity simulation models for a payload decelerated by one or more parachutes is given, including details and implementation features usually omitted as the focus of the research in this field is typically on the investigation of mission design issues, rather than addressing general implementation guidelines for the development of a reconfigurable simulation tool. The dynamics of the system are modeled through a simple multibody model that represents the expected behavior of an entry vehicle during the terminal deceleration phase. The simulators are designed according to a comprehensive vision that enforces the simplification of the coupling mechanism between the payload and the parachute, with an adequate level of physical insight still available. The results presented for a realistic case study define the sensitivity of the simulation outputs to the functional complexity of the mathematical model. Far from being an absolute address for the software designer, this paper tries to contribute to the area of interest with some technical considerations and clarifications.
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.
System Design Description Salt Well Liquid Pumping Dynamic Simulation
International Nuclear Information System (INIS)
HARMSEN, R.W.
1999-01-01
The Salt Well Liquid (SWL) Pumping Dynamic Simulation used by the single-shell tank (SST) Interim Stabilization Project is described. A graphical dynamic simulation predicts SWL removal from 29 SSTs using an exponential function and unique time constant for each SST. Increasing quarterly efficiencies are applied to adjust the pumping rates during fiscal year 2000
Machine learning molecular dynamics for the simulation of infrared spectra.
Gastegger, Michael; Behler, Jörg; Marquetand, Philipp
2017-10-01
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.
Development of an educational nuclear research reactor simulator
International Nuclear Information System (INIS)
Arafa, Amany Abdel Aziz; Saleh, Hassan Ibrahim; Ashoub, Nagieb
2014-01-01
This paper introduces the development of a research reactor educational simulator based on LabVIEW that allows the training of operators and studying different accident scenarios and the effects of operational parameters on the reactor behavior. Using this simulator, the trainee can test the interaction between the input parameters and the reactor activities. The LabVIEW acts as an engine implements the reactor mathematical models. In addition, it is used as a tool for implementing the animated graphical user interface. This simulator provides the training requirements for both of the reactor staff and the nuclear engineering students. Therefore, it uses dynamic animation to enhance learning and interest for a trainee on real system problems and provides better visual effects, improved communications, and higher interest levels. The benefits of conducting such projects are to develop the expertise in this field and save costs of both operators training and simulation courses.
Development of an educational nuclear research reactor simulator
Energy Technology Data Exchange (ETDEWEB)
Arafa, Amany Abdel Aziz; Saleh, Hassan Ibrahim [Atomic Energy Authority, Cairo (Egypt). Radiation Engineering Dept.; Ashoub, Nagieb [Atomic Energy Authority, Cairo (Egypt). Reactor Physics Dept.
2014-12-15
This paper introduces the development of a research reactor educational simulator based on LabVIEW that allows the training of operators and studying different accident scenarios and the effects of operational parameters on the reactor behavior. Using this simulator, the trainee can test the interaction between the input parameters and the reactor activities. The LabVIEW acts as an engine implements the reactor mathematical models. In addition, it is used as a tool for implementing the animated graphical user interface. This simulator provides the training requirements for both of the reactor staff and the nuclear engineering students. Therefore, it uses dynamic animation to enhance learning and interest for a trainee on real system problems and provides better visual effects, improved communications, and higher interest levels. The benefits of conducting such projects are to develop the expertise in this field and save costs of both operators training and simulation courses.
Theory, Modeling and Simulation: Research progress report 1994--1995
Energy Technology Data Exchange (ETDEWEB)
Garrett, B.C.; Dixon, D.A.; Dunning, T.H.
1997-01-01
The Pacific Northwest National Laboratory (PNNL) has established the Environmental Molecular Sciences Laboratory (EMSL). In April 1994, construction began on the new EMSL, a collaborative research facility devoted to advancing the understanding of environmental molecular science. Research in the Theory, Modeling, and Simulation (TM and S) program will play a critical role in understanding molecular processes important in restoring DOE`s research, development, and production sites, including understanding the migration and reactions of contaminants in soils and ground water, developing processes for isolation and processing of pollutants, developing improved materials for waste storage, understanding the enzymatic reactions involved in the biodegradation of contaminants, and understanding the interaction of hazardous chemicals with living organisms. The research objectives of the TM and S program are fivefold: to apply available electronic structure and dynamics techniques to study fundamental molecular processes involved in the chemistry of natural and contaminated systems; to extend current electronic structure and dynamics techniques to treat molecular systems of future importance and to develop new techniques for addressing problems that are computationally intractable at present; to apply available molecular modeling techniques to simulate molecular processes occurring in the multi-species, multi-phase systems characteristic of natural and polluted environments; to extend current molecular modeling techniques to treat ever more complex molecular systems and to improve the reliability and accuracy of such simulations; and to develop technologies for advanced parallel architectural computer systems. Research highlights of 82 projects are given.
Generation of diurnal variation for influent data for dynamic simulation.
Langergraber, G; Alex, J; Weissenbacher, N; Woerner, D; Ahnert, M; Frehmann, T; Halft, N; Hobus, I; Plattes, M; Spering, V; Winkler, S
2008-01-01
When using dynamic simulation for fine tuning of the design of activated sludge (AS) plants diurnal variations of influent data are required. For this application usually only data from the design process and no measured data are available. In this paper a simple method to generate diurnal variations of wastewater flow and concentrations is described. The aim is to generate realistic influent data in terms of flow, concentrations and TKN/COD ratios and not to predict the influent of the AS plant in detail. The work has been prepared within the framework of HSG-Sim (Hochschulgruppe Simulation, http://www.hsgsim.org), a group of researchers from Germany, Austria, Luxembourg, Poland, the Netherlands and Switzerland. (c) IWA Publishing 2008.
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing
2012-01-01
The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
Directory of Open Access Journals (Sweden)
Ji-Long Zhang
Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.
Building a dynamic code to simulate new reactor concepts
International Nuclear Information System (INIS)
Catsaros, N.; Gaveau, B.; Jaekel, M.-T.; Maillard, J.; Maurel, G.; Savva, P.; Silva, J.; Varvayanni, M.
2012-01-01
Highlights: ► We develop a stochastic neutronic code based on an existing High Energy Physics code. ► The code simulates innovative reactor designs including Accelerator Driven Systems. ► Core materials evolution will be dynamically simulated, including fuel burnup. ► Continuous feedback between the main inter-related parameters will be established. ► A description of the current research development and achievements is also given. - Abstract: Innovative nuclear reactor designs have been proposed, such as the Accelerator Driven Systems (ADSs), the “candle” reactors, etc. These reactor designs introduce computational nuclear technology problems the solution of which necessitates a new, global and dynamic computational approach of the system. A continuous feedback procedure must be established between the main inter-related parameters of the system such as the chemical, physical and isotopic composition of the core, the neutron flux distribution and the temperature field. Furthermore, as far as ADSs are concerned, the ability of the computational tool to simulate the nuclear cascade created from the interaction of accelerated protons with the spallation target as well as the produced neutrons, is also required. The new Monte Carlo code ANET (Advanced Neutronics with Evolution and Thermal hydraulic feedback) is being developed based on the GEANT3 High Energy Physics code, aiming to progressively satisfy all the above requirements. A description of the capabilities and methodologies implemented in the present version of ANET is given here, together with some illustrative applications of the code.
Dual Quaternion Variational Integrator for Rigid Body Dynamic Simulation
Xu, Jiafeng; Halse, Karl Henning
2016-01-01
In rigid body dynamic simulations, often the algorithm is required to deal with general situations where both reference point and inertia matrix are arbitrarily de- fined. We introduce a novel Lie group variational integrator using dual quaternion for simulating rigid body dynamics in all six degrees of freedom. Dual quaternion is used to represent rigid body kinematics and one-step Lie group method is used to derive dynamic equations. The combination of these two becomes the first Lie group ...
A note on simulation and dynamical hierarchies
Energy Technology Data Exchange (ETDEWEB)
Rasmussen, S.; Barrett, C.L. [Los Alamos National Lab., NM (United States)]|[Santa Fe Institute, Sante Fe, NM (United States); Baas, N.A. [Trondheim Univ. (Norway). Dept. of Mathematical Sciences; Olesen, M.W. [Los Alamos National Lab., NM (United States)
1996-02-22
This paper summarizes some of the problems associated with the generation of higher order emergent structures in formal dynamical systems as well as some of the formal properties of dynamical systems capable of generating higher order structures.
Visualizing functional motions of membrane transporters with molecular dynamics simulations.
Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad
2013-01-29
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.
Surface Dynamic Process Simulation with the Use of Cellular Automata
International Nuclear Information System (INIS)
Adamska-Szatko, M.; Bala, J.
2010-01-01
Cellular automata are known for many applications, especially for physical and biological simulations. Universal cellular automata can be used for modelling complex natural phenomena. The paper presents simulation of surface dynamic process. Simulation uses 2-dimensional cellular automata algorithm. Modelling and visualisation were created by in-house developed software with standard OpenGL graphic library. (authors)
High tech supply chain simulation based on dynamical systems model
Yuan, X.; Ashayeri, J.
2013-01-01
During the last 45 years, system dynamics as a continuous type of simulation has been used for simulating various problems, ranging from economic to engineering and managerial when limited (historical) information is available. Control theory is another alternative for continuous simulation that
Observations of Crew Dynamics during Mars Analog Simulations
Cusack, Stacy L.
2010-01-01
This presentation reviews the crew dynamics during two simulations of Mars Missions. Using an analog of a Mars habitat in two locations, Flashline Mars Arctic Research Station (FMARS) which is located on Devon Island at 75 deg North in the Canadian Arctic, and the Mars Desert Research Station (MDRS) which is located in the south of Utah, the presentation examines the crew dynamics in relation to the leadership style of the commander of the mission. The difference in the interaction of the two crews were shown to be related to the leadership style and the age group in the crew. As much as possible the habitats and environment was to resemble a Mars outpost. The difference between the International Space Station and a Mars missions is reviewed. The leadership styles are reviewed and the contrast between the FMARS and the MDRS leadership styles were related to crew productivity, and the personal interactions between the crew members. It became evident that leadership styles and interpersonal skill had more affect on mission success and crew dynamics than other characteristics.
Hsieh, Shang-Hsien
1993-01-01
The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.
Real time simulation method for fast breeder reactors dynamics
International Nuclear Information System (INIS)
Miki, Tetsushi; Mineo, Yoshiyuki; Ogino, Takamichi; Kishida, Koji; Furuichi, Kenji.
1985-01-01
The development of multi-purpose real time simulator models with suitable plant dynamics was made; these models can be used not only in training operators but also in designing control systems, operation sequences and many other items which must be studied for the development of new type reactors. The prototype fast breeder reactor ''Monju'' is taken as an example. Analysis is made on various factors affecting the accuracy and computer load of its dynamic simulation. A method is presented which determines the optimum number of nodes in distributed systems and time steps. The oscillations due to the numerical instability are observed in the dynamic simulation of evaporators with a small number of nodes, and a method to cancel these oscillations is proposed. It has been verified through the development of plant dynamics simulation codes that these methods can provide efficient real time dynamics models of fast breeder reactors. (author)
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 $\\tilde{H}$. $\\tilde......{E}(h)$ is employed to determine the relation with the corresponding energy, $E$ for the analytic dynamics with $h=0$ and the zero-order estimate $E_0(h)$ of the energy for discrete dynamics, appearing in the literature for MD with VA. We derive a corresponding time reversible VA algorithm for canonical dynamics...
[Animal experimentation, computer simulation and surgical research].
Carpentier, Alain
2009-11-01
We live in a digital world In medicine, computers are providing new tools for data collection, imaging, and treatment. During research and development of complex technologies and devices such as artificial hearts, computer simulation can provide more reliable information than experimentation on large animals. In these specific settings, animal experimentation should serve more to validate computer models of complex devices than to demonstrate their reliability.
Shekhar, Adarsh
Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in
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.
Kinematics and dynamics analysis of a novel serial-parallel dynamic simulator
International Nuclear Information System (INIS)
Hu, Bo; Zhang, Lian Dong; Yu, Jingjing
2016-01-01
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
Europlanet Research Infrastructure: Planetary Simulation Facilities
Davies, G. R.; Mason, N. J.; Green, S.; Gómez, F.; Prieto, O.; Helbert, J.; Colangeli, L.; Srama, R.; Grande, M.; Merrison, J.
2008-09-01
EuroPlanet The Europlanet Research Infrastructure consortium funded under FP7 aims to provide the EU Planetary Science community greater access for to research infrastructure. A series of networking and outreach initiatives will be complimented by joint research activities and the formation of three Trans National Access distributed service laboratories (TNA's) to provide a unique and comprehensive set of analogue field sites, laboratory simulation facilities, and extraterrestrial sample analysis tools. Here we report on the infrastructure that comprises the second TNA; Planetary Simulation Facilities. 11 laboratory based facilities are able to recreate the conditions found in the atmospheres and on the surfaces of planetary systems with specific emphasis on Martian, Titan and Europa analogues. The strategy has been to offer some overlap in capabilities to ensure access to the highest number of users and to allow for progressive and efficient development strategies. For example initial testing of mobility capability prior to the step wise development within planetary atmospheres that can be made progressively more hostile through the introduction of extreme temperatures, radiation, wind and dust. Europlanet Research Infrastructure Facilties: Mars atmosphere simulation chambers at VUA and OU These relatively large chambers (up to 1 x 0.5 x 0.5 m) simulate Martian atmospheric conditions and the dual cooling options at VUA allows stabilised instrument temperatures while the remainder of the sample chamber can be varied between 220K and 350K. Researchers can therefore assess analytical protocols for instruments operating on Mars; e.g. effect of pCO2, temperature and material (e.g., ± ice) on spectroscopic and laser ablation techniques while monitoring the performance of detection technologies such as CCD at low T & variable p H2O & pCO2. Titan atmosphere and surface simulation chamber at OU The chamber simulates Titan's atmospheric composition under a range of
Dynamic fault simulation of wind turbines using commercial simulation tools
DEFF Research Database (Denmark)
Lund, Torsten; Eek, Jarle; Uski, Sanna
2005-01-01
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. The devi......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....... 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....
Review of Dynamic Modeling and Simulation of Large Scale Belt Conveyor System
He, Qing; Li, Hong
Belt conveyor is one of the most important devices to transport bulk-solid material for long distance. Dynamic analysis is the key to decide whether the design is rational in technique, safe and reliable in running, feasible in economy. It is very important to study dynamic properties, improve efficiency and productivity, guarantee conveyor safe, reliable and stable running. The dynamic researches and applications of large scale belt conveyor are discussed. The main research topics, the state-of-the-art of dynamic researches on belt conveyor are analyzed. The main future works focus on dynamic analysis, modeling and simulation of main components and whole system, nonlinear modeling, simulation and vibration analysis of large scale conveyor system.
Rare event simulation for dynamic fault trees
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
Rare Event Simulation for Dynamic Fault Trees
Ruijters, Enno Jozef Johannes; Reijsbergen, D.P.; de Boer, Pieter-Tjerk; Stoelinga, Mariëlle Ida Antoinette; Tonetta, Stefano; Schoitsch, Erwin; Bitsch, Friedemann
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
Dynamic bounds coupled with Monte Carlo simulations
Rajabali Nejad, Mohammadreza; Meester, L.E.; van Gelder, P.H.A.J.M.; Vrijling, J.K.
2011-01-01
For the reliability analysis of engineering structures a variety of methods is known, of which Monte Carlo (MC) simulation is widely considered to be among the most robust and most generally applicable. To reduce simulation cost of the MC method, variance reduction methods are applied. This paper
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp; Tchipev, Nikola
2012-01-01
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
Unified Nonlinear Flight Dynamics and Aeroelastic Simulator Tool, Phase I
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...
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu
2011-01-01
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
GUMICS4 Synthetic and Dynamic Simulations of the ECLAT Project
Facsko, G.; Palmroth, M. M.; Gordeev, E.; Hakkinen, L. V.; Honkonen, I. J.; Janhunen, P.; Sergeev, V. A.; Kauristie, K.; Milan, S. E.
2012-12-01
The European Commission funded the European Cluster Assimilation Techniques (ECLAT) project as a collaboration of five leader European universities and research institutes. A main contribution of the Finnish Meteorological Institute (FMI) is to provide a wide range of global MHD runs with the Grand Unified Magnetosphere Ionosphere Coupling simulation (GUMICS). The runs are divided in two categories: synthetic runs investigating the extent of solar wind drivers that can influence magnetospheric dynamics, as well as dynamic runs using measured solar wind data as input. Here we consider the first set of runs with synthetic solar wind input. The solar wind density, velocity and the interplanetary magnetic field had different magnitudes and orientations; furthermore two F10.7 flux values were selected for solar radiation minimum and maximum values. The solar wind parameter values were constant such that a constant stable solution was archived. All configurations were run several times with three different (-15°, 0°, +15°) tilt angles in the GSE X-Z plane. The Cray XT supercomputer of the FMI provides a unique opportunity in global magnetohydrodynamic simulation: running the GUMICS-4 based on one year real solar wind data. Solar wind magnetic field, density, temperature and velocity data based on Advanced Composition Explorer (ACE) and WIND measurements are downloaded from the OMNIWeb open database and a special input file is created for each Cluster orbit. All data gaps are replaced with linear interpolations between the last and first valid data values before and after the data gap. Minimum variance transformation is applied for the Interplanetary Magnetic Field data to clean and avoid the code of divergence. The Cluster orbits are divided into slices allowing parallel computation and each slice has an average tilt angle value. The file timestamps start one hour before the perigee to provide time for building up a magnetosphere in the simulation space. The real
ISS Material Science Research Rack HWIL Interface Simulation
Williams, Philip J.; Ballard, Gary H.; Crumbley, Robert T. (Technical Monitor)
2002-01-01
In this paper, the first Material Science Research Rack (MSRR-1) hardware-in-the-loop (HWIL) interface simulation is described. Dynamic Concepts developed this HWIL simulation system with funding and management provided by the Flight Software group (ED14) of NASA-MSFC's Avionics Department. The HWIL system has been used both as a flight software development environment and as a software qualification tool. To fulfill these roles, the HWIL simulator accurately models the system dynamics of many MSRR-1 subsystems and emulates most of the internal interface signals. The modeled subsystems include the Experiment Modules, the Thermal Environment Control System, the Vacuum Access System, the Solid State Power Controller Module, and the Active Rack Isolation Systems. The emulated signals reside on three separate MIL-STD-1553B digital communication buses, the ISS Medium Rate Data Link, and several analog controller and sensor signals. To enhance the range of testing, it was necessary to simulate several off-nominal conditions that may occur in the interfacing subsystems.
Research nuclear reactor start-up simulator
International Nuclear Information System (INIS)
Sofo Haro, M.; Cantero, P.
2009-01-01
This work presents the design and FPGA implementation of a research nuclear reactor start-up simulator. Its aim is to generate a set of signals that allow replacing the neutron detector for stimulated signals, to feed the measurement electronic of the start-up channels, to check its operation, together with the start-up security logic. The simulator presented can be configured on three independent channels and adjust the shape of the output pulses. Furthermore, each channel can be configured in 'rate' mode, where you can specify the growth rate of the pulse frequency in %/s. Result and details of the implementation on FPGA of the different functional blocks are given. (author)
Parallel Monte Carlo simulation of aerosol dynamics
Zhou, K.; He, Z.; Xiao, M.; Zhang, Z.
2014-01-01
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
Graphics supercomputer for computational fluid dynamics research
Liaw, Goang S.
1994-11-01
The objective of this project is to purchase a state-of-the-art graphics supercomputer to improve the Computational Fluid Dynamics (CFD) research capability at Alabama A & M University (AAMU) and to support the Air Force research projects. A cutting-edge graphics supercomputer system, Onyx VTX, from Silicon Graphics Computer Systems (SGI), was purchased and installed. Other equipment including a desktop personal computer, PC-486 DX2 with a built-in 10-BaseT Ethernet card, a 10-BaseT hub, an Apple Laser Printer Select 360, and a notebook computer from Zenith were also purchased. A reading room has been converted to a research computer lab by adding some furniture and an air conditioning unit in order to provide an appropriate working environments for researchers and the purchase equipment. All the purchased equipment were successfully installed and are fully functional. Several research projects, including two existing Air Force projects, are being performed using these facilities.
Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C
2013-11-07
Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.
Energy Technology Data Exchange (ETDEWEB)
NONE
2003-03-01
Joint meeting of the 6th Simulation Science Symposium and the NIFS Collaboration Research 'Large Scale Computer Simulation' was held on December 12-13, 2002 at National Institute for Fusion Science, with the aim of promoting interdisciplinary collaborations in various fields of computer simulations. The present meeting attended by more than 40 people consists of the 11 invited and 22 contributed papers, of which topics were extended not only to fusion science but also to related fields such as astrophysics, earth science, fluid dynamics, molecular dynamics, computer science etc. (author)
Simulation of capillary flow with a dynamic contact angle
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.
Simulating market dynamics : Interactions between consumer psychology and social networks
Janssen, M.A; 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
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...
Nonlinear dynamics research in the former Soviet Union
International Nuclear Information System (INIS)
McKenney, B.L.; Krafsig, J.; Moon, F.C.; Shlesinger, M.F.
1992-08-01
This assessment of nonlinear dynamics research in the former Soviet Union was performed by seven US scientists and engineers active in the fields examined. The topics covered include: solid-state systems and circuits, information theory and signal analysis, chaos in mechanical systems, turbulence and vortex dynamics, ocean processes, image processing, and lasers and nonlinear optics. The field of nonlinear dynamics and chaos blossomed in academic settings in both the West and the former Soviet Union during the 1980s. The field went from mathematical abstraction to interesting engineering application areas. Several generalizations can be drawn from the review of Soviet work: Soviet work generally began earlier than Western work, and, in areas that do not require extensive computational resources, that work has kept up with, and often leads, the West. This is especially true in the mathematical analysis of nonlinear phenomena. Soviet researchers have shown an ability to combine numerical or analytic ideas with laboratory experimentation in a smoother, less erratic fashion than Western researchers. Furthermore, contrary to Western practice, the same researchers often do both theoretical and experimental work. In areas that require numerical verification of ideas in the field, the Western work is leading that of the former Soviet Union. This is especially true in the areas of signal processing, simulations of turbulence, and communications. No evidence was found of any significant penetration of ideas of nonlinear dynamics into technological applications of a military or commercial area in the former Soviet Union. Opportunities abound, but specific applications are not apparent
Dynamic simulation of a direct carbonate fuel cell power plant
Energy Technology Data Exchange (ETDEWEB)
Ernest, J.B. [Fluor Daniel, Inc., Irvine, CA (United States); Ghezel-Ayagh, H.; Kush, A.K. [Fuel Cell Engineering, Danbury, CT (United States)
1996-12-31
Fuel Cell Engineering Corporation (FCE) is commercializing a 2.85 MW Direct carbonate Fuel Cell (DFC) power plant. The commercialization sequence has already progressed through construction and operation of the first commercial-scale DFC power plant on a U.S. electric utility, the 2 MW Santa Clara Demonstration Project (SCDP), and the completion of the early phases of a Commercial Plant design. A 400 kW fuel cell stack Test Facility is being built at Energy Research Corporation (ERC), FCE`s parent company, which will be capable of testing commercial-sized fuel cell stacks in an integrated plant configuration. Fluor Daniel, Inc. provided engineering, procurement, and construction services for SCDP and has jointly developed the Commercial Plant design with FCE, focusing on the balance-of-plant (BOP) equipment outside of the fuel cell modules. This paper provides a brief orientation to the dynamic simulation of a fuel cell power plant and the benefits offered.
Simulating the evolution of industries using a dynamic behavioural model
Kunc, Martin
2004-01-01
Investment decisions determine that not only the evolution of industries is hard to forecast with certainty but also industries may have different dynamic behaviour and evolutionary paths. In this paper we present a behavioural framework to simulate the evolution of industries. Two factors determine the dynamic behaviour of an industry: managerial decision-making and the interconnected set of resources. Managerial decision-making significantly affects the dynamic behaviour of firms. Bounded r...
Computational fluid dynamics (CFD) simulation of hot air flow ...
African Journals Online (AJOL)
Computational Fluid Dynamics simulation of air flow distribution, air velocity and pressure field pattern as it will affect moisture transient in a cabinet tray dryer is performed using SolidWorks Flow Simulation (SWFS) 2014 SP 4.0 program. The model used for the drying process in this experiment was designed with Solid ...
Molecular dynamics simulations of ballistic He penetration into W fuzz
Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.
2016-01-01
Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers
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...
Innovative tools for real-time simulation of dynamic systems
Palli, Gianluca; Carloni, Raffaella; Melchiorri, Claudio
2008-01-01
In this paper, we present a software architecture, based on RTAI-Linux, for the real-time simulation of dynamic systems and for the rapid prototyping of digital controllers. Our aim is to simplify the testing phase of digital controllers by providing the real-time simulation of the plant with the
Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter
DEFF Research Database (Denmark)
Toxvaerd, Søren
2001-01-01
Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...
Dynamics Modeling and Simulation of Large Transport Airplanes in Upset Conditions
Foster, John V.; Cunningham, Kevin; Fremaux, Charles M.; Shah, Gautam H.; Stewart, Eric C.; Rivers, Robert A.; Wilborn, James E.; Gato, William
2005-01-01
As part of NASA's Aviation Safety and Security Program, research has been in progress to develop aerodynamic modeling methods for simulations that accurately predict the flight dynamics characteristics of large transport airplanes in upset conditions. The motivation for this research stems from the recognition that simulation is a vital tool for addressing loss-of-control accidents, including applications to pilot training, accident reconstruction, and advanced control system analysis. The ultimate goal of this effort is to contribute to the reduction of the fatal accident rate due to loss-of-control. Research activities have involved accident analyses, wind tunnel testing, and piloted simulation. Results have shown that significant improvements in simulation fidelity for upset conditions, compared to current training simulations, can be achieved using state-of-the-art wind tunnel testing and aerodynamic modeling methods. This paper provides a summary of research completed to date and includes discussion on key technical results, lessons learned, and future research needs.
Gamma ray observatory dynamics simulator in Ada (GRODY)
International Nuclear Information System (INIS)
1990-09-01
This experiment involved the parallel development of dynamics simulators for the Gamma Ray Observatory in both FORTRAN and Ada for the purpose of evaluating the applicability of Ada to the NASA/Goddard Space Flight Center's flight dynamics environment. The experiment successfully demonstrated that Ada is a viable, valuable technology for use in this environment. In addition to building a simulator, the Ada team evaluated training approaches, developed an Ada methodology appropriate to the flight dynamics environment, and established a baseline for evaluating future Ada projects
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.
Topology in dynamical lattice QCD simulations
International Nuclear Information System (INIS)
Gruber, Florian
2012-01-01
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.
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
AceCloud: Molecular Dynamics Simulations in the Cloud.
Harvey, M J; De Fabritiis, G
2015-05-26
We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.
A dynamic simulation of the Hanford site grout facility
International Nuclear Information System (INIS)
Zimmerman, B.D.; Klimper, S.C.; Williamson, G.F.
1992-01-01
Computer-based dynamic simulation can be a powerful, low-cost tool for investigating questions concerning timing, throughput capability, and ability of engineering facilities and systems to meet established milestones. The simulation project described herein was undertaken to develop a dynamic simulation model of the Hanford site grout facility and its associated systems at the US Department of Energy's (DOE's) Hanford site in Washington State. The model allows assessment of the effects of engineering design and operation trade-offs and of variable programmatic constraints, such as regulatory review, on the ability of the grout system to meet milestones established by DOE for low-level waste disposal
Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry
Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.
2018-04-01
The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.
Approximation of quantum observables by molecular dynamics simulations
Sandberg, Mattias
2016-01-01
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.
Approximation of quantum observables by molecular dynamics simulations
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.
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...
Dynamic simulation of steam generator failures
Energy Technology Data Exchange (ETDEWEB)
Meister, G [Institut fuer Nukleare Sicherheitsforschung, Kernforschungsanlage Juelich GmbH, Juelich (Germany)
1988-07-01
A computer program will be described which is capable to simulate severe transients in a gas heated steam generator. Such transients may arise in the safety analysis of accidents resulting from failures in the heat removal system of an HTGR power plant. Important failure modes which have to be considered are ruptures of one or more steam generator tubes leading to water or steam ejection into the primary system or anomalous operating conditions which my cause damage due to excessive thermal stress. Examples are the complete dryout as a consequence of feedwater interrupt in connection with continuing gas heating and the reflooding of the secondary channel with cold feedwater after dryout. The steam generator program which is capable to simulate accidents of this type is written as a module which can be implemented into a program system fur the simulation of the total heat rejection system. It based on an advanced mathematical model for the two phase flow taking deviations from thermal equilibrium into account. Mass, energy and momentum balances for the primary and secondary fluid and the heat diffusion equations for the heat exchanging wall form a system of coupled differential equations which is solved numerically by an algorithm which is stiffly stable and suppresses effectively oscillations of numerical origin. Results of the simulation of transients of the type mentioned above will be presented and discussed. (author)
Dynamic simulation of steam generator failures
International Nuclear Information System (INIS)
Meister, G.
1988-01-01
A computer program will be described which is capable to simulate severe transients in a gas heated steam generator. Such transients may arise in the safety analysis of accidents resulting from failures in the heat removal system of an HTGR power plant. Important failure modes which have to be considered are ruptures of one or more steam generator tubes leading to water or steam ejection into the primary system or anomalous operating conditions which my cause damage due to excessive thermal stress. Examples are the complete dryout as a consequence of feedwater interrupt in connection with continuing gas heating and the reflooding of the secondary channel with cold feedwater after dryout. The steam generator program which is capable to simulate accidents of this type is written as a module which can be implemented into a program system fur the simulation of the total heat rejection system. It based on an advanced mathematical model for the two phase flow taking deviations from thermal equilibrium into account. Mass, energy and momentum balances for the primary and secondary fluid and the heat diffusion equations for the heat exchanging wall form a system of coupled differential equations which is solved numerically by an algorithm which is stiffly stable and suppresses effectively oscillations of numerical origin. Results of the simulation of transients of the type mentioned above will be presented and discussed. (author)
Analytical system dynamics modeling and simulation
Fabien, Brian C
2008-01-01
This book offering a modeling technique based on Lagrange's energy method includes 125 worked examples. Using this technique enables one to model and simulate systems as diverse as a six-link, closed-loop mechanism or a transistor power amplifier.
Dynamic Interactions for Network Visualization and Simulation
2009-03-01
projects.htm, Site accessed January 5, 2009. 12. John S. Weir, Major, USAF, Mediated User-Simulator Interactive Command with Visualization ( MUSIC -V). Master’s...Computing Sciences in Colleges, December 2005). 14. Enrique Campos -Nanez, “nscript user manual,” Department of System Engineer- ing University of
Distributed dynamic simulations of networked control and building performance applications.
Yahiaoui, Azzedine
2018-02-01
The use of computer-based automation and control systems for smart sustainable buildings, often so-called Automated Buildings (ABs), has become an effective way to automatically control, optimize, and supervise a wide range of building performance applications over a network while achieving the minimum energy consumption possible, and in doing so generally refers to Building Automation and Control Systems (BACS) architecture. Instead of costly and time-consuming experiments, this paper focuses on using distributed dynamic simulations to analyze the real-time performance of network-based building control systems in ABs and improve the functions of the BACS technology. The paper also presents the development and design of a distributed dynamic simulation environment with the capability of representing the BACS architecture in simulation by run-time coupling two or more different software tools over a network. The application and capability of this new dynamic simulation environment are demonstrated by an experimental design in this paper.
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...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...
Molecular dynamics simulation of a chemical reaction
International Nuclear Information System (INIS)
Gorecki, J.; Gryko, J.
1988-06-01
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
A Coupling Vibration Test Bench and the Simulation Research of a Maglev Vehicle
Directory of Open Access Journals (Sweden)
Weihua Ma
2015-01-01
Full Text Available To study the characteristics of the coupling vibration between a maglev vehicle and its track beam system and to improve the performance of the levitation system, a new type of vibration test bench was developed. Take a single maglev frame as the study object; simulation of the coupling vibration of the maglev vehicle, levitation system, and track beam were achieved. In addition, all types of real track irregularity excitations can be simulated using hydraulic actuators of the test bench. To expand the research scope, a simulation model was developed that can conduct the simulation research synergistically with the test bench. Based on a dynamics model of the test bench, the dynamics simulation method determined the influence on the levitation control performance of three factors: the track beam support stiffness, the track beam mass, and the track irregularity. The vibration resonance phenomenon of the vehicle/track system was reproduced by the dynamics simulation, and a portion of the simulation results were validated by the test results. By combining the test bench and the dynamics model, experiments can be guided by the simulation results, and the experimental results can validate the dynamics simulation results.
Energy Technology Data Exchange (ETDEWEB)
Tian, Wei [Univ. of Miami, FL (United States). Dept. of Civil, Architectural and Environmental Engineering; Sevilla, Thomas Alonso [Univ. of Miami, FL (United States). Dept. of Civil, Architectural and Environmental Engineering; Zuo, Wangda [Univ. of Miami, FL (United States). Dept. of Civil, Architectural and Environmental Engineering; Sohn, Michael D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Energy Analysis and Environmental Impacts Div.
2017-06-08
Historically, multizone models are widely used in building airflow and energy performance simulations due to their fast computing speed. However, multizone models assume that the air in a room is well mixed, consequently limiting their application. In specific rooms where this assumption fails, the use of computational fluid dynamics (CFD) models may be an alternative option. Previous research has mainly focused on coupling CFD models and multizone models to study airflow in large spaces. While significant, most of these analyses did not consider the coupled simulation of the building airflow with the building's Heating, Ventilation, and Air-Conditioning (HVAC) systems. This paper tries to fill the gap by integrating the models for HVAC systems with coupled multizone and CFD simulations for airflows, using the Modelica simul ation platform. To improve the computational efficiency, we incorporated a simplified CFD model named fast fluid dynamics (FFD). We first introduce the data synchronization strategy and implementation in Modelica. Then, we verify the implementation using two case studies involving an isothermal and a non-isothermal flow by comparing model simulations to experiment data. Afterward, we study another three cases that are deemed more realistic. This is done by attaching a variable air volume (VAV) terminal box and a VAV system to previous flows to assess the capability of the models in studying the dynamic control of HVAC systems. Finally, we discuss further research needs on the coupled simulation using the models.
Chain networking revealed by molecular dynamics simulation
Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing
Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)
Electrical Dynamic Simulation Activities in Forsmark NPP
International Nuclear Information System (INIS)
Lamell, Per
2015-01-01
The original power system analysis was done in the seventies in former ASEA AB software. For approximate twenty years no major new studies was done because of limited numbers of renewal projects. In the end of the nineties the plant started to update the selectivity planning and study of the loading of the safety bus-bars. The simulation and start of the development of simulation models was done in a tool named Simpow. Simpow was also an ASEA/ABB AB software developed from the program used in the seventies. To continue to work with Simpow was a decision made after doing an extensive review of on the marked available commercially software. Also at that time we start to do our first attempt building electrical simulation models of unit 1 and 2 according to the original documentation. The development of models for the unit 1, 2 and 3 became more intensive some years after the millennium. Partly because of event July 25, 2006 and also because of the renewal of unit 1 and 2 and had subsequently been initiated for unit 3 also. Today we have initiated a conversion of our models to a new program called PowerFactory. That due to the withdrawal of support and development on SIMPOW a couple of years ago. To development relevance, accuracy and detail, models are an important issue for FKA (Forsmark Kraftgrupp AB). The model is initially created according to the plant documentation and also including requested information from the original supplier. Continued development and updates of the model is done according to the data received from the contractors via the demands according to requirements in our technical documents on different electrical components in renewal projects. The development of the model is driven by known weaknesses, depending of the type of studies and necessary data related to events. An important part that will be described is to have a verified simulation tool and validated models. An example is that the models have been validated by making start and
Molecular dynamics simulation of propagating cracks
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.
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.
Monte Carlo simulated dynamical magnetization of single-chain magnets
Energy Technology Data Exchange (ETDEWEB)
Li, Jun; Liu, Bang-Gui, E-mail: bgliu@iphy.ac.cn
2015-03-15
Here, a dynamical Monte-Carlo (DMC) method is used to study temperature-dependent dynamical magnetization of famous Mn{sub 2}Ni system as typical example of single-chain magnets with strong magnetic anisotropy. Simulated magnetization curves are in good agreement with experimental results under typical temperatures and sweeping rates, and simulated coercive fields as functions of temperature are also consistent with experimental curves. Further analysis indicates that the magnetization reversal is determined by both thermal-activated effects and quantum spin tunnelings. These can help explore basic properties and applications of such important magnetic systems. - Highlights: • Monte Carlo simulated magnetization curves are in good agreement with experimental results. • Simulated coercive fields as functions of temperature are consistent with experimental results. • The magnetization reversal is understood in terms of the Monte Carlo simulations.
Autonomous dynamic decision making in a nuclear fuel cycle simulator
International Nuclear Information System (INIS)
Pelakauskas, Martynas; Auzans, Aris; Schneider, Erich A.; Tkaczyk, Alan H.
2013-01-01
Highlights: • Objective criteria based decision making in a nuclear fuel cycle simulator. • Simulation driven by an evolving performance metric. • Implementation of the model in a nuclear fuel cycle simulator. • Verification of dynamic decision making based on uranium price evolution. -- Abstract: Growing energy demand and the push to move toward carbon-free ways of electricity generation have renewed the world's interest in nuclear energy. Due to the high technical and economic uncertainties related to nuclear energy, simulation tools have become a necessity in order to plan and evaluate possible nuclear fuel cycles (NFCs). Most of the NFC simulators today work by running the simulation with a user-defined set of facility build orders and preferences. While this allows for a simple way to change the simulation conditions, it may not always lead to optimal results and strongly relies on the user defining the correct parameters. This study looks into the possibility of using the expected cost of electricity (CoE) as the driving build decision variable instead of relying on user-defined build orders. This is a first step toward a more general decision making strategy in dynamic fuel cycle simulation. For this purpose, additional modules were implemented in an NFC simulator, VEGAS, with the consumption dependent price of uranium as a time-varying NFC cost component that drives the cost competitiveness of available NFC options. The model was demonstrated to verify the correct operation of a CoE-driven NFC simulator
Aerodynamic research of a racing car based on wind tunnel test and computational fluid dynamics
Directory of Open Access Journals (Sweden)
Wang Jianfeng
2018-01-01
Full Text Available Wind tunnel test and computational fluid dynamics (CFD simulation are two main methods for the study of automotive aerodynamics. CFD simulation software solves the results in calculation by using the basic theory of aerodynamic. Calculation will inevitably lead to bias, and the wind tunnel test can effectively simulate the real driving condition, which is the most effective aerodynamics research method. This paper researches the aerodynamic characteristics of the wing of a racing car. Aerodynamic model of a racing car is established. Wind tunnel test is carried out and compared with the simulation results of computational fluid dynamics. The deviation of the two methods is small, and the accuracy of computational fluid dynamics simulation is verified. By means of CFD software simulation, the coefficients of six aerodynamic forces are fitted and the aerodynamic equations are obtained. Finally, the aerodynamic forces and torques of the racing car travel in bend are calculated.
Directory of Open Access Journals (Sweden)
CAROLINA DELGADO HURTADO
2017-12-01
Full Text Available Research capacities are developed scientific skills that enable universities to accomplish the dissemination of high-quality scientific knowledge. Nowadays, the modeling of their dynamics is one of the most important concerns for the stakeholders related to the scientific activity, including university managers, private sector and government. In this context, the present article aims to approach the issue of modeling the capacities of the Universities’ research systems, presenting Systems Dynamics as an effective methodological tool for the treatment of data contained in intellectual capital indicators, allowing to estimate parameters, conditions and scenarios. The main contribution lays on the modeling and simulations accomplished for several scenarios, which display the critical variables and the more sensitive ones when building or strengthening research capacities. The establishment of parameters through regression techniques allowed to more accurately model the dynamics of the variables. This is an interesting contribution in terms of the accuracy of the simulations that later might be used to propose and carry out changes related to the management of the universities research. Future research with alternative modeling for social systems will allow to broaden the scope of the study.
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.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
International Nuclear Information System (INIS)
Gottwald, Fabian; Karsten, Sven; 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 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
Molecular dynamics simulation of ribosome jam
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.
Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
Okumura, Hisashi
2008-09-28
Partial multicanonical algorithm is proposed for molecular dynamics and Monte Carlo simulations. The partial multicanonical simulation samples a wide range of a part of the potential-energy terms, which is necessary to sample the conformational space widely, whereas a wide range of total potential energy is sampled in the multicanonical algorithm. Thus, one can concentrate the effort to determine the weight factor only on the important energy terms in the partial multicanonical simulation. The partial multicanonical, multicanonical, and canonical molecular dynamics algorithms were applied to an alanine dipeptide in explicit water solvent. The canonical simulation sampled the states of P(II), C(5), alpha(R), and alpha(P). The multicanonical simulation covered the alpha(L) state as well as these states. The partial multicanonical simulation also sampled the C(7) (ax) state in addition to the states that were sampled by the multicanonical simulation. In the partial multicanonical simulation, furthermore, backbone dihedral angles phi and psi rotated more frequently than those in the multicanonical and canonical simulations. These results mean that the partial multicanonical algorithm has a higher sampling efficiency than the multicanonical and canonical algorithms.
Exploration and thinking of dynamic scientific and technical intelligence research
International Nuclear Information System (INIS)
Zhang Xupu; Xia Yun
2014-01-01
This article discusses the concept and types of dynamic scientific and technical intelligence, describes the characteristics and role of dynamic scientific and technical intelligence, and analyzes methods and procedures of dynamic scientific and technical intelligence research. Combined with the status quo of dynamic scientific and technical intelligence research in library of China Institute of Atomic Energy, this article makes some suggestions for strengthening dynamic scientific and technical intelligence research. (authors)
DYNSIR; A dynamic simulator for the chemical process
International Nuclear Information System (INIS)
Park, Hyun Soo; Yoo, Jae Hyung; Byeon, Kee Hoh; Park, Jeong Hwa; Park, Seong Won
1990-03-01
A program code for dynamic simulation of arbitrary chemical process, called DYNSIR, is developed. The code can simulate rather arbitrary arrangements of individual chemical processing units whose models are described by ordinary differential equations. The code structure to handle input/output, memory and data management, numerical interactive or predetermined changes in parameter values during the simulation. Individual model is easy to maintain since the modular approach is used. The integration routine is highly effective because of the development of algorithm for modular integration method using the cubic spline. DYNSIR's data structures are not the index but the pointer structure. This pointer structure allows the dynamic memory allocation for the memory management. The dynamic memory allocation methods is to minimize the amount of memories and to overcome the limitation of the number of variables to be used. Finally, it includes various functions, such as the input preprocessor, the effective error processing, and plotting and reporting routines. (author)
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)
Molecular dynamics simulation studies of tailored nanostructured polymers
Liu, Lixin
With recent advancements in the synthesis and characterization of polymeric materials, scientists are able to create multi-scale novel polymers with various cases of chemical functionalities, diversified topologies, as well as cross-linking networks. Due to those remarkable achievements, there are a broad range of possible applications of smart polymers in catalysis, in environmental remediation, and especially in drug-delivery. Because of rising interest in developing therapeutic drug binding to specific treating target, polymer chemists are in particular interests in design and engineering the drug delivery materials to be not only bio-compatible, but also to be capable of self-assembly at various in-vivo physiological stimulus. Both experimental and theoretical work indicate that the thermodynamic properties relating to the hydrophobic effect play an important role in determining self-assembly process. At the same time, computational simulation and modeling are powerful instruments to contribute to microscopic thermodynamics' understanding toward self-assembly phenomenon. Along with statistical approaches, constructing empirical model based on simulation results would also help predict for further development of tailored nano-structured materials. My Research mainly focused on investigating physical and chemical characteristics of polymer materials through molecular dynamics simulation and probing the fundamental thermodynamic driving force of self-assembly behavior. We tried to surmount technological obstacles in computational chemistry and build an efficient scheme to identify the physical and chemical Feature of molecules, to reproduce underlying properties, to understand the origin of thermodynamic signatures, and to speed up current trial and error process in screening new materials.
The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation
Chen, Jundong
2018-03-01
Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.
DEFF Research Database (Denmark)
Papaleo, Elena
2015-01-01
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...... 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...... 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....
Assessing Group Dynamics in a Mars Simulation
Bishop, S. L.
2007-10-01
International interest in psychosocial functioning generally and issues of group and inter-group function for space crews has increased as focus has shifted towards longer duration spaceflight and, particularly, the issues involved in sending a human crew to Mars (Kanas, et al., 2001; Dawson, 2002). Planning documents for a human mission to Mars such as the NASA Design Reference Mission (DRM 1.0) emphasize the need for adaptability of crewmembers and autonomy in the crew as a whole (Hoffman and Kaplan, 1997). Similarly a major study by the International Space University (ISU, 1991) emphasized the need for autonomy and initiative for a Mars crew given that many of the scenarios that will be encountered on Mars cannot be rehearsed on earth and given the lack of any realistic possibility for rescue of the crew. This research project was only one subset of data collected during the larger AustroMars Expedition at the Mars Desert Research Facility (MDRS) in 2006. The participating crew comprises part of a multi-year investigation on teams utilizing the MDRS facility. The program of research has included numerous researchers since 2002 with a progressive evolution of key foci addressing stress, personality, coping, adaptation, cognitive functioning, and group identity assessed across the duration period of the individual missions.
Molecular Dynamics Simulations of displacement cascades in metallic systems
International Nuclear Information System (INIS)
Doan, N.V.; Tietze, H.
1995-01-01
We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)
Stochastic Simulation of Cardiac Ventricular Myocyte Calcium Dynamics and Waves
Tuan, Hoang-Trong Minh; Williams, George S. B.; Chikando, Aristide C.; Sobie, Eric A.; Lederer, W. Jonathan; Jafri, M. Saleet
2011-01-01
A three dimensional model of calcium dynamics in the rat ventricular myocyte was developed to study the mechanism of calcium homeostasis and pathological calcium dynamics during calcium overload. The model contains 20,000 calcium release units (CRUs) each containing 49 ryanodine receptors. The model simulates calcium sparks with a realistic spontaneous calcium spark rate. It suggests that in addition to the calcium spark-based leak, there is an invisible calcium leak caused by the stochastic ...
Coalescence of silver unidimensional structures by molecular dynamics simulation
International Nuclear Information System (INIS)
Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.
2007-01-01
The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)
Beam dynamics simulation in the X-ray Compton source
Energy Technology Data Exchange (ETDEWEB)
Gladkikh, P.; Karnaukhov, I.; Telegin, Yu.; Shcherbakov, A. E-mail: shcherbakov@kipt.kharkov.ua; Zelinsky, A
2002-05-01
At the National Science Center 'Kharkov Institute of Physics and Technology' the X-ray source based on Compton scattering has been developed. The computer code for simulation of electron beam dynamics with taking into account the Compton scattering effect based on Monte Carlo method is described in this report. The first results of computer simulation of beam dynamics with electron-photon interaction, parameters of electron and photon beams are presented. Calculations were carried out with the lattice of synchrotron light source SRS-800 Ukrainian Synchrotron Center.
Beam dynamics simulation in the X-ray Compton source
International Nuclear Information System (INIS)
Gladkikh, P.; Karnaukhov, I.; Telegin, Yu.; Shcherbakov, A.; Zelinsky, A.
2002-01-01
At the National Science Center 'Kharkov Institute of Physics and Technology' the X-ray source based on Compton scattering has been developed. The computer code for simulation of electron beam dynamics with taking into account the Compton scattering effect based on Monte Carlo method is described in this report. The first results of computer simulation of beam dynamics with electron-photon interaction, parameters of electron and photon beams are presented. Calculations were carried out with the lattice of synchrotron light source SRS-800 Ukrainian Synchrotron Center
Beam dynamics simulation in the X-ray Compton source
Gladkikh, P; Telegin, Yu P; Shcherbakov, A; Zelinsky, A
2002-01-01
At the National Science Center 'Kharkov Institute of Physics and Technology' the X-ray source based on Compton scattering has been developed. The computer code for simulation of electron beam dynamics with taking into account the Compton scattering effect based on Monte Carlo method is described in this report. The first results of computer simulation of beam dynamics with electron-photon interaction, parameters of electron and photon beams are presented. Calculations were carried out with the lattice of synchrotron light source SRS-800 Ukrainian Synchrotron Center.
Dynamic modeling, simulation and control of energy generation
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
Lessons Learned From Dynamic Simulations of Advanced Fuel Cycles
International Nuclear Information System (INIS)
Piet, Steven J.; Dixon, Brent W.; Jacobson, Jacob J.; Matthern, Gretchen E.; Shropshire, David E.
2009-01-01
Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe 'lessons learned' from dynamic simulations but attempt to answer the 'so what' question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof
Dynamic simulation of the NET In-Vessel Handling Unit
International Nuclear Information System (INIS)
Reim, J.
1991-01-01
During the conceptual design phase of the Next European Torus (NET) a large remote maintenance transporter system, the In-Vessel Handling Unit (IVHU), is being developed. It consists of an articulated boom with four rotational joints, which is mounted on a carrier outside the vessel. This boom will be able to carry master-slave manipulators or special work units. The engineering design is supported by dynamic computations. Main topics of the dynamic simulation are the evaluation of IVHU performance, selection and optimisation of the actuator design and of the control algorithms. This simulation task requires full three-dimensional modelling regarding structural elasticity and non-linear actuator dynamics. The Multibody dynamics of the transporter system are modelled with a commerical analysis package. Elastic links and a precise dynamic actuator model are introduced by applied forces, spring elements and differential equations. The actuator model comprises electric motors, gears and linear control algorithms. Non-linear effects which have an influence on control stability and accuracy are taken into account. Most important effects are backlash and static friction. The simulations concentrate on test and optimisation of the control layout and performance studies for critical remote handling tasks. Simulations for control layout and critical remote maintenance tasks correspond to the design objectives of the transporter system. (orig.)
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.
Object Oriented Toolbox for Modelling and Simulation of Dynamical Systems
DEFF Research Database (Denmark)
Poulsen, Mikael Zebbelin; Wagner, Falko Jens; Thomsen, Per Grove
1998-01-01
This paper presents the results of an ongoing project, dealing with design and implementation of a simulation toolbox based on object oriented modelling techniques. The paper describes an experimental implementation of parts of such a toolbox in C++, and discusses the experiences drawn from that ...... that process. Essential to the work is the focus on simulation of complex dynamical systems, from modelling the single components/subsystems to building complete systemssuch a toolbox in C++, and discusses the experiences drawn from that process....
Influence of wheel-rail contact modelling on vehicle dynamic simulation
Burgelman, Nico; Sichani, Matin Sh.; Enblom, Roger; Berg, Mats; Li, Zili; Dollevoet, Rolf
2015-08-01
This paper presents a comparison of four models of rolling contact used for online contact force evaluation in rail vehicle dynamics. Until now only a few wheel-rail contact models have been used for online simulation in multibody software (MBS). Many more models exist and their behaviour has been studied offline, but a comparative study of the mutual influence between the calculation of the creep forces and the simulated vehicle dynamics seems to be missing. Such a comparison would help researchers with the assessment of accuracy and calculation time. The contact methods investigated in this paper are FASTSIM, Linder, Kik-Piotrowski and Stripes. They are compared through a coupling between an MBS for the vehicle simulation and Matlab for the contact models. This way the influence of the creep force calculation on the vehicle simulation is investigated. More specifically this study focuses on the influence of the contact model on the simulation of the hunting motion and on the curving behaviour.
Dynamic Hybrid Simulation of the Lunar Wake During ARTEMIS Crossing
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.
Directory of Open Access Journals (Sweden)
Elena ePapaleo
2015-05-01
Full Text Available 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.
Xu, Zhongfeng; Yang, Zong-Liang
2012-01-01
An improved dynamical downscaling method (IDD) with general circulation model (GCM) bias corrections is developed and assessed over North America. A set of regional climate simulations is performed with the Weather Research and Forecasting Model
Dynamic wind turbine models in power system simulation tool DIgSILENT
Hansen, A.D.; Jauch, C.; Sørensen, Poul Ejnar; Iov, F.; Blaabjerg, F.
2004-01-01
The present report describes the dynamic wind turbine models implemented in the power system simulation tool DIgSILENT (Version 12.0). The developed models are a part of the results of a national research project, whose overall objective is to create amodel database in different simulation tools. This model database should be able to support the analysis of the interaction between the mechanical structure of the wind turbine and the electrical grid during different operational modes. The repo...
The Research on Modeling and Simulation of TFE Polymerization Process
Directory of Open Access Journals (Sweden)
Jing Gao Sun
2014-01-01
Full Text Available PTFE (polytetrafluoroethylene is the fluorinated straight-chain polymer, made by the polymerization of tetrafluoroethylene monomer; it is used widely because of its excellent performance and can be obtained by the polymerization of body, solutions, suspensions, and emulsions. But only the last two are the main ways. This research paper makes simulation based on Polymer Plus. It uses the emulsion polymerization method at background to carry out a semibatch reactor system. Upon the actual production conditions, simulation process under the steady state conditions is used to analyze the effects of the changes on operating conditions; the corresponding dynamic model is created to analyze the impact of the changes of conditions on the entire system. Moreover, the amount of APS which plays an important part in this reaction is discussed for getting the most suitable amount of initiator. Because of less research work on this job, it is so difficult to find the related data from the literature. Therefore, this research will have a great significance for the process of the tetrafluoroethylene emulsion polymerization in the future.
Validating clustering of molecular dynamics simulations using polymer models
Directory of Open Access Journals (Sweden)
Phillips Joshua L
2011-11-01
Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our
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...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system...
A statistical-dynamical downscaling procedure for global climate simulations
International Nuclear Information System (INIS)
Frey-Buness, A.; Heimann, D.; Sausen, R.; Schumann, U.
1994-01-01
A statistical-dynamical downscaling procedure for global climate simulations is described. The procedure is based on the assumption that any regional climate is associated with a specific frequency distribution of classified large-scale weather situations. The frequency distributions are derived from multi-year episodes of low resolution global climate simulations. Highly resolved regional distributions of wind and temperature are calculated with a regional model for each class of large-scale weather situation. They are statistically evaluated by weighting them with the according climate-specific frequency. The procedure is exemplarily applied to the Alpine region for a global climate simulation of the present climate. (orig.)
A Unique Software System For Simulation-to-Flight Research
Chung, Victoria I.; Hutchinson, Brian K.
2001-01-01
"Simulation-to-Flight" is a research development concept to reduce costs and increase testing efficiency of future major aeronautical research efforts at NASA. The simulation-to-flight concept is achieved by using common software and hardware, procedures, and processes for both piloted-simulation and flight testing. This concept was applied to the design and development of two full-size transport simulators, a research system installed on a NASA B-757 airplane, and two supporting laboratories. This paper describes the software system that supports the simulation-to-flight facilities. Examples of various simulation-to-flight experimental applications were also provided.
Dynamic simulation of a steam generator by neural networks
International Nuclear Information System (INIS)
Masini, R.; Padovani, E.; Ricotti, M.E.; Zio, E.
1999-01-01
Numerical simulation by computers of the dynamic evolution of complex systems and components is a fundamental phase of any modern engineering design activity. This is of particular importance for risk-based design projects which require that the system behavior be analyzed under several and often extreme conditions. The traditional methods of simulation typically entail long, iterative, processes which lead to large simulation times, often exceeding the transients real time. Artificial neural networks (ANNs) may be exploited in this context, their advantages residing mainly in the speed of computation, in the capability of generalizing from few examples, in the robustness to noisy and partially incomplete data and in the capability of performing empirical input-output mapping without complete knowledge of the underlying physics. In this paper we present a novel approach to dynamic simulation by ANNs based on a superposition scheme in which a set of networks are individually trained, each one to respond to a different input forcing function. The dynamic simulation of a steam generator is considered as an example to show the potentialities of this tool and to point out the difficulties and crucial issues which typically arise when attempting to establish an efficient neural network simulator. The structure of the networks system is such to feedback, at each time step, a portion of the past evolution of the transient and this allows a good reproduction of also non-linear dynamic behaviors. A nice characteristic of the approach is that the modularization of the training reduces substantially its burden and gives this neural simulation tool a nice feature of transportability. (orig.)
Developing Soil Models for Dynamic Impact Simulations
Fasanella, Edwin L.; Lyle, Karen H.; Jackson, Karen E.
2009-01-01
This paper describes fundamental soils characterization work performed at NASA Langley Research Center in support of the Subsonic Rotary Wing (SRW) Aeronautics Program and the Orion Landing System (LS) Advanced Development Program (ADP). LS-DYNA(Registered TradeMark)1 soil impact model development and test-analysis correlation results are presented for: (1) a 38-ft/s vertical drop test of a composite fuselage section, outfitted with four blocks of deployable energy absorbers (DEA), onto sand, and (2) a series of impact tests of a 1/2-scale geometric boilerplate Orion capsule onto soil. In addition, the paper will discuss LS-DYNA contact analysis at the soil/structure interface, methods used to estimate frictional forces, and the sensitivity of the model to density, moisture, and compaction.
Simulation Analysis of Helicopter Ground Resonance Nonlinear Dynamics
Zhu, Yan; Lu, Yu-hui; Ling, Ai-min
2017-07-01
In order to accurately predict the dynamic instability of helicopter ground resonance, a modeling and simulation method of helicopter ground resonance considering nonlinear dynamic characteristics of components (rotor lead-lag damper, landing gear wheel and absorber) is presented. The numerical integral method is used to calculate the transient responses of the body and rotor, simulating some disturbance. To obtain quantitative instabilities, Fast Fourier Transform (FFT) is conducted to estimate the modal frequencies, and the mobile rectangular window method is employed in the predictions of the modal damping in terms of the response time history. Simulation results show that ground resonance simulation test can exactly lead up the blade lead-lag regressing mode frequency, and the modal damping obtained according to attenuation curves are close to the test results. The simulation test results are in accordance with the actual accident situation, and prove the correctness of the simulation method. This analysis method used for ground resonance simulation test can give out the results according with real helicopter engineering tests.
Simulation of Protein Structure, Dynamics and Function in Organic Media
National Research Council Canada - National Science Library
Daggett, Valerie
1998-01-01
The overall goal of our ONR-sponsored research is to pursue realistic molecular modeling strudies pertinnent to the related properties of protein stability, dynamics, structure, function, and folding in aqueous solution...
Energy Technology Data Exchange (ETDEWEB)
Wang, Chao [Pacific Northwest National Laboratory, Physical and Computational Sciences Directorate, Richland WA; Xu, Zhijie [Pacific Northwest National Laboratory, Physical and Computational Sciences Directorate, Richland WA; Lai, Kevin [Pacific Northwest National Laboratory, Physical and Computational Sciences Directorate, Richland WA; Whyatt, Greg [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland WA; Marcy, Peter W. [Los Alamos National Laboratory, Statistical Sciences Group, Los Alamos NM; Sun, Xin [Oak Ridge National Laboratory, Energy and Transportation Science Division, Oak Ridge TN
2017-10-24
The first part of this paper (Part 1) presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO2) capture. To generate data for WWC model validation, CO2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work has the ability to account for both chemical absorption and desorption of CO2 in MEA. In addition, the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry’s constant and gas diffusivity in the non-reacting nitrous oxide (N2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO2 reaction rate constants after using the N2O/CO2 analogy method. The calibrated model can be used to predict the CO2 mass transfer in a WWC for a wider range of operating conditions.
Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E
2017-01-01
Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...... to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration....... The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure...
Using simulation to assess the opportunities of dynamic waste collection
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
Using Simulation to Assess the Opportunities of Dynamic Waste Collection
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
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...
Accurate simulation dynamics of microscopic filaments using "caterpillar" Oseen hydrodynamics
Bailey, A.G.; Lowe, C.P.; Pagonabarraga, I.; Cosentino Lagomarsino, M.
2009-01-01
Microscopic semiflexible filaments suspended in a viscous fluid are widely encountered in biophysical problems. The classic example is the flagella used by microorganisms to generate propulsion. Simulating the dynamics of these filaments numerically is complicated because of the coupling between the
Effects of transition on wind tunnel simulation of vehicel dynamics
Ericsson, L. E.
Among the many problems the test engineer faces when trying to simulate full-scale vehicle dynamics in a wind tunnel test is the fact that the test usually will be performed at Reynolds numbers far below those existing on the full-scale vehicle. It is found that a severe scaling problem may exist even in the case of attached flow. The strong coupling existing between boundary layer transition and vehicle motion can cause the wind tunnel results to be very misleading, in some cases dangerously so. For example, the subscale test could fail to show a dynamic stability problem existing in full-scale flight, or, conversely, show one that does not exist. When flow separation occurs together with boundary layer transition, the scaling problem becomes more complicated, and the potential for dangerously misleading subscale test results increases. The existing literature is reviewed to provide examples of the different types of dynamic simulation problems that the test engineer is likely to face. It should be emphasized that the difficulties presented by transition effects in the case of wind tunnel simulation of vehicle dynamics apply to the same extent to numeric simulation methods.
Ab initio molecular dynamics simulation of laser melting of silicon
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
Simulating Poverty and Inequality Dynamics in Developing Countries
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…
Simulation of the substrate cavity dynamics of quercetinase
van den Bosch, M; Swart, M; van Gunsteren, WF; Canters, GW
2004-01-01
Molecular dynamics (MD) simulations have been performed on quercetin 2,3 dioxygenase (2,3QD) to study the mobility and flexibility of the substrate cavity. 2,3QD is the only firmly established Cu-containing dioxygenase known so far. It catalyses the breakage of the O-heterocycle of flavonols. The
Microsecond atomic-scale molecular dynamics simulations of polyimides
Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.
2013-01-01
We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long
Simulating an arbitrary number of flavors of dynamical overlap fermions
International Nuclear Information System (INIS)
DeGrand, T.; Schaefer, S.
2006-05-01
We present a set of related Hybrid Monte Carlo methods to simulate an arbitrary number of dynamical overlap fermions. Each fermion is represented by a chiral pseudo-fermion field. The new algorithm reduces critical slowing down in the chiral limit and for sectors of nontrivial topology. (Orig.)
Efficient dynamic simulation of flexible link manipulators with PID control
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
Molecular dynamics simulations and free energy profile of ...
Indian Academy of Sciences (India)
aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.
Molecular dynamics simulations of lipid vesicle fusion in atomic detail
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
Dynamical simulation of heavy ion collisions; VUU and QMD method
International Nuclear Information System (INIS)
Niita, Koji
1992-01-01
We review two simulation methods based on the Vlasov-Uehling-Uhlenbeck (VUU) equation and Quantum Molecular Dynamics (QMD), which are the most widely accepted theoretical framework for the description of intermediate-energy heavy-ion reactions. We show some results of the calculations and compare them with the experimental data. (author)
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.
A new simulation algorithm for lattice QCD with dynamical quarks
Bunk, B.; Jegerlehner, B.; Luscher, M.; Simma, H.; Sommer, R.; Bunk, B; Jansen, K; Jegerlehner, B; Luscher, M; Simma, H
1994-01-01
A previously introduced multi-boson technique for the simulation of QCD with dynamical quarks is described and some results of first test runs on a 6^3\\times12 lattice with Wilson quarks and gauge group SU(2) are reported.
Proceedings of the meeting on large scale computer simulation research
International Nuclear Information System (INIS)
2004-04-01
The meeting to summarize the collaboration activities for FY2003 on the Large Scale Computer Simulation Research was held January 15-16, 2004 at Theory and Computer Simulation Research Center, National Institute for Fusion Science. Recent simulation results, methodologies and other related topics were presented. (author)
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.
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)
2015-12-07
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
International Nuclear Information System (INIS)
Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter
2015-01-01
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level
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.
Liquid-vapor coexistence by molecular dynamics simulation
International Nuclear Information System (INIS)
Baranyai, Andras; Cummings, Peter T.
2000-01-01
We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics
On the characteristics of a numerical fluid dynamics simulator
International Nuclear Information System (INIS)
Winkler, K.H.A.; Norman, M.L.; Norton, J.L.
1986-01-01
John von Neumann envisioned scientists and mathematicians analyzing and controlling their numerical experiments on nonlinear dynamic systems interactively. The authors describe their concept of a real-time Numerical Fluid Dynamics Simulator NFDS. The authors envision the NFDS to be composed of simulation processors, data storage devices, and image processing devices of extremely high power and capacity, interconnected by very high throughput communication channels. They present individual component performance requirements for both real-time and playback operating modes of the NFDS, using problems of current interest in fluid dynamics as examples. Scaling relations are derived showing the dependence of system requirements on the dimensionality and complexity of the numerical model. The authors conclude by extending their analysis to the system requirements posed in modeling the more involved physics of radiation hydrodynamics
Beam dynamics simulation of W-band photo injector
International Nuclear Information System (INIS)
Zhu Xiongwei
2002-01-01
The authors present a beam dynamics simulation study on 1.6 cell, high gradient W-Band photocathode RF gun which is capable of generating and accelerating 300 pC electron bunch. The design system is made up of 91.392 GHz photocathode RF gun and 91.392 GHz travelling wave linac cells. Based on the numerical simulation using SUPERFISH and PARMELA and the conventional RF linac scaling law, the design will produce 300 pC at 1.74 MeV with bunch length 0.72 ps and normalized transverse emittance 0.55 mm mrad. The authors study the beam dynamics in high frequency and high gradient; due to the high gradient, the ponderomotive effect plays an important role in beam dynamics; the authors found the ponderomotive effect still exist with only the fundamental space harmonics (synchrotron mode) due to the coupling of the transverse and longitudinal motion
Simulation and experimental research on line throwing rocket with flight
Wen-bin Gu; Ming Lu; Jian-qing Liu; Qin-xing Dong; Zhen-xiong Wang; Jiang-hai Chen
2014-01-01
The finite segment method is used to model the line throwing rocket system. A dynamic model of line throwing rocket with flight motion based on Kane's method is presented by the kinematics description of the system and the consideration of the forces acting on the system. The experiment designed according to the parameters of the dynamic model is made. The simulation and experiment results, such as range, velocity and flight time, are compared and analyzed. The simulation results are basicall...
Bolhuis, Peter
Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.
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.
Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.
2009-01-01
and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...... dynamics (MD) simulations of a hydrophilic air-water-silica system using the MD package FASTTUBE. We employ quantum chemistry calculation to obtain air-silica interaction parameters for the simulations. Our simulations are based in the following force fields: i) The silica-silica interaction is based...... of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems. For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence of air. Hence...
Simulation of the Dynamic Inefficiency of the CMS Pixel Detector
INSPIRE-00380273
2015-05-07
The Pixel Detector is the innermost part of the CMS Tracker. It therefore has to prevail in the harshest environment in terms of particle fluence and radiation. There are several mechanisms that may decrease the efficiency of the detector. These are mainly caused by data acquisition (DAQ) problems and/or Single Event Upsets (SEU). Any remaining efficiency loss is referred to as the dynamic inefficiency. It is caused by various mechanisms inside the Readout Chip (ROC) and depends strongly on the data occupancy. In the 2012 data, at high values of instantaneous luminosity the inefficiency reached 2\\% (in the region closest to the interaction point) which is not negligible. In the 2015 run higher instantaneous luminosity is expected, which will result in lower efficiencies; therefore this effect needs to be understood and simulated. A data-driven method has been developed to simulate dynamic inefficiency, which has been shown to successfully simulate the effects.
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
International Nuclear Information System (INIS)
Wei Gu; Garcia, A.E.; Schoenborn, B.P.
1994-01-01
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
Haptization of molecular dynamics simulation with thermal display
International Nuclear Information System (INIS)
Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki
2010-01-01
Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)
Parallel alternating direction preconditioner for isogeometric simulations of explicit dynamics
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.
A Thermodynamic Library for Simulation and Optimization of Dynamic Processes
DEFF Research Database (Denmark)
Ritschel, Tobias Kasper Skovborg; Gaspar, Jozsef; Jørgensen, John Bagterp
2017-01-01
Process system tools, such as simulation and optimization of dynamic systems, are widely used in the process industries for development of operational strategies and control for process systems. These tools rely on thermodynamic models and many thermodynamic models have been developed for different...... compounds and mixtures. However, rigorous thermodynamic models are generally computationally intensive and not available as open-source libraries for process simulation and optimization. In this paper, we describe the application of a novel open-source rigorous thermodynamic library, ThermoLib, which...... is designed for dynamic simulation and optimization of vapor-liquid processes. ThermoLib is implemented in Matlab and C and uses cubic equations of state to compute vapor and liquid phase thermodynamic properties. The novelty of ThermoLib is that it provides analytical first and second order derivatives...
Molecular dynamics simulations of a lithium/sodium carbonate mixture.
Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo
2016-03-01
The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates.
Software life cycle dynamic simulation model: The organizational performance submodel
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.
Why we simulate negated information: a dynamic pragmatic account.
Tian, Ye; Breheny, Richard; Ferguson, Heather J
2010-12-01
A well-established finding in the simulation literature is that participants simulate the positive argument of negation soon after reading a negative sentence, prior to simulating a scene consistent with the negated sentence (Kaup, Ludtke, & Zwaan, 2006; Kaup, Yaxley, Madden, Zwaan, & Ludtke, 2007). One interpretation of this finding is that negation requires two steps to process: first represent what is being negated then "reject" that in favour of a representation of a negation-consistent state of affairs (Kaup et al., 2007). In this paper we argue that this finding with negative sentences could be a by-product of the dynamic way that language is interpreted relative to a common ground and not the way that negation is represented. We present a study based on Kaup et al. (2007) that tests the competing accounts. Our results suggest that some negative sentences are not processed in two steps, but provide support for the alternative, dynamic account.
Probing the limits of metal plasticity with molecular dynamics simulations
Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas; Bulatov, Vasily V.
2017-10-01
Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every ``jiggle and wiggle'' of atomic motion, whereas dislocation dynamics models do not. Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85-340 nm) and timescales (1 ns-1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong
Computational fluid dynamics simulations and validations of results
CSIR Research Space (South Africa)
Sitek, MA
2013-09-01
Full Text Available Wind flow influence on a high-rise building is analyzed. The research covers full-scale tests, wind-tunnel experiments and numerical simulations. In the present paper computational model used in simulations is described and the results, which were...
Simulation language of DSNP: dynamic simulator for nuclear power-plants
International Nuclear Information System (INIS)
Saphier, D.
1978-09-01
The Dynamic Simulator for Nuclear Power-plants (DSNP) is a system of programs and data sets by which a nuclear power plant or part thereof can be simulated at different levels of sophistication. The acronym DSNP is used interchangeably for the DSNP language, for the DSNP precompiler, for the DSNP libraries, and for the DSNP document generator. The DSNP language is a set of simple block oriented statements, which together with the appropriate data, comprise a simulation of a nuclear power plant. The majority of the DSNP statements will result in the inclusion of a simulated physical module into the program. FORTRAN statements can be inserted with no restrictions among DSNP statements
Thermal transport in semicrystalline polyethylene by molecular dynamics simulation
Lu, Tingyu; Kim, Kyunghoon; Li, Xiaobo; Zhou, Jun; Chen, Gang; Liu, Jun
2018-01-01
Recent research has highlighted the potential to achieve high-thermal-conductivity polymers by aligning their molecular chains. Combined with other merits, such as low-cost, corrosion resistance, and light weight, such polymers are attractive for heat transfer applications. Due to their quasi-one-dimensional structural nature, the understanding on the thermal transport in those ultra-drawn semicrystalline polymer fibers or films is still lacking. In this paper, we built the ideal repeating units of semicrystalline polyethylene and studied their dependence of thermal conductivity on different crystallinity and interlamellar topology using the molecular dynamics simulations. We found that the conventional models, such as the Choy-Young's model, the series model, and Takayanagi's model, cannot accurately predict the thermal conductivity of the quasi-one-dimensional semicrystalline polyethylene. A modified Takayanagi's model was proposed to explain the dependence of thermal conductivity on the bridge number at intermediate and high crystallinity. We also analyzed the heat transfer pathways and demonstrated the substantial role of interlamellar bridges in the thermal transport in the semicrystalline polyethylene. Our work could contribute to the understanding of the structure-property relationship in semicrystalline polymers and shed some light on the development of plastic heat sinks and thermal management in flexible electronics.
Fluid dynamics parallel computer development at NASA Langley Research Center
Townsend, James C.; Zang, Thomas A.; Dwoyer, Douglas L.
1987-01-01
To accomplish more detailed simulations of highly complex flows, such as the transition to turbulence, fluid dynamics research requires computers much more powerful than any available today. Only parallel processing on multiple-processor computers offers hope for achieving the required effective speeds. Looking ahead to the use of these machines, the fluid dynamicist faces three issues: algorithm development for near-term parallel computers, architecture development for future computer power increases, and assessment of possible advantages of special purpose designs. Two projects at NASA Langley address these issues. Software development and algorithm exploration is being done on the FLEX/32 Parallel Processing Research Computer. New architecture features are being explored in the special purpose hardware design of the Navier-Stokes Computer. These projects are complementary and are producing promising results.
Simulating Data for Clinical Research: A Tutorial
Beaujean, A. Alexander
2018-01-01
Simulation studies use computer-generated data to examine questions of interest that have traditionally been used to study properties of statistics and estimating algorithms. With the recent advent of powerful processing capabilities in affordable computers along with readily usable software, it is now feasible to use a simulation study to aid in…
Research on Dynamic Coupled Characteristics of A Tracked Vehicle Gearbox
Directory of Open Access Journals (Sweden)
Hui Liu
2011-12-01
Full Text Available A tracked vehicle gearbox is divided into two subsystems-housing and gear train. Dynamic behaviors of the two subsystems are coupled practically. And the coupled characteristics describe the integrative dynamic behaviors of gearbox. This study proposes a coupled simulation model to investigate the interrelationship between dynamics of two subsystems. Multi-source excitations are numerically calculated to provide boundary conditions. The flexibility of transmission shafts and housing is mathematically described based on mode superposition. The coupled dynamic characteristics are analyzed with dynamics simulation computation. The flexibility of housing is one of the main causes to induce the fluctuation of dynamic responses of transmission shafts. The experimental results show that the proposed method is accurate through comparison of simulation results and test data.
The Fermi-Pasta-Ulam problem: Simulation and modern dynamics
International Nuclear Information System (INIS)
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
Fast Simulation of Dynamic Ultrasound Images Using the GPU.
Storve, Sigurd; Torp, Hans
2017-10-01
Simulated ultrasound data is a valuable tool for development and validation of quantitative image analysis methods in echocardiography. Unfortunately, simulation time can become prohibitive for phantoms consisting of a large number of point scatterers. The COLE algorithm by Gao et al. is a fast convolution-based simulator that trades simulation accuracy for improved speed. We present highly efficient parallelized CPU and GPU implementations of the COLE algorithm with an emphasis on dynamic simulations involving moving point scatterers. We argue that it is crucial to minimize the amount of data transfers from the CPU to achieve good performance on the GPU. We achieve this by storing the complete trajectories of the dynamic point scatterers as spline curves in the GPU memory. This leads to good efficiency when simulating sequences consisting of a large number of frames, such as B-mode and tissue Doppler data for a full cardiac cycle. In addition, we propose a phase-based subsample delay technique that efficiently eliminates flickering artifacts seen in B-mode sequences when COLE is used without enough temporal oversampling. To assess the performance, we used a laptop computer and a desktop computer, each equipped with a multicore Intel CPU and an NVIDIA GPU. Running the simulator on a high-end TITAN X GPU, we observed two orders of magnitude speedup compared to the parallel CPU version, three orders of magnitude speedup compared to simulation times reported by Gao et al. in their paper on COLE, and a speedup of 27000 times compared to the multithreaded version of Field II, using numbers reported in a paper by Jensen. We hope that by releasing the simulator as an open-source project we will encourage its use and further development.
Synthesis of recurrent neural networks for dynamical system simulation.
Trischler, Adam P; D'Eleuterio, Gabriele M T
2016-08-01
We review several of the most widely used techniques for training recurrent neural networks to approximate dynamical systems, then describe a novel algorithm for this task. The algorithm is based on an earlier theoretical result that guarantees the quality of the network approximation. We show that a feedforward neural network can be trained on the vector-field representation of a given dynamical system using backpropagation, then recast it as a recurrent network that replicates the original system's dynamics. After detailing this algorithm and its relation to earlier approaches, we present numerical examples that demonstrate its capabilities. One of the distinguishing features of our approach is that both the original dynamical systems and the recurrent networks that simulate them operate in continuous time. Copyright © 2016 Elsevier Ltd. All rights reserved.
Simulation of noisy dynamical system by Deep Learning
Yeo, Kyongmin
2017-11-01
Deep learning has attracted huge attention due to its powerful representation capability. However, most of the studies on deep learning have been focused on visual analytics or language modeling and the capability of the deep learning in modeling dynamical systems is not well understood. In this study, we use a recurrent neural network to model noisy nonlinear dynamical systems. In particular, we use a long short-term memory (LSTM) network, which constructs internal nonlinear dynamics systems. We propose a cross-entropy loss with spatial ridge regularization to learn a non-stationary conditional probability distribution from a noisy nonlinear dynamical system. A Monte Carlo procedure to perform time-marching simulations by using the LSTM is presented. The behavior of the LSTM is studied by using noisy, forced Van der Pol oscillator and Ikeda equation.
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.
Efficient Neural Network Modeling for Flight and Space Dynamics Simulation
Directory of Open Access Journals (Sweden)
Ayman Hamdy Kassem
2011-01-01
Full Text Available This paper represents an efficient technique for neural network modeling of flight and space dynamics simulation. The technique will free the neural network designer from guessing the size and structure for the required neural network model and will help to minimize the number of neurons. For linear flight/space dynamics systems, the technique can find the network weights and biases directly by solving a system of linear equations without the need for training. Nonlinear flight dynamic systems can be easily modeled by training its linearized models keeping the same network structure. The training is fast, as it uses the linear system knowledge to speed up the training process. The technique is tested on different flight/space dynamic models and showed promising results.
System dynamic simulation: A new method in social impact assessment (SIA)
Energy Technology Data Exchange (ETDEWEB)
Karami, Shobeir, E-mail: shobeirkarami@gmail.com [Agricultural Extension and Education, Shiraz University (Iran, Islamic Republic of); Karami, Ezatollah, E-mail: ekarami@shirazu.ac.ir [Agricultural Extension and Education, Shiraz University (Iran, Islamic Republic of); Buys, Laurie, E-mail: l.buys@qut.edu.au [Creative Industries Faculty, School of Design, Queensland University of Technology (Australia); Drogemuller, Robin, E-mail: robin.drogemuller@qut.edu.au [Creative Industries Faculty, School of Design, Queensland University of Technology (Australia)
2017-01-15
Many complex social questions are difficult to address adequately with conventional methods and techniques, due to the complicated dynamics, and hard to quantify social processes. Despite these difficulties researchers and practitioners have attempted to use conventional methods not only in evaluative modes but also in predictive modes to inform decision making. The effectiveness of SIAs would be increased if they were used to support the project design processes. This requires deliberate use of lessons from retrospective assessments to inform predictive assessments. Social simulations may be a useful tool for developing a predictive SIA method. There have been limited attempts to develop computer simulations that allow social impacts to be explored and understood before implementing development projects. In light of this argument, this paper aims to introduce system dynamic (SD) simulation as a new predictive SIA method in large development projects. We propose the potential value of the SD approach to simulate social impacts of development projects. We use data from the SIA of Gareh-Bygone floodwater spreading project to illustrate the potential of SD simulation in SIA. It was concluded that in comparison to traditional SIA methods SD simulation can integrate quantitative and qualitative inputs from different sources and methods and provides a more effective and dynamic assessment of social impacts for development projects. We recommend future research to investigate the full potential of SD in SIA in comparing different situations and scenarios.
System dynamic simulation: A new method in social impact assessment (SIA)
International Nuclear Information System (INIS)
Karami, Shobeir; Karami, Ezatollah; Buys, Laurie; Drogemuller, Robin
2017-01-01
Many complex social questions are difficult to address adequately with conventional methods and techniques, due to the complicated dynamics, and hard to quantify social processes. Despite these difficulties researchers and practitioners have attempted to use conventional methods not only in evaluative modes but also in predictive modes to inform decision making. The effectiveness of SIAs would be increased if they were used to support the project design processes. This requires deliberate use of lessons from retrospective assessments to inform predictive assessments. Social simulations may be a useful tool for developing a predictive SIA method. There have been limited attempts to develop computer simulations that allow social impacts to be explored and understood before implementing development projects. In light of this argument, this paper aims to introduce system dynamic (SD) simulation as a new predictive SIA method in large development projects. We propose the potential value of the SD approach to simulate social impacts of development projects. We use data from the SIA of Gareh-Bygone floodwater spreading project to illustrate the potential of SD simulation in SIA. It was concluded that in comparison to traditional SIA methods SD simulation can integrate quantitative and qualitative inputs from different sources and methods and provides a more effective and dynamic assessment of social impacts for development projects. We recommend future research to investigate the full potential of SD in SIA in comparing different situations and scenarios.
Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).
Energy Technology Data Exchange (ETDEWEB)
Wang, Chao [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical and Computational Sciences Directorate; Xu, Zhijie [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical and Computational Sciences Directorate; Lai, Kevin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical and Computational Sciences Directorate; Whyatt, Greg [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Energy and Environment Directorate; Marcy, Peter W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sun, Xin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Energy and Transportation Science Division
2017-10-24
Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO_{2}) capture. In this study, to generate data for WWC model validation, CO_{2} mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO_{2} in MEA. In addition, the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO_{2} across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N_{2}O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO_{2} reaction rate constants after using the N_{2}O/CO_{2} analogy method. Finally, the calibrated model can be used to predict the CO_{2} mass transfer in a WWC for a wider range of operating conditions.
Research in Modeling and Simulation for Airspace Systems Innovation
Ballin, Mark G.; Kimmel, William M.; Welch, Sharon S.
2007-01-01
This viewgraph presentation provides an overview of some of the applied research and simulation methodologies at the NASA Langley Research Center that support aerospace systems innovation. Risk assessment methodologies, complex systems design and analysis methodologies, and aer ospace operations simulations are described. Potential areas for future research and collaboration using interactive and distributed simula tions are also proposed.
Extracting Markov Models of Peptide Conformational Dynamics from Simulation Data.
Schultheis, Verena; Hirschberger, Thomas; Carstens, Heiko; Tavan, Paul
2005-07-01
A high-dimensional time series obtained by simulating a complex and stochastic dynamical system (like a peptide in solution) may code an underlying multiple-state Markov process. We present a computational approach to most plausibly identify and reconstruct this process from the simulated trajectory. Using a mixture of normal distributions we first construct a maximum likelihood estimate of the point density associated with this time series and thus obtain a density-oriented partition of the data space. This discretization allows us to estimate the transfer operator as a matrix of moderate dimension at sufficient statistics. A nonlinear dynamics involving that matrix and, alternatively, a deterministic coarse-graining procedure are employed to construct respective hierarchies of Markov models, from which the model most plausibly mapping the generating stochastic process is selected by consideration of certain observables. Within both procedures the data are classified in terms of prototypical points, the conformations, marking the various Markov states. As a typical example, the approach is applied to analyze the conformational dynamics of a tripeptide in solution. The corresponding high-dimensional time series has been obtained from an extended molecular dynamics simulation.
Seeking new mutation clues from Bacillus licheniformis amylase by molecular dynamics simulations
Lu, Tao
2009-07-01
Amylase is one of the most important industrial enzymes in the world. Researchers have been searching for a highly thermal stable mutant for many years, but most focus on point mutations of one or few nitrogenous bases. According to this molecular dynamic simulation of amylase from Bacillus licheniformis (BLA), the deletion of some nitrogenous bases would be more efficacious than point mutations. The simulation reveals strong fluctuation of the BLA structure at optimum temperature. The fluctuation of the outer domains of BLA is stronger than that of the core domain. Molecular simulation provides a clue to design thermal stable amylases through deletion mutations in the outer domain.
Simulation of plume dynamics by the Lattice Boltzmann Method
Mora, Peter; Yuen, David A.
2017-09-01
The Lattice Boltzmann Method (LBM) is a semi-microscopic method to simulate fluid mechanics by modelling distributions of particles moving and colliding on a lattice. We present 2-D simulations using the LBM of a fluid in a rectangular box being heated from below, and cooled from above, with a Rayleigh of Ra = 108, similar to current estimates of the Earth's mantle, and a Prandtl number of 5000. At this Prandtl number, the flow is found to be in the non-inertial regime where the inertial terms denoted I ≪ 1. Hence, the simulations presented lie within the regime of relevance for geodynamical problems. We obtain narrow upwelling plumes with mushroom heads and chutes of downwelling fluid as expected of a flow in the non-inertial regime. The method developed demonstrates that the LBM has great potential for simulating thermal convection and plume dynamics relevant to geodynamics, albeit with some limitations.
Molecular dynamics simulation of amplitude modulation atomic force microscopy
International Nuclear Information System (INIS)
Hu, Xiaoli; Martini, Ashlie; Egberts, Philip; Dong, Yalin
2015-01-01
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. (paper)
Simulation of Forest Cover Dynamics for Eastern Eurasian Boreal Forests
Shugart, H. H.; Yan, X.; Zhang, N.; Isaev, A. S.; Shuman, J. K.
2006-12-01
We are developing and testing a boreal zone forest dynamics model capable of simulating the forest cover dynamics of the Eurasian boreal forest, a major biospheric ecosystem with potentially large roles in the planetary carbon cycle and in the feedback between terrestrial surface and the atmosphere. In appreciating the role of this region in the coupling between atmosphere and terrestrial surface, on must understand the interactions between CO2 source/sink relationships (associated with growing or clearing forests) and the albedo effects (from changes in terrestrial surface cover). There is some evidence that in the Eurasian Boreal zone, the Carbon budget effects from forest change may oppose the albedo changes. This creates complex feedbacks between surface and atmosphere and motivates the need for a forest dynamics model that simultaneous represents forest vegetation and carbon storage and release. A forest dynamics model applied to Eastern Eurasia, FAREAST, has been tested using three types of information: 1. Direct species composition comparisons between simulated and observed mature forests at the same locations; 2. Forest type comparisons between simulated and observed forests along altitudinal gradients of several different mountains; 3. Comparison with forest stands in different succession stages of simulated forests. Model comparisons with independent data indicate the FAREAST model is capable of representing many of the broad features of the forests of Northeastern China. After model validation in the Northeast China region, model applications were developed for the forests of the Russian Far East. Continental-scale forest cover can be simulated to a relatively realistic degree using a forest gap model with standard representations of individual-plant processes. It appears that such a model, validated relatively locally in this case, in Northeastern China, can then be applied over a much larger region and under conditions of climatic change.
Simulating soil phosphorus dynamics for a phosphorus loss quantification tool.
Vadas, Peter A; Joern, Brad C; Moore, Philip A
2012-01-01
Pollution of fresh waters by agricultural phosphorus (P) is a water quality concern. Because soils can contribute significantly to P loss in runoff, it is important to assess how management affects soil P status over time, which is often done with models. Our objective was to describe and validate soil P dynamics in the Annual P Loss Estimator (APLE) model. APLE is a user-friendly spreadsheet model that simulates P loss in runoff and soil P dynamics over 10 yr for a given set of runoff, erosion, and management conditions. For soil P dynamics, APLE simulates two layers in the topsoil, each with three inorganic P pools and one organic P pool. It simulates P additions to soil from manure and fertilizer, distribution among pools, mixing between layers due to tillage and bioturbation, leaching between and out of layers, crop P removal, and loss by surface runoff and erosion. We used soil P data from 25 published studies to validate APLE's soil P processes. Our results show that APLE reliably simulated soil P dynamics for a wide range of soil properties, soil depths, P application sources and rates, durations, soil P contents, and management practices. We validated APLE specifically for situations where soil P was increasing from excessive P inputs, where soil P was decreasing due to greater outputs than inputs, and where soil P stratification occurred in no-till and pasture soils. Successful simulations demonstrate APLE's potential to be applied to major management scenarios related to soil P loss in runoff and erosion. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.
Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories
Directory of Open Access Journals (Sweden)
Jenny Farmer
2017-11-01
Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.
Computer simulations of liquid crystals: Defects, deformations and dynamics
Billeter, Jeffrey Lee
1999-11-01
Computer simulations play an increasingly important role in investigating fundamental issues in the physics of liquid crystals. Presented here are the results of three projects which utilize the unique power of simulations to probe questions which neither theory nor experiment can adequately answer. Throughout, we use the (generalized) Gay-Berne model, a widely-used phenomenological potential which captures the essential features of the anisotropic mesogen shapes and interactions. First, we used a Molecular Dynamics simulation with 65536 Gay-Berne particles to study the behaviors of topological defects in a quench from the isotropic to the nematic phase. Twist disclination loops were the dominant defects, and we saw evidence for dynamical scaling. We observed the loops separating, combining and collapsing, and we also observed numerous non-singular type-1 lines which appeared to be intimately involved with many of the loop processes. Second, we used a Molecular Dynamics simulation of a sphere embedded in a system of 2048 Gay-Berne particles to study the effects of radial anchoring of the molecules at the sphere's surface. A saturn ring defect configuration was observed, and the ring caused a driven sphere (modelling the falling ball experiment) to experience an increased resistance as it moved through the nematic. Deviations from a linear relationship between the driving force and the terminal speed are attributed to distortions of the saturn ring which we observed. The existence of the saturn ring confirms theoretical predictions for small spheres. Finally, we constructed a model for wedge-shaped molecules and used a linear response approach in a Monte Carlo simulation to investigate the flexoelectric behavior of a system of 256 such wedges. Novel potential models as well as novel analytical and visualization techniques were developed for these projects. Once again, the emphasis throughout was to investigate questions which simulations alone can adequately answer.
Quantum dynamical simulations of local field enhancement in metal nanoparticles.
Negre, Christian F A; Perassi, Eduardo M; Coronado, Eduardo A; Sánchez, Cristián G
2013-03-27
Field enhancements (Γ) around small Ag nanoparticles (NPs) are calculated using a quantum dynamical simulation formalism and the results are compared with electrodynamic simulations using the discrete dipole approximation (DDA) in order to address the important issue of the intrinsic atomistic structure of NPs. Quite remarkably, in both quantum and classical approaches the highest values of Γ are located in the same regions around single NPs. However, by introducing a complete atomistic description of the metallic NPs in optical simulations, a different pattern of the Γ distribution is obtained. Knowing the correct pattern of the Γ distribution around NPs is crucial for understanding the spectroscopic features of molecules inside hot spots. The enhancement produced by surface plasmon coupling is studied by using both approaches in NP dimers for different inter-particle distances. The results show that the trend of the variation of Γ versus inter-particle distance is different for classical and quantum simulations. This difference is explained in terms of a charge transfer mechanism that cannot be obtained with classical electrodynamics. Finally, time dependent distribution of the enhancement factor is simulated by introducing a time dependent field perturbation into the Hamiltonian, allowing an assessment of the localized surface plasmon resonance quantum dynamics.
Using system dynamics simulation for assessment of hydropower system safety
King, L. M.; Simonovic, S. P.; Hartford, D. N. D.
2017-08-01
Hydropower infrastructure systems are complex, high consequence structures which must be operated safely to avoid catastrophic impacts to human life, the environment, and the economy. Dam safety practitioners must have an in-depth understanding of how these systems function under various operating conditions in order to ensure the appropriate measures are taken to reduce system vulnerability. Simulation of system operating conditions allows modelers to investigate system performance from the beginning of an undesirable event to full system recovery. System dynamics simulation facilitates the modeling of dynamic interactions among complex arrangements of system components, providing outputs of system performance that can be used to quantify safety. This paper presents the framework for a modeling approach that can be used to simulate a range of potential operating conditions for a hydropower infrastructure system. Details of the generic hydropower infrastructure system simulation model are provided. A case study is used to evaluate system outcomes in response to a particular earthquake scenario, with two system safety performance measures shown. Results indicate that the simulation model is able to estimate potential measures of system safety which relate to flow conveyance and flow retention. A comparison of operational and upgrade strategies is shown to demonstrate the utility of the model for comparing various operational response strategies, capital upgrade alternatives, and maintenance regimes. Results show that seismic upgrades to the spillway gates provide the largest improvement in system performance for the system and scenario of interest.
The molecular dynamics simulation of ion-induced ripple growth
International Nuclear Information System (INIS)
Suele, P.; Heinig, K.-H.
2009-01-01
The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength (λ) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths (λ 35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in λ long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for λ>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.
The architecture of Newton, a general-purpose dynamics simulator
Cremer, James F.; Stewart, A. James
1989-01-01
The architecture for Newton, a general-purpose system for simulating the dynamics of complex physical objects, is described. The system automatically formulates and analyzes equations of motion, and performs automatic modification of this system equations when necessitated by changes in kinematic relationships between objects. Impact and temporary contact are handled, although only using simple models. User-directed influence of simulations is achieved using Newton's module, which can be used to experiment with the control of many-degree-of-freedom articulated objects.
Computational fluid dynamics simulations of light water reactor flows
International Nuclear Information System (INIS)
Tzanos, C.P.; Weber, D.P.
1999-01-01
Advances in computational fluid dynamics (CFD), turbulence simulation, and parallel computing have made feasible the development of three-dimensional (3-D) single-phase and two-phase flow CFD codes that can simulate fluid flow and heat transfer in realistic reactor geometries with significantly reduced reliance, especially in single phase, on empirical correlations. The objective of this work was to assess the predictive power and computational efficiency of a CFD code in the analysis of a challenging single-phase light water reactor problem, as well as to identify areas where further improvements are needed
Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution
Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.
2011-01-01
Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molec...
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
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.
Frank, Martin
2015-01-01
Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).
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.
Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining
International Nuclear Information System (INIS)
Khasin, M.; Kosloff, R.
2010-01-01
An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables--the elements of the spectrum-generating algebra--is simulated by a surrogate open-system dynamics, which can be interpreted as weak measurement of the target observables, performed on the evolving system. The open-system state can be represented by a mixture of pure states, localized in the phase space. The localization reduces the scaling of the computational resources with the Hilbert-space dimension n by factor n 3/2 (ln n) -1 compared to conventional sparse-matrix methods. The guidelines for the choice of parameters for the simulation are presented and the scaling of the computational resources with the Hilbert-space dimension of the system is estimated. The algorithm is applied to the simulation of the dynamics of systems of 2x10 4 and 2x10 6 cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.
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%.
Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ
DEFF Research Database (Denmark)
Euro, Liliya; Haapanen, Outi; Róg, Tomasz
2017-01-01
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......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...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...
Dynamic modeling and simulation of a real world billiard
International Nuclear Information System (INIS)
Hartl, Alexandre E.; Miller, Bruce N.; 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. -- Highlights: → We create a model of a gravitational billiard that includes rotation and dissipation. → Predictions of the model are compared with the experiments of Felt and Olafsen. → The simulations correctly predict the essential features of the experiments.
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.
Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates
Energy Technology Data Exchange (ETDEWEB)
Zhang Junfang [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia); Rivero, Mayela [CSIRO Petroleum, PO Box 1130, Bentley, Western Australia, 6102 (Australia); Choi, S K [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia)
2007-02-14
We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 A. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.
Deformation mechanisms in nanotwinned copper by molecular dynamics simulation
Energy Technology Data Exchange (ETDEWEB)
Zhao, Xing [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China); Lu, Cheng, E-mail: chenglu@uow.edu.au [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Tieu, Anh Kiet; Pei, Linqing; Zhang, Liang; Su, Lihong [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Zhan, Lihua [State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China)
2017-02-27
Nanotwinned materials exhibit simultaneous ultrahigh strength and high ductility which is attributed to the interactions between dislocations and twin boundaries but the specific deformation mechanisms are rarely seen in experiments at the atomic level. Here we use large scale molecular dynamics simulations to explore this intricate interplay during the plastic deformation of nanotwinned Cu. We demonstrate that the dominant deformation mechanism transits dynamically from slip transfer to twin boundary migration to slip-twin interactions as the twin boundary orientation changes from horizontal to slant, and then to a vertical direction. Building on the fundamental physics of dislocation processes from computer simulations and combining the available experimental investigations, we unravel the underlying deformation mechanisms for nanotwinned Cu, incorporating all three distinct dislocation processes. Our results give insights into systematically engineering the nanoscale twins to fabricate nanotwinned metals or alloys that have high strength and considerable ductility.
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.
DYNSYL: a general-purpose dynamic simulator for chemical processes
International Nuclear Information System (INIS)
Patterson, G.K.; Rozsa, R.B.
1978-01-01
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
Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations
Norman, Michael L.
1997-01-01
Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.
Dynamic skin deformation simulation using musculoskeletal model and soft tissue dynamics
Institute of Scientific and Technical Information of China (English)
Akihiko Murai; Q. Youn Hong; Katsu Yamane; Jessica K. Hodgins
2017-01-01
Deformation of skin and muscle is essential for bringing an animated character to life. This deformation is difficult to animate in a realistic fashion using traditional techniques because of the subtlety of the skin deformations that must move appropriately for the character design. In this paper, we present an algorithm that generates natural, dynamic, and detailed skin deformation (movement and jiggle) from joint angle data sequences. The algorithm has two steps: identification of parameters for a quasi-static muscle deformation model, and simulation of skin deformation. In the identification step, we identify the model parameters using a musculoskeletal model and a short sequence of skin deformation data captured via a dense marker set. The simulation step first uses the quasi-static muscle deformation model to obtain the quasi-static muscle shape at each frame of the given motion sequence (slow jump). Dynamic skin deformation is then computed by simulating the passive muscle and soft tissue dynamics modeled as a mass–spring–damper system. Having obtained the model parameters, we can simulate dynamic skin deformations for subjects with similar body types from new motion data. We demonstrate our method by creating skin deformations for muscle co-contraction and external impacts from four different behaviors captured as skeletal motion capture data. Experimental results show that the simulated skin deformations are quantitatively and qualitatively similar to measured actual skin deformations.
Dynamic skin deformation simulation using musculoskeletal model and soft tissue dynamics
Institute of Scientific and Technical Information of China (English)
Akihiko Murai; Q.Youn Hong; Katsu Yamane; Jessica K.Hodgins
2017-01-01
Deformation of skin and muscle is essential for bringing an animated character to life. This deformation is difficult to animate in a realistic fashion using traditional techniques because of the subtlety of the skin deformations that must move appropriately for the character design. In this paper, we present an algorithm that generates natural, dynamic, and detailed skin deformation(movement and jiggle) from joint angle data sequences. The algorithm has two steps: identification of parameters for a quasi-static muscle deformation model, and simulation of skin deformation. In the identification step, we identify the model parameters using a musculoskeletal model and a short sequence of skin deformation data captured via a dense marker set. The simulation step first uses the quasi-static muscle deformation model to obtain the quasi-static muscle shape at each frame of the given motion sequence(slow jump). Dynamic skin deformation is then computed by simulating the passive muscle and soft tissue dynamics modeled as a mass–spring–damper system. Having obtained the model parameters, we can simulate dynamic skin deformations for subjects with similar body types from new motion data. We demonstrate our method by creating skin deformations for muscle co-contraction and external impacts from four different behaviors captured as skeletal motion capture data. Experimental results show that the simulated skin deformations are quantitatively and qualitatively similar to measured actual skin deformations.
Dynamic information architecture system (DIAS) : multiple model simulation management
International Nuclear Information System (INIS)
Simunich, K. L.; Sydelko, P.; Dolph, J.; Christiansen, J.
2002-01-01
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 can schedule other events; create or remove Entities from the
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
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.)
Reactor numerical simulation and hydraulic test research
International Nuclear Information System (INIS)
Yang, L. S.
2009-01-01
In recent years, the computer hardware was improved on the numerical simulation on flow field in the reactor. In our laboratory, we usually use the Pro/e or UG commercial software. After completed topology geometry, ICEM-CFD is used to get mesh for computation. Exact geometrical similarity is maintained between the main flow paths of the model and the prototype, with the exception of the core simulation design of the fuel assemblies. The drive line system is composed of drive mechanism, guide bush assembly, fuel assembly and control rod assembly, and fitted with the rod level indicator and drive mechanism power device
Cuetos, Alejandro; Patti, Alessandro
2015-08-01
We propose a simple but powerful theoretical framework to quantitatively compare Brownian dynamics (BD) and dynamic Monte Carlo (DMC) simulations of multicomponent colloidal suspensions. By extending our previous study focusing on monodisperse systems of rodlike colloids, here we generalize the formalism described there to multicomponent colloidal mixtures and validate it by investigating the dynamics in isotropic and liquid crystalline phases containing spherical and rodlike particles. In order to investigate the dynamics of multicomponent colloidal systems by DMC simulations, it is key to determine the elementary time step of each species and establish a unique timescale. This is crucial to consistently study the dynamics of colloidal particles with different geometry. By analyzing the mean-square displacement, the orientation autocorrelation functions, and the self part of the van Hove correlation functions, we show that DMC simulation is a very convenient and reliable technique to describe the stochastic dynamics of any multicomponent colloidal system. Our theoretical formalism can be easily extended to any colloidal system containing size and/or shape polydisperse particles.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
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.
Molecular Dynamics Simulations of Tensile Behavior of Copper
Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.
2014-01-01
Molecular dynamics simulations on tensile deformation of initially defect free single crystal copper nanowire oriented in {100} has been carried out at 10 K under adiabatic and isothermal loading conditions. The tensile behaviour was characterized by sharp rise in stress in elastic regime followed by sudden drop at the point of dislocation nucleation. The important finding is that the variation in dislocation density is correlated with the observed stress-strain response. Several interesting ...
Modeling and simulation of high-speed milling centers dynamics
Msaddek , El Bechir; Bouaziz , Zoubeir; Baili , Maher; Dessein , Gilles
2011-01-01
International audience; High-speed machining is a milling operation in industrial production of aeronautic parts, molds, and dies. The parts production is being reduced because of the slowing down of the machining resulting from the tool path discontinuity machining strategy. In this article, we propose a simulation tool of the machine dynamic behavior, in complex parts machining. For doing this, analytic models have been developed expressing the cutting tool feed rate. Afterwards, a simulati...
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane
Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping
2012-01-01
We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present new results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition...
Dynamic simulation for effective workforce management in new product development
M. Mutingi
2012-01-01
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 mana...
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....
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
International Nuclear Information System (INIS)
Swygenhoven, H. van; Caro, A.
1997-01-01
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
Molecular dynamics simulation of cascade damage in gold
International Nuclear Information System (INIS)
Alonso, E.; Caturla, M.J.; Tang, M.; Huang, H.; Diaz de la Rubia, T.
1997-01-01
High-energy cascades have been simulated in gold using molecular dynamics with a modified embedded atom method potential. The results show that both vacancy and interstitial clusters form with high probability as a result of intracascade processes. The formation of clusters has been interpreted in terms of the high pressures generated in the core of the cascade during the early stages. The authors provide evidence that correlation between interstitial and vacancy clustering exists
Simulation of dynamic systems with Matlab and Simulink
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-
Simulating endogenous dynamics of activity-travel behavior : results of numerical simulations
Psarra, I.; Liao, F.; Arentze, T.A.; Timmermans, H.J.P.
2013-01-01
Modelling the dynamics of activity-travel behavior constitutes the next challenge on the international research agenda. Long-term dynamics relate to changes in opportunities or constraints, such as residential and job choice, while short-term decisions relate to day-to-day experiences. Due to a
New modelling strategy for IRIS dynamic response simulation
International Nuclear Information System (INIS)
Cammi, A.; Ricotti, M. E.; Casella, F.; Schiavo, F.
2004-01-01
The pressurized light water cooled, medium power (1000 MWt) IRIS (International Reactor Innovative and Secure) has been under development for four years by an international consortium of over 21 organizations from ten countries. The plant conceptual design was completed in 2001 and the preliminary design is nearing completion. The pre-application licensing process with NRC started in October, 2002 and IRIS is one of the designs considered by US utilities as part of the ESP (Early Site Permit) process. In this paper the development of an adequate modeling and simulation tool for Dynamics and Control tasks is presented. The key features of the developed simulator are: a) Modularity: the system model is built by connecting the models of its components, which are written independently of their boundary conditions; b) Openness: the code of each component model is clearly readable and close to the original equations and easily customised by the experienced user; c) Efficiency: the simulation code is fast; d) Tool support: the simulation tool is based on reliable, tested and well-documented software. To achieve these objectives, the Modelica language was used as a basis for the development of the simulator. The Modelica language is the results of recent advances in the field of object-oriented, multi-physics, dynamic system modelling. The language definition is open-source and it has already been successfully adopted in several industrial fields. To provide the required capabilities for the analysis, specific models for nuclear reactor components have been developed, to be applied for the dynamic simulation of the IRIS integral reactor, albeit keeping general validity for PWR plants. The following Modelica models have been written to satisfy the IRIS modelling requirements and are presented in this paper: neutronics point kinetic, fuel heat transfer, control rods model, including the innovative internal drive mechanism type, and a once-through type steam generator, thus
Direct identification of predator-prey dynamics in gyrokinetic simulations
Energy Technology Data Exchange (ETDEWEB)
Kobayashi, Sumire, E-mail: sumire.kobayashi@lpp.polytechnique.fr; Gürcan, Özgür D [Laboratoire de Physique des Plasmas, CNRS, Paris-Sud, Ecole Polytechnique, UMR7648, F-91128 Palaiseau (France); Diamond, Patrick H. [University of California, San Diego, La Jolla, California 92093-0319 (United States)
2015-09-15
The interaction between spontaneously formed zonal flows and small-scale turbulence in nonlinear gyrokinetic simulations is explored in a shearless closed field line geometry. It is found that when clear limit cycle oscillations prevail, the observed turbulent dynamics can be quantitatively captured by a simple Lotka-Volterra type predator-prey model. Fitting the time traces of full gyrokinetic simulations by such a reduced model allows extraction of the model coefficients. Scanning physical plasma parameters, such as collisionality and density gradient, it was observed that the effective growth rates of turbulence (i.e., the prey) remain roughly constant, in spite of the higher and varying level of primary mode linear growth rates. The effective growth rate that was extracted corresponds roughly to the zonal-flow-modified primary mode growth rate. It was also observed that the effective damping of zonal flows (i.e., the predator) in the parameter range, where clear predator-prey dynamics is observed, (i.e., near marginal stability) agrees with the collisional damping expected in these simulations. This implies that the Kelvin-Helmholtz-like instability may be negligible in this range. The results imply that when the tertiary instability plays a role, the dynamics becomes more complex than a simple Lotka-Volterra predator prey.
Dynamic simulation of variable capacity refrigeration systems under abnormal conditions
International Nuclear Information System (INIS)
Liang Nan; Shao Shuangquan; Tian Changqing; Yan Yuying
2010-01-01
There are often abnormal working conditions at evaporator outlet of a refrigeration system, such as two-phase state in transient process, and it is essential to investigate such transient behaviours for system design and control strategy. In this paper, a dynamic lumped parameter model is developed to simulate the transient behaviours of refrigeration system with variable capacity in both normal and abnormal working conditions. The appropriate discriminant method is adopted to switch the normal and abnormal conditions smoothly and to eliminate the simulated data oscillation. In order to verify the dynamic model, we built a test system with variable frequency compressor, water-cooling condenser, evaporator and electronic expansion valve. Calculated values from the mathematical model show reasonable agreement with the experimental data. The simulation results show that the transient behaviours of the variable capacity refrigeration system in the abnormal working conditions can be calculated reliably with the dynamic model when the compressor rotary speed or the opening of electronic expansion valve changes abruptly.
Literature for flight simulator (motion) requirements research
2010-10-29
This is the yearly snapshot of the literature examined in the framework of the Federal Aviation Administration/Volpe Center Flight Simulator Human Factors Program and entered in an EndNote database. It describes 1131 documents, 118 more than last y...
Brownian dynamic simulations and experiments of MR fluids
International Nuclear Information System (INIS)
Segovia-Gutiérrez, J P; Vicente, J de; Hidalgo, R; Puertas, A M
2013-01-01
The use of computational techniques in magnetorheology is not new. I general, these approaches assume dipolar magnetic interactions, hard sphere repulsions, and no-slip conditions. In this contribution we focus on the dynamics of the equilibrium state in the presence of uniaxial DC fields. To achieve this goal we make use of Brownian Dynamic Simulations. We highlight the importance of the Brownian forces versus magnetic dipolar interaction in the range of low magnetic field strengths. We monitor the formation of columnar structures and their dynamics, in competition with the Brownian motion, until a hexatic crystal phase appears at high field strengths for monodisperse systems. The shear viscosity is computed from the Einstein relation and eventually compared with experimental data at very low-shear rates. A reasonably good agreement between both data sets is observed.
Molecular dynamics simulations of lysozyme in water/sugar solutions
Energy Technology Data Exchange (ETDEWEB)
Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)
2008-04-18
Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.
Modelling of windmill induction generators in dynamic simulation programs
DEFF Research Database (Denmark)
Akhmatov, Vladislav; Knudsen, Hans
1999-01-01
with and without a model of the mechanical shaft. The reason for the discrepancies are explained, and it is shown that the phenomenon is due partly to the presence of DC offset currents in the induction machine stator, and partly to the mechanical shaft system of the wind turbine and the generator rotor......For AC networks with large amounts of induction generators-in case of e.g. windmills-the paper demonstrates a significant discrepancy in the simulated voltage recovery after faults in weak networks, when comparing result obtained with dynamic stability programs and transient programs, respectively....... It is shown that it is possible to include a transient model in dynamic stability programs and thus obtain correct results also in dynamic stability programs. A mechanical model of the shaft system has also been included in the generator model...
Langevin dynamics simulations of large frustrated Josephson junction arrays
International Nuclear Information System (INIS)
Groenbech-Jensen, N.; Bishop, A.R.; Lomdahl, P.S.
1991-01-01
Long-time Langevin dynamics simulations of large (N x N,N = 128) 2-dimensional arrays of Josephson junctions in a uniformly frustrating external magnetic field are reported. The results demonstrate: (1) Relaxation from an initially random flux configuration as a universal fit to a glassy stretched-exponential type of relaxation for the intermediate temperatures T(0.3 T c approx-lt T approx-lt 0.7 T c ), and an activated dynamic behavior for T ∼ T c ; (2) a glassy (multi-time, multi-length scale) voltage response to an applied current. Intrinsic dynamical symmetry breaking induced by boundaries as nucleation sites for flux lattice defects gives rise to transverse and noisy voltage response
Langevin dynamics simulations of large frustrated Josephson junction arrays
International Nuclear Information System (INIS)
Gronbech-Jensen, N.; Bishop, A.R.; Lomdahl, P.S.
1991-01-01
Long-time Langevin dynamics simulations of large (N x N, N = 128) 2-dimensional arrays of Josephson junctions in a uniformly frustrating external magnetic field are reported. The results demonstrate: Relaxation from an initially random flux configuration as a ''universal'' fit to a ''glassy'' stretched-exponential type of relaxation for the intermediate temperatures T (0.3 T c approx-lt T approx-lt 0.7 T c ), and an ''activated dynamic'' behavior for T ∼ T c A glassy (multi-time, multi-length scale) voltage response to an applied current. Intrinsic dynamical symmetry breaking induced by boundaries as nucleation sites for flux lattice defects gives rise to transverse and noisy voltage response
Dynamics of Research Team Formation in Complex Networks
Sun, Caihong; Wan, Yuzi; Chen, Yu
Most organizations encourage the formation of teams to accomplish complicated tasks, and vice verse, effective teams could bring lots benefits and profits for organizations. Network structure plays an important role in forming teams. In this paper, we specifically study the dynamics of team formation in large research communities in which knowledge of individuals plays an important role on team performance and individual utility. An agent-based model is proposed, in which heterogeneous agents from research communities are described and empirically tested. Each agent has a knowledge endowment and a preference for both income and leisure. Agents provide a variable input (‘effort’) and their knowledge endowments to production. They could learn from others in their team and those who are not in their team but have private connections in community to adjust their own knowledge endowment. They are allowed to join other teams or work alone when it is welfare maximizing to do so. Various simulation experiments are conducted to examine the impacts of network topology, knowledge diffusion among community network, and team output sharing mechanisms on the dynamics of team formation.
Molecular dynamics simulation of thermophysical properties of undercooled liquid cobalt
International Nuclear Information System (INIS)
Han, X J; Wang, J Z; Chen, M; Guo, Z Y
2004-01-01
Molecular dynamics simulations with two different embedded-atom-method (EAM) potentials are applied to calculate the density, specific heat and self-diffusion coefficient of liquid cobalt at temperatures above and below the melting temperature. Simulation shows that Pasianot's EAM model of cobalt constructed on the basis of a hcp structure is more successful than Stoop's EAM model in the framework of a fcc structure in predicting the thermophysical properties of liquid cobalt. Simulations with Pasianot's EAM model indicate that the density fits into ρ = 7.49-9.17 x 10 -4 (T- T m ) g cm -3 , and the self-diffusion coefficient is given by D = 1.291 x 10 -7 exp(-48 795.71/RT) m 2 s -1 . Dissimilar to the linear dependence of the density and the Arrhenius dependence of the self-diffusion coefficient on temperature, the specific heat shows almost a constant value of 38.595 ± 0.084 J mol -1 K -1 within the temperature range of simulation. The simulated properties of liquid cobalt are compared with experimental data available. Comparisons show reasonable agreements between the simulated results from Pasianot's EAM model and experimental data
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.
Vision-Augmented Molecular Dynamics Simulation of Nanoindentation
Directory of Open Access Journals (Sweden)
Rajab Al-Sayegh
2015-01-01
Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.
A Dynamical Training and Design Simulator for Active Catheters
Directory of Open Access Journals (Sweden)
Georges Dumont
2004-12-01
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.
Dynamic simulation of collisions of heavy high-speed trucks with concrete barriers
International Nuclear Information System (INIS)
Itoh, Yoshito; Liu, Chunlu; Kusama, Ryuichi
2007-01-01
Real vehicle collision experiments on full-scale road safety barriers are important to determine the outcome of a vehicle versus barrier impact accident. However, such experiments require large investment of time and money. Numerical simulation has therefore been imperative as an alternative method for testing concrete barriers. In this research, spring subgrade models were first developed to simulate the ground boundary of concrete barriers. Both heavy trucks and concrete barriers were modeled using finite element methods (FEM) to simulate dynamic collision performances. Comparison of the results generated from computer simulations and on-site full-scale experiments demonstrated that the developed models could be applied to simulate the collision of heavy trucks with concrete barriers to provide the data to design new road safety barriers and analyze existing ones
Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides
International Nuclear Information System (INIS)
Ogawa, Hiroshi
2015-01-01
Highlights: • Hydrogen–dislocation interaction was simulated by molecular dynamics method. • Different distribution of H atoms were observed at edge and screw dislocation. • Planner distribution of hydrogen may be caused by partialized edge dislocation. • Hydrogen diffusivity was reduced in both edge and screw dislocation models. • Pipe diffusion was observed for edge dislocation but not for screw dislocation. - Abstract: Kinetics of interstitial hydrogen atoms near dislocation cores were analyzed by atomistic simulation. Classical molecular dynamics method was applied to model structures of edge and screw dislocations in α-phase vanadium hydride. Simulation showed that hydrogen atoms aggregate near dislocation cores. The spatial distribution of hydrogen has a planner shape at edge dislocation due to dislocation partialization, and a cylindrical shape at screw dislocation. Simulated self-diffusion coefficients of hydrogen atoms in dislocation models were a half- to one-order lower than that of dislocation-free model. Arrhenius plot of self-diffusivity showed slightly different activation energies for edge and screw dislocations. Directional dependency of hydrogen diffusion near dislocation showed high and low diffusivity along edge and screw dislocation lines, respectively, hence so called ‘pipe diffusion’ possibly occur at edge dislocation but does not at screw dislocation
Simulated impacts of insect defoliation on forest carbon dynamics
International Nuclear Information System (INIS)
Medvigy, D; Clark, K L; Skowronski, N S; Schäfer, K V R
2012-01-01
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. (letter)
A hybrid algorithm for parallel molecular dynamics simulations
Mangiardi, Chris M.; Meyer, R.
2017-10-01
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.
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...... 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...... zones connected by open areas with pressure and buoyancy driven air flow. The two programs are interconnected in an iterative procedure. The paper shows also an evaluation of the air quality in the main area of the buildings based on CFD predictions. It is shown that an interconnection between a CFD...
Molecular dynamics simulation of bubble nucleation in explosive boiling
International Nuclear Information System (INIS)
Zou Yu; Chinese Academy of Sciences, Beijing; Huai Xiulan; Liang Shiqiang
2009-01-01
Molecular dynamics (MD) simulation is carried out for the bubble nucleation of liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. The results indicate that the initial equilibrium temperature of liquid and molecular cluster size affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of bubble nucleation, the potential energy of the system slowly increases. In the bubble nucleation of explosive boiling, the lower the initial equilibrium temperature, the larger the size of the molecular cluster, and the more the heat transferred into the system of the simulation cell, causing the increase potential energy in a larger range. (authors)
A Dynamic Compliance Cervix Phantom Robot for Latent Labor Simulation.
Luk, Michelle Jennifer; Lobb, Derek; Smith, James Andrew
2018-05-09
Physical simulation systems are commonly used in training of midwifery and obstetrics students, but none of these systems offers a dynamic compliance aspect that would make them more truly representative of cervix ripening. In this study, we introduce a unique soft robot phantom that simulates the cervix softening during the latent labor phase of birth. This proof-of-concept robotic phantom can be dilated by 1 cm and effaced by 35% through the application of a Foley catheter-like loading mechanism. Furthermore, psychophysics trials demonstrate how untrained subjects can identify hard and soft states of the phantom with specificities of 91% and 87%, respectively. Both results indicated the appropriateness for application of this soft robot technology to birth training simulators.
Lightweight computational steering of very large scale molecular dynamics simulations
International Nuclear Information System (INIS)
Beazley, D.M.
1996-01-01
We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages
Beam dynamics simulations using a parallel version of PARMILA
International Nuclear Information System (INIS)
Ryne, R.D.
1996-01-01
The computer code PARMILA has been the primary tool for the design of proton and ion linacs in the United States for nearly three decades. Previously it was sufficient to perform simulations with of order 10000 particles, but recently the need to perform high resolution halo studies for next-generation, high intensity linacs has made it necessary to perform simulations with of order 100 million particles. With the advent of massively parallel computers such simulations are now within reach. Parallel computers already make it possible, for example, to perform beam dynamics calculations with tens of millions of particles, requiring over 10 GByte of core memory, in just a few hours. Also, parallel computers are becoming easier to use thanks to the availability of mature, Fortran-like languages such as Connection Machine Fortran and High Performance Fortran. We will describe our experience developing a parallel version of PARMILA and the performance of the new code
Beam dynamics simulations using a parallel version of PARMILA
International Nuclear Information System (INIS)
Ryne, Robert
1996-01-01
The computer code PARMILA has been the primary tool for the design of proton and ion linacs in the United States for nearly three decades. Previously it was sufficient to perform simulations with of order 10000 particles, but recently the need to perform high resolution halo studies for next-generation, high intensity linacs has made it necessary to perform simulations with of order 100 million particles. With the advent of massively parallel computers such simulations are now within reach. Parallel computers already make it possible, for example, to perform beam dynamics calculations with tens of millions of particles, requiring over 10 GByte of core memory, in just a few hours. Also, parallel computers are becoming easier to use thanks to the availability of mature, Fortran-like languages such as Connection Machine Fortran and High Performance Fortran. We will describe our experience developing a parallel version of PARMILA and the performance of the new code. (author)
Dynamic simulation of the 2 MWt slowpoke heating reactor
International Nuclear Information System (INIS)
Tseng, C.M.; Lepp, R.M.
1982-04-01
A 2 MWt SLOWPOKE reactor, intended for commercial space heating, is being developed at the Chalk River Nuclear Laboratories. A small-signal dynamic simulation of this reactor, without closed-loop control, was developed. Basic equations were used to describe the physical phenomena in each kf the eight reactor subsystems. These equations were then linearized about the normal operation conditions and rearranged in a dimensionless form for implementation. The overall simulation is non-linear. Slow transient responses (minutes to days) of the simulation to both reactivity and temperature perturbations were measured at full power. In all cases the system reached a new steady state in times varying from 12 h to 250 h. These results illustrate the benefits of the inherent negative reactivity feedback of this reactor concept. The addition of closed-loop control using core outlet temperature as the controlled variable to move a beryllium reflector is also examined
Molecular dynamics simulation of gold cluster growth during sputter deposition
Energy Technology Data Exchange (ETDEWEB)
Abraham, J. W., E-mail: abraham@theo-physik.uni-kiel.de; Bonitz, M., E-mail: bonitz@theo-physik.uni-kiel.de [Institut für Theoretische Physik und Astrophysik, Christian-Albrechts-Universität zu Kiel, Leibnizstraße 15, D-24098 Kiel (Germany); Strunskus, T.; Faupel, F. [Institut für Materialwissenschaft, Lehrstuhl für Materialverbunde, Christian-Albrechts-Universität zu Kiel, Kaiserstraße 2, D-24143 Kiel (Germany)
2016-05-14
We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.
Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.
2017-03-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.
Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I
Energy Technology Data Exchange (ETDEWEB)
Schmalz, Mark S
2011-07-24
Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G} for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient
Global Dynamic Numerical Simulations of Plate Tectonic Reorganizations
Morra, G.; Quevedo, L.; Butterworth, N.; Matthews, K. J.; Müller, D.
2010-12-01
We use a new numerical approach for global geodynamics to investigate the origin of present global plate motion and to identify the causes of the last two global tectonic reorganizations occurred about 50 and 100 million years ago (Ma) [1]. While the 50 Ma event is the most well-known global plate-mantle event, expressed by the bend in the Hawaiian-Emperor volcanic chain, a prominent plate reorganization at about 100 Ma, although presently little studied, is clearly indicated by a major bend in the fracture zones in the Indian Ocean and by a change in Pacific plate motion [2]. Our workflow involves turning plate reconstructions into surface meshes that are subsequently employed as initial conditions for global Boundary Element numerical models. The tectonic setting that anticipates the reorganizations is processed with the software GPlates, combining the 3D mesh of the paleo-plate morphology and the reconstruction of paleo-subducted slabs, elaborated from tectonic history [3]. All our models involve the entire planetary system, are fully dynamic, have free surface, are characterized by a spectacular computational speed due to the simultaneous use of the multi-pole algorithm and the Boundary Element formulation and are limited only by the use of sharp material property variations [4]. We employ this new tool to unravel the causes of plate tectonic reorganizations, producing and comparing global plate motion with the reconstructed ones. References: [1] Torsvik, T., Müller, R.D., Van der Voo, R., Steinberger, B., and Gaina, C., 2008, Global Plate Motion Frames: Toward a unified model: Reviews in Geophysics, VOL. 46, RG3004, 44 PP., 2008 [2] Wessel, P. and Kroenke, L.W. Pacific absolute plate motion since 145 Ma: An assessment of the fixed hot spot hypothesis. Journal of Geophysical Research, Vol 113, B06101, 2008 [3] L. Quevedo, G. Morra, R. D. Mueller. Parallel Fast Multipole Boundary Element Method for Crustal Dynamics, Proceeding 9th World Congress and 4th Asian
Monte Carlo-based simulation of dynamic jaws tomotherapy
Energy Technology Data Exchange (ETDEWEB)
Sterpin, E.; Chen, Y.; Chen, Q.; Lu, W.; Mackie, T. R.; Vynckier, S. [Department of Molecular Imaging, Radiotherapy and Oncology, Universite Catholique de Louvain, 54 Avenue Hippocrate, 1200 Brussels, Belgium and Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705 (United States); TomoTherapy Inc., 1240 Deming Way, Madison, Wisconsin 53717 (United States); 21 Century Oncology., 1240 D' onofrio, Madison, Wisconsin 53719 (United States); TomoTherapy Inc., 1240 Deming Way, Madison, Wisconsin 53717 and Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705 (United States); Department of Radiotherapy and Oncology, Universite Catholique de Louvain, St-Luc University Hospital, 10 Avenue Hippocrate, 1200 Brussels (Belgium)
2011-09-15
Purpose: Original TomoTherapy systems may involve a trade-off between conformity and treatment speed, the user being limited to three slice widths (1.0, 2.5, and 5.0 cm). This could be overcome by allowing the jaws to define arbitrary fields, including very small slice widths (<1 cm), which are challenging for a beam model. The aim of this work was to incorporate the dynamic jaws feature into a Monte Carlo (MC) model called TomoPen, based on the MC code PENELOPE, previously validated for the original TomoTherapy system. Methods: To keep the general structure of TomoPen and its efficiency, the simulation strategy introduces several techniques: (1) weight modifiers to account for any jaw settings using only the 5 cm phase-space file; (2) a simplified MC based model called FastStatic to compute the modifiers faster than pure MC; (3) actual simulation of dynamic jaws. Weight modifiers computed with both FastStatic and pure MC were compared. Dynamic jaws simulations were compared with the convolution/superposition (C/S) of TomoTherapy in the ''cheese'' phantom for a plan with two targets longitudinally separated by a gap of 3 cm. Optimization was performed in two modes: asymmetric jaws-constant couch speed (''running start stop,'' RSS) and symmetric jaws-variable couch speed (''symmetric running start stop,'' SRSS). Measurements with EDR2 films were also performed for RSS for the formal validation of TomoPen with dynamic jaws. Results: Weight modifiers computed with FastStatic were equivalent to pure MC within statistical uncertainties (0.5% for three standard deviations). Excellent agreement was achieved between TomoPen and C/S for both asymmetric jaw opening/constant couch speed and symmetric jaw opening/variable couch speed, with deviations well within 2%/2 mm. For RSS procedure, agreement between C/S and measurements was within 2%/2 mm for 95% of the points and 3%/3 mm for 98% of the points, where dose is
Monte Carlo-based simulation of dynamic jaws tomotherapy
International Nuclear Information System (INIS)
Sterpin, E.; Chen, Y.; Chen, Q.; Lu, W.; Mackie, T. R.; Vynckier, S.
2011-01-01
Purpose: Original TomoTherapy systems may involve a trade-off between conformity and treatment speed, the user being limited to three slice widths (1.0, 2.5, and 5.0 cm). This could be overcome by allowing the jaws to define arbitrary fields, including very small slice widths (<1 cm), which are challenging for a beam model. The aim of this work was to incorporate the dynamic jaws feature into a Monte Carlo (MC) model called TomoPen, based on the MC code PENELOPE, previously validated for the original TomoTherapy system. Methods: To keep the general structure of TomoPen and its efficiency, the simulation strategy introduces several techniques: (1) weight modifiers to account for any jaw settings using only the 5 cm phase-space file; (2) a simplified MC based model called FastStatic to compute the modifiers faster than pure MC; (3) actual simulation of dynamic jaws. Weight modifiers computed with both FastStatic and pure MC were compared. Dynamic jaws simulations were compared with the convolution/superposition (C/S) of TomoTherapy in the ''cheese'' phantom for a plan with two targets longitudinally separated by a gap of 3 cm. Optimization was performed in two modes: asymmetric jaws-constant couch speed (''running start stop,'' RSS) and symmetric jaws-variable couch speed (''symmetric running start stop,'' SRSS). Measurements with EDR2 films were also performed for RSS for the formal validation of TomoPen with dynamic jaws. Results: Weight modifiers computed with FastStatic were equivalent to pure MC within statistical uncertainties (0.5% for three standard deviations). Excellent agreement was achieved between TomoPen and C/S for both asymmetric jaw opening/constant couch speed and symmetric jaw opening/variable couch speed, with deviations well within 2%/2 mm. For RSS procedure, agreement between C/S and measurements was within 2%/2 mm for 95% of the points and 3%/3 mm for 98% of the points, where dose is greater than 30% of the prescription dose (gamma analysis
Lee, Kyoung O; Holmes, Thomas W; Calderon, Adan F; Gardner, Robin P
2012-05-01
Using a Monte Carlo (MC) simulation, random walks were used for pebble tracking in a two-dimensional geometry in the presence of a biased gravity field. We investigated the effect of viscosity damping in the presence of random Gaussian fluctuations. The particle tracks were generated by Molecular Dynamics (MD) simulation for a Pebble Bed Reactor. The MD simulations were conducted in the interaction of noncohesive Hertz-Mindlin theory where the random walk MC simulation has a correlation with the MD simulation. This treatment can easily be extended to include the generation of transient gamma-ray spectra from a single pebble that contains a radioactive tracer. Then the inverse analysis thereof could be made to determine the uncertainty of the realistic measurement of transient positions of that pebble by any given radiation detection system designed for that purpose. Copyright Â© 2011 Elsevier Ltd. All rights reserved.
DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS
JUFFER, AH; BERENDSEN, HJC
1993-01-01
A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the
Marrink, SJ; Mark, AE
2003-01-01
Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at
A Numerical Approach for Hybrid Simulation of Power System Dynamics Considering Extreme Icing Events
DEFF Research Database (Denmark)
Chen, Lizheng; Zhang, Hengxu; Wu, Qiuwei
2017-01-01
numerical simulation scheme integrating icing weather events with power system dynamics is proposed to extend power system numerical simulation. A technique is developed to efficiently simulate the interaction of slow dynamics of weather events and fast dynamics of power systems. An extended package for PSS...
Dynamic simulation of a forced circulation evaporating system
International Nuclear Information System (INIS)
Lee, J.S.; Lee, K.J.
1993-01-01
A dynamic simulation program has been developed to simulate the forced circulation evaporating system of the Kori PWR Power Plant in Korea which is used to treat liquid waste containing boric acid. Energy and mass balances for the vapor and liquid phases are used to describe the interaction among system components such as the vapor body, heater jacket and condenser. In order to simulate entrainment carryover in the sieve tray column and wire mesh pad, Kister's and Carpenter-Othmer's correlations are adopted, respectively. A new correlation formula is also suggested to simulate the geometric effect of the vapor body. A fuzzy heuristic controller and conventional controllers such as P (proportional), PI (proportional-integral) and PID (proportional-integral-derivative) controls are incorporated to observe their responses to a given disturbance. The simulations show good agreement with the real operation data. It is also identified that the vapor velocity or flow rate in the sieve tray column determines the system decontamination factor (DF), and that the longer the vapor body is, the less entrainment carryover occurs out of the vapor body. In addition, the wire mesh pad is identified as maintaining very high deentrainment efficiency even though the vapor velocity may show large fluctuations. With respect to system control, the fuzzy heuristic controller approaches a new steady state faster than conventional controllers. Also the fuzzy controller maintains higher DF during transients and is stronger against time delay in the control components. (Author)
Towards realistic molecular dynamics simulations of grain boundary mobility
International Nuclear Information System (INIS)
Zhou, J.; Mohles, V.
2011-01-01
In order to investigate grain boundary migration by molecular dynamics (MD) simulations a new approach involving a crystal orientation-dependent driving force has been developed by imposing an appropriate driving force on grain boundary atoms and enlarging the effective range of driving force. The new approach has been validated by the work of the driving force associated with the motion of grain boundaries. With the new approach the relation between boundary migration velocity and driving force is found to be nonlinear, as was expected from rate theory for large driving forces applied in MD simulations. By evaluating grain boundary mobility nonlinearly for a set of symmetrical tilt boundaries in aluminum at high temperature, high-angle grain boundaries were shown to move much faster than low-angle grain boundaries. This agrees well with experimental findings for recrystallization and grain growth. In comparison with the available data the simulated mobility of a 38.21 o Σ7 boundary was found to be significantly lower than other MD simulation results and comparable with the experimental values. Furthermore, the average volume involved during atomic jumps for boundary migration is determined in MD simulations for the first time. The large magnitude of the volume indicates that grain boundary migration is accomplished by the correlated motion of atom groups.
Dissipative particle dynamics simulations for biological tissues: rheology and competition
International Nuclear Information System (INIS)
Basan, Markus; Prost, Jacques; Joanny, Jean-François; Elgeti, Jens
2011-01-01
In this work, we model biological tissues using a simple, mechanistic simulation based on dissipative particle dynamics. We investigate the continuum behavior of the simulated tissue and determine its dependence on the properties of the individual cell. Cells in our simulation adhere to each other, expand in volume, divide after reaching a specific size checkpoint and undergo apoptosis at a constant rate, leading to a steady-state homeostatic pressure in the tissue. We measure the dependence of the homeostatic state on the microscopic parameters of our model and show that homeostatic pressure, rather than the unconfined rate of cell division, determines the outcome of tissue competitions. Simulated cell aggregates are cohesive and round up due to the effect of tissue surface tension, which we measure for different tissues. Furthermore, mixtures of different cells unmix according to their adhesive properties. Using a variety of shear and creep simulations, we study tissue rheology by measuring yield stresses, shear viscosities, complex viscosities as well as the loss tangents as a function of model parameters. We find that cell division and apoptosis lead to a vanishing yield stress and fluid-like tissues. The effects of different adhesion strengths and levels of noise on the rheology of the tissue are also measured. In addition, we find that the level of cell division and apoptosis drives the diffusion of cells in the tissue. Finally, we present a method for measuring the compressibility of the tissue and its response to external stress via cell division and apoptosis
ChainMail based neural dynamics modeling of soft tissue deformation for surgical simulation.
Zhang, Jinao; Zhong, Yongmin; Smith, Julian; Gu, Chengfan
2017-07-20
Realistic and real-time modeling and simulation of soft tissue deformation is a fundamental research issue in the field of surgical simulation. In this paper, a novel cellular neural network approach is presented for modeling and simulation of soft tissue deformation by combining neural dynamics of cellular neural network with ChainMail mechanism. The proposed method formulates the problem of elastic deformation into cellular neural network activities to avoid the complex computation of elasticity. The local position adjustments of ChainMail are incorporated into the cellular neural network as the local connectivity of cells, through which the dynamic behaviors of soft tissue deformation are transformed into the neural dynamics of cellular neural network. Experiments demonstrate that the proposed neural network approach is capable of modeling the soft tissues' nonlinear deformation and typical mechanical behaviors. The proposed method not only improves ChainMail's linear deformation with the nonlinear characteristics of neural dynamics but also enables the cellular neural network to follow the principle of continuum mechanics to simulate soft tissue deformation.
Dynamic simulation of motion effects in IMAT lung SBRT.
Zou, Wei; Yin, Lingshu; Shen, Jiajian; Corradetti, Michael N; Kirk, Maura; Munbodh, Reshma; Fang, Penny; Jabbour, Salma K; Simone, Charles B; Yue, Ning J; Rengan, Ramesh; Teo, Boon-Keng Kevin
2014-11-01
Intensity modulated arc therapy (IMAT) has been widely adopted for Stereotactic Body Radiotherapy (SBRT) for lung cancer. While treatment dose is optimized and calculated on a static Computed Tomography (CT) image, the effect of the interplay between the target and linac multi-leaf collimator (MLC) motion is not well described and may result in deviations between delivered and planned dose. In this study, we investigated the dosimetric consequences of the inter-play effect on target and organs at risk (OAR) by simulating dynamic dose delivery using dynamic CT datasets. Fifteen stage I non-small cell lung cancer (NSCLC) patients with greater than 10 mm tumor motion treated with SBRT in 4 fractions to a dose of 50 Gy were retrospectively analyzed for this study. Each IMAT plan was initially optimized using two arcs. Simulated dynamic delivery was performed by associating the MLC leaf position, gantry angle and delivered beam monitor units (MUs) for each control point with different respiratory phases of the 4D-CT using machine delivery log files containing time stamps of the control points. Dose maps associated with each phase of the 4D-CT dose were calculated in the treatment planning system and accumulated using deformable image registration onto the exhale phase of the 4D-CT. The original IMAT plans were recalculated on the exhale phase of the CT for comparison with the dynamic simulation. The dose coverage of the PTV showed negligible variation between the static and dynamic simulation. There was less than 1.5% difference in PTV V95% and V90%. The average inter-fraction and cumulative dosimetric effects among all the patients were less than 0.5% for PTV V95% and V90% coverage and 0.8 Gy for the OARs. However, in patients where target is close to the organs, large variations were observed on great vessels and bronchus for as much as 4.9 Gy and 7.8 Gy. Limited variation in target dose coverage and OAR constraints were seen for each SBRT fraction as well as over all
Miao, Linling; Young, Charles D.; Sing, Charles E.
2017-07-01
Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.
Molecular dynamics simulations of solutions at constant chemical potential
Perego, C.; Salvalaglio, M.; Parrinello, M.
2015-04-01
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.
Simulation error propagation for a dynamic rod worth measurement technique
International Nuclear Information System (INIS)
Kastanya, D.F.; Turinsky, P.J.
1996-01-01
KRSKO nuclear station, subsequently adapted by Westinghouse, introduced the dynamic rod worth measurement (DRWM) technique for measuring pressurized water reactor rod worths. This technique has the potential for reduced test time and primary loop waste water versus alternatives. The measurement is performed starting from a slightly supercritical state with all rods out (ARO), driving a bank in at the maximum stepping rate, and recording the ex-core detectors responses and bank position as a function of time. The static bank worth is obtained by (1) using the ex-core detectors' responses to obtain the core average flux (2) using the core average flux in the inverse point-kinetics equations to obtain the dynamic bank worth (3) converting the dynamic bank worth to the static bank worth. In this data interpretation process, various calculated quantities obtained from a core simulator are utilized. This paper presents an analysis of the sensitivity to the impact of core simulator errors on the deduced static bank worth
Analyzing, Modeling, and Simulation for Human Dynamics in Social Network
Directory of Open Access Journals (Sweden)
Yunpeng Xiao
2012-01-01
Full Text Available This paper studies the human behavior in the top-one social network system in China (Sina Microblog system. By analyzing real-life data at a large scale, we find that the message releasing interval (intermessage time obeys power law distribution both at individual level and at group level. Statistical analysis also reveals that human behavior in social network is mainly driven by four basic elements: social pressure, social identity, social participation, and social relation between individuals. Empirical results present the four elements' impact on the human behavior and the relation between these elements. To further understand the mechanism of such dynamic phenomena, a hybrid human dynamic model which combines “interest” of individual and “interaction” among people is introduced, incorporating the four elements simultaneously. To provide a solid evaluation, we simulate both two-agent and multiagent interactions with real-life social network topology. We achieve the consistent results between empirical studies and the simulations. The model can provide a good understanding of human dynamics in social network.
Dynamical properties of fractal networks: Scaling, numerical simulations, and physical realizations
International Nuclear Information System (INIS)
Nakayama, T.; Yakubo, K.; Orbach, R.L.
1994-01-01
This article describes the advances that have been made over the past ten years on the problem of fracton excitations in fractal structures. The relevant systems to this subject are so numerous that focus is limited to a specific structure, the percolating network. Recent progress has followed three directions: scaling, numerical simulations, and experiment. In a happy coincidence, large-scale computations, especially those involving array processors, have become possible in recent years. Experimental techniques such as light- and neutron-scattering experiments have also been developed. Together, they form the basis for a review article useful as a guide to understanding these developments and for charting future research directions. In addition, new numerical simulation results for the dynamical properties of diluted antiferromagnets are presented and interpreted in terms of scaling arguments. The authors hope this article will bring the major advances and future issues facing this field into clearer focus, and will stimulate further research on the dynamical properties of random systems
A spectral approach for discrete dislocation dynamics simulations of nanoindentation
Bertin, Nicolas; Glavas, Vedran; Datta, Dibakar; Cai, Wei
2018-07-01
We present a spectral approach to perform nanoindentation simulations using three-dimensional nodal discrete dislocation dynamics. The method relies on a two step approach. First, the contact problem between an indenter of arbitrary shape and an isotropic elastic half-space is solved using a spectral iterative algorithm, and the contact pressure is fully determined on the half-space surface. The contact pressure is then used as a boundary condition of the spectral solver to determine the resulting stress field produced in the simulation volume. In both stages, the mechanical fields are decomposed into Fourier modes and are efficiently computed using fast Fourier transforms. To further improve the computational efficiency, the method is coupled with a subcycling integrator and a special approach is devised to approximate the displacement field associated with surface steps. As a benchmark, the method is used to compute the response of an elastic half-space using different types of indenter. An example of a dislocation dynamics nanoindentation simulation with complex initial microstructure is presented.
Parareal in Time for Dynamic Simulations of Power Systems
Energy Technology Data Exchange (ETDEWEB)
Gurrala, Gurunath [ORNL; Dimitrovski, Aleksandar D [ORNL; Pannala, Sreekanth [ORNL; Simunovic, Srdjan [ORNL; Starke, Michael R [ORNL
2015-01-01
In recent years, there have been significant developments in parallel algorithms and high performance parallel computing platforms. Parareal in time algorithm has become popular for long transient simulations (e.g., molecular dynamics, fusion, reacting flows). Parareal is a parallel algorithm which divides the time interval into sub-intervals and solves them concurrently. This paper investigates the applicability of the parareal algorithm to power system dynamic simulations. Preliminary results on the application of parareal for multi-machine power systems are reported in this paper. Two widely used test systems, WECC 3-generator 9-bus system, New England 10-generator 39- bus system, is used to explore the effectiveness of the parareal. Severe 3 phase bus faults are simulated using both the classical and detailed models of multi-machine power systems. Actual Speedup of 5-7 times is observed assuming ideal parallelization. It has been observed that the speedup factors of the order of 20 can be achieved by using fast coarse approximations of power system models. Dependency of parareal convergence on fault duration and location has been observed.
Dynamic Simulation of Human Gait Model With Predictive Capability.
Sun, Jinming; Wu, Shaoli; Voglewede, Philip A
2018-03-01
In this paper, it is proposed that the central nervous system (CNS) controls human gait using a predictive control approach in conjunction with classical feedback control instead of exclusive classical feedback control theory that controls based on past error. To validate this proposition, a dynamic model of human gait is developed using a novel predictive approach to investigate the principles of the CNS. The model developed includes two parts: a plant model that represents the dynamics of human gait and a controller that represents the CNS. The plant model is a seven-segment, six-joint model that has nine degrees-of-freedom (DOF). The plant model is validated using data collected from able-bodied human subjects. The proposed controller utilizes model predictive control (MPC). MPC uses an internal model to predict the output in advance, compare the predicted output to the reference, and optimize the control input so that the predicted error is minimal. To decrease the complexity of the model, two joints are controlled using a proportional-derivative (PD) controller. The developed predictive human gait model is validated by simulating able-bodied human gait. The simulation results show that the developed model is able to simulate the kinematic output close to experimental data.
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel
International Nuclear Information System (INIS)
Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.
2011-01-01
This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12σ, 14σ and 16σ and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.
Huge-scale molecular dynamics simulation of multibubble nuclei
Watanabe, Hiroshi
2013-12-01
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.
Dynamic Simulation of Water Networks to Control and Reduce Physical Unaccounted-for Water
Directory of Open Access Journals (Sweden)
Nima Zorriasateyn
2005-09-01
Full Text Available A significant percentage of unaccounted-for water consists of leakage in water distribution networks in Iran. To detect leakage area with less costs and time spending and then identify the exact place of it with special instruments, would be economical and a better water resource management. In this research, a real case has been selected and examined with dynamic simulation using MIKE NET. The method that has been carried out in this research based on maximizing the correlation coefficient and minimizing the sum of error squares between pressure measured inputs (observed data and calculated pressure (by model. According to the results, dynamic simulation of municipal water distribution system can be used as a guide to determine the place and the amount of leakage.Thereby the area of large leakage can be simulated with appropriate accuracy through measured pressure. Therefor from management aspect, dynamic simulation can be used to decrease time consumption and to save costs for detecting leakage.
Development of the Object-Oriented Dynamic Simulation Models Using Visual C++ Freeware
Directory of Open Access Journals (Sweden)
Alexander I. Kozynchenko
2016-01-01
Full Text Available The paper mostly focuses on the methodological and programming aspects of developing a versatile desktop framework to provide the available basis for the high-performance simulation of dynamical models of different kinds and for diverse applications. So the paper gives some basic structure for creating a dynamical simulation model in C++ which is built on the Win32 platform with an interactive multiwindow interface and uses the lightweight Visual C++ Express as a free integrated development environment. The resultant simulation framework could be a more acceptable alternative to other solutions developed on the basis of commercial tools like Borland C++ or Visual C++ Professional, not to mention the domain specific languages and more specialized ready-made software such as Matlab, Simulink, and Modelica. This approach seems to be justified in the case of complex research object-oriented dynamical models having nonstandard structure, relationships, algorithms, and solvers, as it allows developing solutions of high flexibility. The essence of the model framework is shown using a case study of simulation of moving charged particles in the electrostatic field. The simulation model possesses the necessary visualization and control features such as an interactive input, real time graphical and text output, start, stop, and rate control.
EDITORIAL: Changes to Fluid Dynamics Research in 2009 Changes to Fluid Dynamics Research in 2009
Funakoshi, Mitsuaki
2009-02-01
Welcome to the first issue of the modified Fluid Dynamics Research (FDR) journal, which is now being published by IOP Publishing on behalf of the Japan Society of Fluid Mechanics. Since its launch in 1986, FDR has become a well-established international journal that publishes theoretical, numerical and experimental studies contributing to the fundamental understanding and application of fluid phenomena. It has also been an invaluable resource for physicists and researchers in engineering interested in problems relevant to the motion of fluids. From 2009, FDR will be edited by a new international Editorial Board, with the strong intention of establishing the journal further and bringing it to a wider audience. In this new-look FDR, which will be published six times per year, readers will find several special sections containing high quality invited reviews and papers written by leading researchers who have been selected by the international Editorial Board. This is in addition to the regular papers on a variety of topical subjects by active researchers in the field. As before, there are no publication charges for standard articles, and now article numbering has been adopted, enabling accepted papers to be published online more quickly, ahead of print publication. In order to maintain a balanced and up-to-date perspective, we welcome feedback from our readers regarding the content of the journal, as well as suggestions for topics to cover and areas to highlight. Finally, I would like to thank our authors, members of the international Editorial Board, and the staff at IOP Publishing for producing this first issue. We hope you will enjoy reading this renewed and exciting journal for the international fluid dynamics community.
Simulation of generation and dynamics of polarization singularities with circular Airy beams.
Ye, Dong; Peng, Xinyu; Zhou, Muchun; Xin, Yu; Song, Minmin
2017-11-01
The generation and dynamics of polarization singularities have been underresearched for years, while the focusing property of the topological configuration has not been explored much. In this paper, we simulated the generation of low-order polarization singularities with a circular Airy beam and explored the focusing property of the synthetic light field during propagation due to the autofocusing of the component. Our work researched the focusing properties of the polarization singularity configuration, which may help to develop its application prospect.
SIMULATED ANIMAL EXPERIMENTS IN TEACHING AND RESEARCH
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Chirag B. Mistry, Shreya M. Shah, Jagatkumar D. Bhatt
2015-07-01
Full Text Available Animal experiments are of paramount importance in the pre-clinical screening of new chemical entity. On the other hand, various regulatory guidelines for animal experiments are becoming more stringent in the face of worldwide protests by animal rights activists. Moreover, simulated animal experiments’ softwares are being developed and they can be implemented in the postgraduate and graduate students’ curriculum for demonstration of standard physiological and pharmacological principles compared to real time animal experiments. In fact, implementation of virtual experiment will decrease hand on experience of animal experiments among medical students, but after medical graduation, animal experiment is lest utilized during their day to day clinical practice. Similarly, in case of postgraduate pharmacology curriculum, computer based virtual animal experiments can facilitate teaching and learning in a short span of time with various protocols, without sacrificing any animal for already established experimental outcomes.
Emulation of dynamic simulators with application to hydrology
Energy Technology Data Exchange (ETDEWEB)
Machac, David, E-mail: david.machac@eawag.ch [Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Systems Analysis, Integrated Assessment and Modelling, 8600 Dübendorf (Switzerland); ETH Zurich, Department of Environmental Systems Science, 8092 Zurich (Switzerland); Reichert, Peter [Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Systems Analysis, Integrated Assessment and Modelling, 8600 Dübendorf (Switzerland); ETH Zurich, Department of Environmental Systems Science, 8092 Zurich (Switzerland); Albert, Carlo [Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Systems Analysis, Integrated Assessment and Modelling, 8600 Dübendorf (Switzerland)
2016-05-15
Many simulation-intensive tasks in the applied sciences, such as sensitivity analysis, parameter inference or real time control, are hampered by slow simulators. Emulators provide the opportunity of speeding up simulations at the cost of introducing some inaccuracy. An emulator is a fast approximation to a simulator that interpolates between design input–output pairs of the simulator. Increasing the number of design data sets is a computationally demanding way of improving the accuracy of emulation. We investigate the complementary approach of increasing emulation accuracy by including knowledge about the mechanisms of the simulator into the formulation of the emulator. To approximately reproduce the output of dynamic simulators, we consider emulators that are based on a system of linear, ordinary or partial stochastic differential equations with a noise term formulated as a Gaussian process of the parameters to be emulated. This stochastic model is then conditioned to the design data so that it mimics the behavior of the nonlinear simulator as a function of the parameters. The drift terms of the linear model are designed to provide a simplified description of the simulator as a function of its key parameters so that the required corrections by the conditioned Gaussian process noise are as small as possible. The goal of this paper is to compare the gain in accuracy of these emulators by enlarging the design data set and by varying the degree of simplification of the linear model. We apply this framework to a simulator for the shallow water equations in a channel and compare emulation accuracy for emulators based on different spatial discretization levels of the channel and for a standard non-mechanistic emulator. Our results indicate that we have a large gain in accuracy already when using the simplest mechanistic description by a single linear reservoir to formulate the drift term of the linear model. Adding some more reservoirs does not lead to a significant
A Newtonian Development of the Mean-Axis Dynamics with Example and Simulation
Keyes, Sally Ann
Mean-axis models of flight dynamics for flexible aircraft are being utilized more frequently in dynamics and controls research. The mean-axis equations of motion are traditionally developed with Lagrangian mechanics and are typically simplified using assumptions regarding the effects of elastic deformation. Although widely accepted in literature, the formulation and assumptions may be confusing to a user outside of the flight dynamics field. In this thesis, the equations of motion are derived from first principles utilizing Newtonian mechanics. Using this framework, the formulation offers new insight into the equations of motion and explanations for the assumptions. A three-lumped-mass idealization of a rolling flexible aircraft is presented as an example of the mean-axis equations of motion. The example is used to investigate the effects of common simplifying assumptions. The equations of motion are developed without any such assumptions, and simulation results allow for a comparison of the exact and simplified dynamics.
Massobrio, Carlo; Bernasconi, Marco; Salmon, Philip S
2015-01-01
This book is a unique reference work in the area of atomic-scale simulation of glasses. For the first time, a highly selected panel of about 20 researchers provides, in a single book, their views, methodologies and applications on the use of molecular dynamics as a tool to describe glassy materials. The book covers a wide range of systems covering ""traditional"" network glasses, such as chalcogenides and oxides, as well as glasses for applications in the area of phase change materials. The novelty of this work is the interplay between molecular dynamics methods (both at the classical and firs
Co-Simulation Control of Robot Arm Dynamics in ADAMS and MATLAB
Luo Haitao; Liu Yuwang; Chen Zhengcang; Leng Yuquan
2013-01-01
The main objective of this study is how to quickly establish the virtual prototyping model of robot arm system and effectively solve trajectory tracking control for a given signal. Taking the 2-DOF robot arm as an example, a co-simulation control method is introduced to research multi-body dynamics. Using Newton-Euler and Lagrange method, respectively establish the dynamics model of robot arm and verify the correctness of equations. Firstly, the physical model of robot arm was built by PROE a...
Agent-based simulation in entrepreneurship research
Yang, S.-J.S.; Chandra, Y.
2009-01-01
Agent-based modeling (ABM) has wide applications in natural and social sciences yet it has not been widely applied in entrepreneurship research. We discuss the nature of ABM, its position among conventional methodologies and then offer a roadmap for developing, testing and extending theories of
Kounalakis, M.; Langford, N. K.; Sagastizabal, R.; Dickel, C.; Bruno, A.; Luthi, F.; Thoen, D. J.; Endo, A.; Dicarlo, L.
The field dipole coupling of quantum light and matter, described by the quantum Rabi model, leads to exotic phenomena when the coupling strength g becomes comparable or larger than the atom and photon frequencies ωq , r. In this ultra-strong coupling regime, excitations are not conserved, leading to collapse-revival dynamics in atom and photon parity and Schrödinger-cat-like atom-photon entanglement. We realize a quantum simulation of the Rabi model using a transmon qubit coupled to a resonator. In this first part, we describe our analog-digital approach to implement up to 90 symmetric Trotter steps, combining single-qubit gates with the Jaynes-Cummings interaction naturally present in our circuit QED system. Controlling the phase of microwave pulses defines a rotating frame and enables simulation of arbitrary parameter regimes of the Rabi model. We demonstrate measurements of qubit parity dynamics showing revivals at g /ωr > 0 . 8 for ωq = 0 and characteristic dynamics for nondegenerate ωq from g / 4 to g. Funding from the EU FP7 Project ScaleQIT, an ERC Grant, the Dutch Research Organization NWO, and Microsoft Research.
Computer simulation of population dynamics inside the urban environment
Andreev, A. S.; Inovenkov, I. N.; Echkina, E. Yu.; Nefedov, V. V.; Ponomarenko, L. S.; Tikhomirov, V. V.
2017-12-01
In this paper using a mathematical model of the so-called “space-dynamic” approach we investigate the problem of development and temporal dynamics of different urban population groups. For simplicity we consider an interaction of only two population groups inside a single urban area with axial symmetry. This problem can be described qualitatively by a system of two non-stationary nonlinear differential equations of the diffusion type with boundary conditions of the third type. The results of numerical simulations show that with a suitable choice of the diffusion coefficients and interaction functions between different population groups we can receive different scenarios of population dynamics: from complete displacement of one population group by another (originally more “aggressive”) to the “peaceful” situation of co-existence of them together.
Phase portrait methods for verifying fluid dynamic simulations
Energy Technology Data Exchange (ETDEWEB)
Stewart, H.B.
1989-01-01
As computing resources become more powerful and accessible, engineers more frequently face the difficult and challenging engineering problem of accurately simulating nonlinear dynamic phenomena. Although mathematical models are usually available, in the form of initial value problems for differential equations, the behavior of the solutions of nonlinear models is often poorly understood. A notable example is fluid dynamics: while the Navier-Stokes equations are believed to correctly describe turbulent flow, no exact mathematical solution of these equations in the turbulent regime is known. Differential equations can of course be solved numerically, but how are we to assess numerical solutions of complex phenomena without some understanding of the mathematical problem and its solutions to guide us
Dynamic Monte Carlo simulations of radiatively accelerated GRB fireballs
Chhotray, Atul; Lazzati, Davide
2018-05-01
We present a novel Dynamic Monte Carlo code (DynaMo code) that self-consistently simulates the Compton-scattering-driven dynamic evolution of a plasma. We use the DynaMo code to investigate the time-dependent expansion and acceleration of dissipationless gamma-ray burst fireballs by varying their initial opacities and baryonic content. We study the opacity and energy density evolution of an initially optically thick, radiation-dominated fireball across its entire phase space - in particular during the Rph matter-dominated fireballs due to Thomson scattering. We quantify the new phases by providing analytical expressions of Lorentz factor evolution, which will be useful for deriving jet parameters.
Molecular dynamics simulations of cluster fission and fusion processes
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia
2004-01-01
Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...
Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts
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Kazuaki Z. Takahashi
2017-01-01
Full Text Available Long-timescale molecular dynamics simulations were performed to estimate the actual physical nature of a united-atom model of polyethylene (PE. Several scaling laws for representative polymer properties are compared to theoretical predictions. Internal structure results indicate a clear departure from theoretical predictions that assume ideal chain statics. Chain motion deviates from predictions that assume ideal motion of short chains. With regard to linear viscoelasticity, the presence or absence of entanglements strongly affects the duration of the theoretical behavior. Overall, the results indicate that Gaussian statics and dynamics are not necessarily established for real atomistic models of PE. Moreover, the actual physical nature should be carefully considered when using atomistic models for applications that expect typical polymer behaviors.
Modeling and simulation of dynamic voltage restorer in power system
International Nuclear Information System (INIS)
Abdel Aziz, M.A.A.M.
2012-01-01
There are many loads subjected to several Power Quality Problems such as voltage sags/swells, unbalance, harmonics distortion, and short interruption. These loads encompass a wide range of equipment which are very sensitive to voltage disturbances. The Dynamic Voltage Restorer (DVR) has recently been introduced to protect sensitive loads from voltage sags and other voltage disturbances in addition to this, it mitigates current harmonics distortion. It is a series connected power electronic based device. It is considered as one of the most efficient and effective solutions. Its appeal includes smaller size and fast dynamic response to disturbances. This work describes a proposal of the DVR to improve power quality distribution (medium voltage) system. The control of the compensation voltage and harmonics cancellation in the DVR is based on Adaptive Noise Canceling (ANC) technique. Simulation results carried out by PSCAD/EMTDC to investigate the performance of the proposed method.
Modelization and numerical simulation of atmospheric aerosols dynamics
International Nuclear Information System (INIS)
Debry, Edouard
2004-01-01
Chemical-transport models are now able to describe in a realistic way gaseous pollutants behavior in the atmosphere. Nevertheless atmospheric pollution also exists as a fine suspended particles, called aerosols which interact with gaseous phase, solar radiation, and have their own dynamic behavior. The goal of this thesis is the modelization and numerical simulation of the General Dynamic Equation of aerosols (GDE). Part I deals with some theoretical aspects of aerosol modelization. Part II is dedicated to the building of one size resolved aerosol model (SIREAM). In part III we perform the reduction of this model in order to use it in dispersion models as POLAIR3D. Several modelization issues are still opened: organic aerosol matter, externally mixed aerosols, coupling with turbulent mixing, and nano-particles. (author) [fr
Molecular dynamics simulations of glycerol glass-forming liquid
International Nuclear Information System (INIS)
Blieck, J.; Affouard, F.; Bordat, P.; Lerbret, A.; Descamps, M.
2005-01-01
Structural and dynamical properties of liquid glycerol have been investigated by Molecular Dynamics simulations. An improved model based on a slight reparametrisation of the all-atoms AMBER force field used in [R. Chelli, P. Procacci, G. Cardini, R.G.D. Valle, S. Califano, Phys. Chem. Chem. Phys. 1 (1999) 871] is presented. The structure remains satisfactory, qualitatively similar to that obtained from the original model. This new model is also found to reproduce significantly better the diffusion coefficient and the correlations times as they can be deduced from neutron spin echo (NSE) experiments. Structural heterogeneities revealed as a pre-peak of the static structure factor S(Q) close to Q ∼ 0.6 A -1 are observed. Our results are also found compatible with predictions of the Mode Coupling Theory
Enhancing protein adsorption simulations by using accelerated molecular dynamics.
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Christian Mücksch
Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.
Cost of QCD simulations with nf = 2 dynamical Wilson fermions
International Nuclear Information System (INIS)
Lippert, Th.
2002-01-01
Cost estimates for simulations of full QCD with n f = 2 Wilson fermions by hybrid Monte Carlo are presented. The extrapolations are based on the average number of iterations, N it , of the iterative solver within the fermionic part of the HMC molecular dynamics, which is closely related to the minimal eigenvalue of M † M. The cost formula is determined as a product of the scaling functions of iterative solver and integrated autocorrelation time of 1/N it as function of the inverse lattice pseudoscalar mass. Timings by SESAM/TχL allow to fix the pre-factor. It is demonstrated that a 2-flavor dynamical determination of light hadron masses with a statistical precision comparable to the corresponding quenched results from CP-PACS is the appropriate task for a 100 Tflops system
Beam dynamics simulation of a double pass proton linear accelerator
Directory of Open Access Journals (Sweden)
Kilean Hwang
2017-04-01
Full Text Available A recirculating superconducting linear accelerator with the advantage of both straight and circular accelerator has been demonstrated with relativistic electron beams. The acceleration concept of a recirculating proton beam was recently proposed [J. Qiang, Nucl. Instrum. Methods Phys. Res., Sect. A 795, 77 (2015NIMAER0168-900210.1016/j.nima.2015.05.056] and is currently under study. In order to further support the concept, the beam dynamics study on a recirculating proton linear accelerator has to be carried out. In this paper, we study the feasibility of a two-pass recirculating proton linear accelerator through the direct numerical beam dynamics design optimization and the start-to-end simulation. This study shows that the two-pass simultaneous focusing without particle losses is attainable including fully 3D space-charge effects through the entire accelerator system.
Dynamic modelling and simulation for control of a cylindrical robotic manipulator
International Nuclear Information System (INIS)
Iqbal, A.; Athar, S.M.
1995-03-01
In this report a dynamic model for the three degrees-of-freedom cylindrical manipulator, INFOMATE has been developed. Although the robot dynamics are highly coupled and non-linear, the developed model is relatively straight forward and compact for control engineering and simulation applications. The model has been simulated using the graphical simulation package SIMULINK. Different aspects of INFOMATE associated with forward dynamics, inverse dynamics and control have been investigated by performing various simulation experiments. These simulation experiments confirm the accuracy and applicability of the dynamic robot model. (author) 18 figs
TIRE MODELS USED IN VEHICLE DYNAMIC APPLICATIONS AND THEIR USING IN VEHICLE ACCIDENT SIMULATIONS
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Osman ELDOĞAN
1995-01-01
Full Text Available Wheel model is very important in vehicle modelling, it is because the contact between vehicle and road is achieved by wheel. Vehicle models can be dynamic models which are used in vehicle design, they can also be models used in accident simulations. Because of the importance of subject, many studies including theoretical, experimental and mixed type have been carried out. In this study, information is given about development of wheel modelling and research studies and also use of these modellings in traffic accident simulations.
A novel dynamic cardiac simulator utilizing pneumatic artificial muscle.
Liu, Hao; Yan, Jie; Zhou, Yuanyuan; Li, Hongyi; Li, Changji
2013-01-01
With the development of methods and skills of minimally invasive surgeries, equipments for doctors' training and practicing are in high demands. Especially for the cardiovascular surgeries, operators are requested to be familiar with the surgical environment of a beating heart. In this paper, we present a new dynamic cardiac simulator utilizing pneumatic artificial muscle to realize heartbeat. It's an artificial left ventricular of which the inner chamber is made of thermoplastic elastomers (TPE) with an anatomical structure of the real human heart. It is covered by another layer of material forming the artificial muscle which actuates the systole and diastole uniformly and omnidirectionally as the cardiac muscle does. Preliminary experiments were conducted to evaluate the performance of the simulator. The results indicated that the pressure at the terminal of the aorta could be controlled within the range of normal human systolic pressure, which quantitatively validated the new actuating mode of the heart-beating is effective.
Computational Fluid Dynamics (CFD) simulations of a Heisenberg Vortex Tube
Bunge, Carl; Sitaraman, Hariswaran; Leachman, Jake
2017-11-01
A 3D Computational Fluid Dynamics (CFD) simulation of a Heisenberg Vortex Tube (HVT) is performed to estimate cooling potential with cryogenic hydrogen. The main mechanism driving operation of the vortex tube is the use of fluid power for enthalpy streaming in a highly turbulent swirl in a dual-outlet tube. This enthalpy streaming creates a temperature separation between the outer and inner regions of the flow. Use of a catalyst on the peripheral wall of the centrifuge enables endothermic conversion of para-ortho hydrogen to aid primary cooling. A κ- ɛ turbulence model is used with a cryogenic, non-ideal equation of state, and para-orthohydrogen species evolution. The simulations are validated with experiments and strategies for parametric optimization of this device are presented.
Coding considerations for standalone molecular dynamics simulations of atomistic structures
Ocaya, R. O.; Terblans, J. J.
2017-10-01
The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.
Molecular dynamics simulation of deformation twin in rocksalt vanadium nitride
International Nuclear Information System (INIS)
Fu, Tao; Peng, Xianghe; Zhao, Yinbo; Li, Tengfei; Li, Qibin; Wang, Zhongchang
2016-01-01
We perform molecular dynamics simulation of nano-indentation with a cylindrical indenter to investigate the formation mechanism of deformation twin in vanadium nitride (VN) with a rocksalt structure. We find that the deformation twins occur during the loading stage, and subsequently conduct a systematic analysis of nucleation, propagation and thickening of a deformation twin. We find that the nucleation of a partial dislocation and its propagation to form a stacking fault are premise of deformation twin formation. The sequential nucleation and propagation of partial dislocation on adjacent parallel {111} planes are found to cause the thickening of the deformation twin. Moreover, the deformation twins can exist in VN at room temperature. - Highlights: • MD simulations of indentation are performed to study the deformation twin in VN. • The deformation twins can occur in VN during the loading stage. • The nucleation, propagation and thickening of a deformation twin are analyzed. • The deformation twins can exist in VN at room temperature.
Fluid Dynamics of Magnetic Nanoparticles in Simulated Blood Vessels
Blue, Lauren; Sewell, Mary Kathryn; Brazel, Christopher S.
2008-11-01
Magnetic nanoparticles (MNPs) can be used to locally target therapies and offer the benefit of using an AC magnetic field to combine hyperthermia treatment with the triggered release of therapeutic agents. Here, we investigate localization of MNPs in a simulated environment to understand the relationship between magnetic field intensity and bulk fluid dynamics to determine MNP retention in a simulated blood vessel. As MNPs travel through blood vessels, they can be slowed or trapped in a specific area by applying a magnetic field. Magnetic cobalt ferrite nanoparticles were synthesized and labeled with a fluorescent rhodamine tag to visualize patterns in a flow cell, as monitored by a fluorescence microscope. Particle retention was determined as a function of flow rate, concentration, and magnetic field strength. Understanding the relationship between magnetic field intensity, flow behavior and nanoparticle characteristics will aid in the development of therapeutic systems specifically targeted to diseased tissue.
Fast stochastic algorithm for simulating evolutionary population dynamics
Tsimring, Lev; Hasty, Jeff; Mather, William
2012-02-01
Evolution and co-evolution of ecological communities are stochastic processes often characterized by vastly different rates of reproduction and mutation and a coexistence of very large and very small sub-populations of co-evolving species. This creates serious difficulties for accurate statistical modeling of evolutionary dynamics. In this talk, we introduce a new exact algorithm for fast fully stochastic simulations of birth/death/mutation processes. It produces a significant speedup compared to the direct stochastic simulation algorithm in a typical case when the total population size is large and the mutation rates are much smaller than birth/death rates. We illustrate the performance of the algorithm on several representative examples: evolution on a smooth fitness landscape, NK model, and stochastic predator-prey system.
Molecular dynamics simulations of field emission from a planar nanodiode
Energy Technology Data Exchange (ETDEWEB)
Torfason, Kristinn; Valfells, Agust; Manolescu, Andrei [School of Science and Engineering, Reykjavik University, Menntavegur 1, IS-101 Reykjavik (Iceland)
2015-03-15
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 [Y. Y. Lau, Y. Liu, and R. K. Parker, Phys. Plasmas 1, 2082 (1994) and Y. Feng and J. P. Verboncoeur, Phys. Plasmas 13, 073105 (2006)]. 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.
Dynamic simulations of many-body electrostatic self-assembly
Lindgren, Eric B.; Stamm, Benjamin; Maday, Yvon; Besley, Elena; Stace, A. J.
2018-03-01
Two experimental studies relating to electrostatic self-assembly have been the subject of dynamic computer simulations, where the consequences of changing the charge and the dielectric constant of the materials concerned have been explored. One series of calculations relates to experiments on the assembly of polymer particles that have been subjected to tribocharging and the simulations successfully reproduce many of the observed patterns of behaviour. A second study explores events observed following collisions between single particles and small clusters composed of charged particles derived from a metal oxide composite. As before, observations recorded during the course of the experiments are reproduced by the calculations. One study in particular reveals how particle polarizability can influence the assembly process. This article is part of the theme issue `Modern theoretical chemistry'.
Molecular dynamics simulation of thermal conductivities of superlattice nanowires
Institute of Scientific and Technical Information of China (English)
YANG; Juekuan(杨决宽); CHEN; Yunfei(陈云飞); YAN; Jingping(颜景平)
2003-01-01
Nonequilibrium molecular dynamics simulations were carried out to investigate heat transfer in superlattice nanowires. Results show that for fixed period length superlattice nanowires, the ratio of the total interfacial thermal resistance to the total thermal resistance and the effective thermal conductivities are invariant with the changes in interface numbers. Increasing the period length leads to an increase in the average interfacial thermal resistance, which indicates that the interfacial thermal resistance depends not only on the materials that constitute the alternating segments of superlattice nanowires, but also on the lattice strain throughout the segments. The modification of the lattice structure due to the lattice mismatch should be taken into account in the acoustic mismatch model. Simulation results also demonstrated the size confinement effect on the thermal conductivities for low dimensional structures, i.e. the thermal conductivities and the interfacial thermal resistance increase as the nanowire cross-sectional area increases.
THE DYNAMICS OF A DISTRIBUTION SYSTEM SIMULATED ON A SPREADSHEET
Directory of Open Access Journals (Sweden)
R. Reinecke
2012-01-01
Full Text Available
ENGLISH ABSTRACT: The dynamics of a typical production-distribution system, namely from manufacturer to distributors to retailers has been simulated with the aid of Lotus 123 on a personal computer. The original simulation program DYNAr10 was run on an IBM 1620 mainframe computer but we successfully converted it to run on a personal computer using LOTUS 123.
This paper deals with problems encountered in using the present MS-DOS limited PC machines to run application programmes written for earlier mainframe machines. It is also shown that results very comparable with those obtained on mainframe machines can be generated on a simple PC.
AFRIKAANSE OPSOMMING: Hierdie referaat beskryf die ervaring van magisterstudente met die omskakeling van die simulasieprogram DYNAMO vir die ondersoek van die dinamika van industriele stelsels van hoofraamrekenaar na 'n persoonlike rekenaar.
Dynamic simulation of the in-tank precipitation process
International Nuclear Information System (INIS)
Hang, T.; Shanahan, K.L.; Gregory, M.V.; Walker, D.D.
1993-01-01
As part of the High-Level Waste Tank Farm at the Savannah River Site (SRS), the In-Tank Precipitation (ITP) facility was designed to decontaminate the radioactive waste supernate by removing cesium as precipitated cesium tetraphenylborate. A dynamic computer model of the ITP process was developed using SPEEDUP TM software to provide guidance in the areas of operation and production forecast, production scheduling, safety, air emission, and process improvements. The model performs material balance calculations in all phase (solid, liquid, and gas) for 50 key chemical constituents to account for inventory accumulation, depletion, and dilution. Calculations include precipitation, benzene radiolytic reactions, evaporation, dissolution, adsorption, filtration, and stripping. To control the ITP batch operation a customized FORTRAN program was generated and linked to SPEEDUP TM simulation This paper summarizes the model development and initial results of the simulation study
An evaluation of Dynamic TOPMODEL for low flow simulation
Coxon, G.; Freer, J. E.; Quinn, N.; Woods, R. A.; Wagener, T.; Howden, N. J. K.
2015-12-01
Hydrological models are essential tools for drought risk management, often providing input to water resource system models, aiding our understanding of low flow processes within catchments and providing low flow predictions. However, simulating low flows and droughts is challenging as hydrological systems often demonstrate threshold effects in connectivity, non-linear groundwater contributions and a greater influence of water resource system elements during low flow periods. These dynamic processes are typically not well represented in commonly used hydrological models due to data and model limitations. Furthermore, calibrated or behavioural models may not be effectively evaluated during more extreme drought periods. A better understanding of the processes that occur during low flows and how these are represented within models is thus required if we want to be able to provide robust and reliable predictions of future drought events. In this study, we assess the performance of dynamic TOPMODEL for low flow simulation. Dynamic TOPMODEL was applied to a number of UK catchments in the Thames region using time series of observed rainfall and potential evapotranspiration data that captured multiple historic droughts over a period of several years. The model performance was assessed against the observed discharge time series using a limits of acceptability framework, which included uncertainty in the discharge time series. We evaluate the models against multiple signatures of catchment low-flow behaviour and investigate differences in model performance between catchments, model diagnostics and for different low flow periods. We also considered the impact of surface water and groundwater abstractions and discharges on the observed discharge time series and how this affected the model evaluation. From analysing the model performance, we suggest future improvements to Dynamic TOPMODEL to improve the representation of low flow processes within the model structure.
Aeroelastic Dynamics Simulation of Two BaffleBased Connected Shells
Directory of Open Access Journals (Sweden)
G. A. Shcheglov
2015-01-01
Full Text Available The present work is an extention study of aeroelastic vibrations of thin-walled structures with a spatial subsonic flow. An original algorithm for solving complex conjugated aeroelasticity problem, allowing to carry out direct numerical simulation of structural oscillations in the spatial flow of an incompressible medium are developed and tested. On the basis of this simulation study of the spectrum comes the driving forces acting on the flow in a spatial component elastic structure mounted on an impenetrable screen.Currently, updating the mathematical models of unsteady loads that act on the spacepurpose elastic designs such as launch vehicles, service tower installed on the launch pad is a challenge. We consider two thin-walled cantilevered rotating shells connected by a system of elastic couplings, installed next to the impenetrable baffle so that the axes of rotation are perpendicular to the baffle. Dynamics of elastic system is investigated numerically, using the vortex element method with the spatial separated flow of an incompressible medium. A feature of the algorithm is the common commercial complex MSC Patran / Nastran which is used in preparing data to calculate the shell dynamics thereby allowing to consider very complex dynamic schemes.The work performs the first calculations of the model problem concerning the forced oscillations of two coupled cylindrical shells in the flow of an incompressible medium. Comparing the load spectra for the elastic and absolutely rigid structure has shown that the frequency spectra vary slightly. Further calculations are required in which it will be necessary to increase the duration of the calculations, sampling in construction of design scheme, and given the large number of vibration modes that require increasing computing power.Experience in calculating aeroelastic dynamics of complex elastic structures taking into account the screen proved to be successful as a whole, thereby allowing to turn to
New Dynamic Library of Reverse Osmosis Plants with Fault Simulation
International Nuclear Information System (INIS)
Luis, Palacin; Fernando, Tadeo; Cesar, de Prada; Elfil, Hamza
2009-01-01
This paper presents an update of a dynamic library of reverse osmosis plants (ROSIM). This library has been developed in order to be used for optimization, simulation, controller testing or fault detection strategies and a simple fault tolerant control is tested. ROSIM is based in a set of components representing the different units of a typical reverse osmosis plant (as sand filters, cartridge filters, exchanger energy recoveries, pumps, membranes, storage tanks, control systems, valves, etc.). Different types of fouling (calcium carbonate, iron hydroxide, biofouling) have been added and the mathematical model of the reverse osmosis membranes, proposed in the original library, has been improved.
Molecular Dynamics Simulations on Evaporation of Droplets with Dissolved Salts
Jin-Liang Xu; Min Chen; Xiao-Dong Wang; Bing-Bing Wang
2013-01-01
Molecular dynamics simulations are used to study the evaporation of water droplets containing either dissolved LiCl, NaCl or KCl salt in a gaseous surrounding (nitrogen) with a constant high temperature of 600 K. The initial droplet has 298 K temperature and contains 1,120 water molecules, 0, 40, 80 or 120 salt molecules. The effects of the salt type and concentration on the evaporation rate are examined. Three stages with different evaporation rates are observed for all cases. In the initial...
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
International Nuclear Information System (INIS)
Mugnai, Mauro L.; Elber, Ron
2015-01-01
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide
Numerical simulation of the RISOe1-airfoil dynamic stall
Energy Technology Data Exchange (ETDEWEB)
Bertagnolio, F.; Soerensen, N. [Risoe National Lab., Wind Energy and Atmospheric Physics Dept., Roskilde (Denmark)
1997-12-31
In this paper we are concerned with the numerical computation of the dynamic stall that occur in the viscous flowfield over an airfoil. These results are compared to experimental data that were obtained with the new designed RISOe1-airfoil, both for a motionless airfoil and for a pitching motion. Moreover, we present some numerical computations of the plunging and lead-lag motions. We also investigate the possibility of using the pitching motion to simulate the plunging and lead-lag situations. (au)
Molecular dynamics computer simulations based on NMR data
International Nuclear Information System (INIS)
Vlieg, J. de.
1989-01-01
In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs
Investigations of Solar Prominence Dynamics Using Laboratory Simulations
International Nuclear Information System (INIS)
Bellan, Paul M.
2008-01-01
Laboratory experiments simulating many of the dynamical features of solar coronal loops have been carried out. These experiments manifest collimation, kinking, jet flows, and S-shapes. Diagnostics include high-speed photography and x-ray detectors. Two loops having opposite or the same magnetic helicity polarities have been merged and it is found that counter-helicity merging provides much greater x-ray emission. A non-MHD particle orbit instability has been discovered whereby ions going in the opposite direction of the current flow direction can be ejected from a magnetic flux tube.
Dynamic computer simulation of the Fort St. Vrain steam turbines
International Nuclear Information System (INIS)
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
Game-based dynamic simulations supporting technical education and training
Directory of Open Access Journals (Sweden)
Tore BjÃƒÂ¸lseth
2006-04-01
Full Text Available Educational games may improve learning by taking advantage of the new knowledge and skills of todayÃ¢Â€Â™s students obtained from extensive use of interactive games. This paper describes how interactive dynamic simulators of advanced technical systems and phenomena can be shaped and adapted as games and competitions supporting technical education and training. Some selected examples at different educational levels are shown, from vocational training to university level courses. The potential benefit and perceived learning effect of this approach is also described and underpinned from comprehensive user feedback.
Design of Experiment Using Simulation of a Discrete Dynamical System
Directory of Open Access Journals (Sweden)
Mašek Jan
2016-12-01
Full Text Available The topic of the presented paper is a promising approach to achieve optimal Design of Experiment (DoE, i.e. spreading of points within a design domain, using a simulation of a discrete dynamical system of interacting particles within an n-dimensional design space. The system of mutually repelling particles represents a physical analogy of the Audze-Eglājs (AE optimization criterion and its periodical modification (PAE, respectively. The paper compares the performance of two approaches to implementation: a single-thread process using the JAVA language environment and a massively parallel solution employing the nVidia CUDA platform.
Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals
International Nuclear Information System (INIS)
Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon
2000-01-01
We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the direction form intersecting stacking faults by slippage along {111} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society
International Nuclear Information System (INIS)
Chang, Ji Woon; Shin, Young Joon; Lee, Tae Hoon; Lee, Ki Young; Kim, Yong Wan; Chang, Jong Hwa; Youn, Cheung
2011-01-01
The Sulfur-Iodine (SI) cycle which can produce hydrogen by using nuclear heat consists of a Bunsen reaction (Section 1), a sulfur acid concentration and decomposition (Section 2), and a hydriodic acid concentration and decomposition (Section 3). The heat required in the SI process can be supplied through an intermediate heat exchanger (IHX) by a Very High Temperature Gas Cooled Reactor (VHTR). The Korea Atomic Energy Research Institute-Dynamic Simulation Code (KAERI-DySCo) based on the Visual C++ is an integration application software that simulates the dynamic behavior of the SI process. KAERI-DySCo was prepared to solve dynamic problem of the seven chemical reactors which consist of Sections 2 and 3. Section 3 is the key part of the SI process, because the strong non-ideality and the partial immiscibility of the binary HI.H 2 O and the ternary HI.I 2 .H 2 O (HIX solution) mixture make it difficult to model and simulate the dynamic behavior of the system. Therefore, it is necessary to compose separately a dynamic simulation program for Section 3 in KAERI-DySCo optimization. In this paper, a simulation program to analyze the dynamic behavior of Section 3 is introduced using the prepared KAERI-DySCo, and results of dynamic simulation are represented by running the program
Description of waste pretreatment and interfacing systems dynamic simulation model
International Nuclear Information System (INIS)
Garbrick, D.J.; Zimmerman, B.D.
1995-05-01
The Waste Pretreatment and Interfacing Systems Dynamic Simulation Model was created to investigate the required pretreatment facility processing rates for both high level and low level waste so that the vitrification of tank waste can be completed according to the milestones defined in the Tri-Party Agreement (TPA). In order to achieve this objective, the processes upstream and downstream of the pretreatment facilities must also be included. The simulation model starts with retrieval of tank waste and ends with vitrification for both low level and high level wastes. This report describes the results of three simulation cases: one based on suggested average facility processing rates, one with facility rates determined so that approximately 6 new DSTs are required, and one with facility rates determined so that approximately no new DSTs are required. It appears, based on the simulation results, that reasonable facility processing rates can be selected so that no new DSTs are required by the TWRS program. However, this conclusion must be viewed with respect to the modeling assumptions, described in detail in the report. Also included in the report, in an appendix, are results of two sensitivity cases: one with glass plant water recycle steams recycled versus not recycled, and one employing the TPA SST retrieval schedule versus a more uniform SST retrieval schedule. Both recycling and retrieval schedule appear to have a significant impact on overall tank usage
Shear test on viscoelastic granular material using Contact Dynamics simulations
Quezada, Juan Carlos; Sagnol, Loba; Chazallon, Cyrille
2017-06-01
By means of 3D contact dynamic simulations, the behavior of a viscoelastic granular material under shear loading is investigated. A viscoelastic fluid phase surrounding the solid particles is simulated by a contact model acting between them. This contact law was implemented in the LMGC90 software, based on the Burgers model. This model is able to simulate also the effect of creep relaxation. To validate the proposed contact model, several direct shear tests were performed, experimentally and numerically using the Leutner device. The numerical samples were created using spheres with two particle size distribution, each one identified for two layers from a road structure. Our results show a reasonable agreement between experimental and numerical data regarding the strain-stress evolution curves and the stress levels measured at failure. The proposed model can be used to simulate the mechanical behavior of multi-layer road structure and to study the influence of traffic on road deformation, cracking and particles pull-out induced by traffic loading.
The computer simulation of 3d gas dynamics in a gas centrifuge
Borman, V. D.; Bogovalov, S. V.; Borisevich, V. D.; Tronin, I. V.; Tronin, V. N.
2016-09-01
We argue on the basis of the results of 2D analysis of the gas flow in gas centrifuges that a reliable calculation of the circulation of the gas and gas content in the gas centrifuge is possible only in frameworks of 3D numerical simulation of gas dynamics in the gas centrifuge (hereafter GC). The group from National research nuclear university, MEPhI, has created a computer code for 3D simulation of the gas flow in GC. The results of the computer simulations of the gas flows in GC are presented. A model Iguassu centrifuge is explored for the simulations. A nonaxisymmetric gas flow is produced due to interaction of the hypersonic rotating flow with the scoops for extraction of the product and waste flows from the GC. The scoops produce shock waves penetrating into a working camera of the GC and form spiral waves there.
The computer simulation of 3d gas dynamics in a gas centrifuge
International Nuclear Information System (INIS)
Borman, V D; Bogovalov, S V; Borisevich, V D; Tronin, I V; Tronin, V N
2016-01-01
We argue on the basis of the results of 2D analysis of the gas flow in gas centrifuges that a reliable calculation of the circulation of the gas and gas content in the gas centrifuge is possible only in frameworks of 3D numerical simulation of gas dynamics in the gas centrifuge (hereafter GC). The group from National research nuclear university, MEPhI, has created a computer code for 3D simulation of the gas flow in GC. The results of the computer simulations of the gas flows in GC are presented. A model Iguassu centrifuge is explored for the simulations. A nonaxisymmetric gas flow is produced due to interaction of the hypersonic rotating flow with the scoops for extraction of the product and waste flows from the GC. The scoops produce shock waves penetrating into a working camera of the GC and form spiral waves there. (paper)
Rajendiran, Nivedita; Durrant, Jacob D
2018-05-05
Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting-edge rendering techniques. We expect Pyrite-generated images to appeal to students and non-specialists alike. A copy of the plugin is available at http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
HVAC-DYNAMIC; A training simulator for dynamic analysis of HVAC plants
Energy Technology Data Exchange (ETDEWEB)
Heintz, M; Novakovic, V [SINTEF Division of Applied Thermodynamic, HVAC Group, Trondheim (Norway); Oegaard, O [SINTEF Division of Automatic Control, Trondheim (Norway); Brustad, G [Computer Aided Modelling, CAMO A/S, Trondheim (Norway)
1989-01-01
HVAC-DYNAMIC is a software tool for the dynamic simulation of Heating, Ventilation and Air Conditioning (HVAC) plants. The program is designed to be used by HVAC engineers during design or troubleshooting of plants and by plant operators in their training. The program is based on a set of the most-used HVAC plant configurations and requires only a minimum of knowledge in numeric methods and programming. A brief presentation of the program structure and examples showing some of the application of the program are given. 4 figs., 4 refs.
HVAC-DYNAMIC: a training simulator for dynamic analysis of HVAC plants
Directory of Open Access Journals (Sweden)
Morten Heintz
1989-07-01
Full Text Available HVAC-DYNAMIC is a software tool for the dynamic simulation of Heating, Ventilation and Air Conditioning (HVAC plants. The program is designed to be used by HVAC engineers during design or troubleshooting of plants and by plant operators in their training. The program is based on a set of the most-used HVAC plant configurations and requires only a minimum of knowledge in numeric methods and programming. A brief presentation of the program structure and examples showing some of the application of the program are given.
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.
2012-01-01
In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...
Research Summary 3-D Computational Fluid Dynamics (CFD) Model Of The Human Respiratory System
The U.S. EPA’s Office of Research and Development (ORD) has developed a 3-D computational fluid dynamics (CFD) model of the human respiratory system that allows for the simulation of particulate based contaminant deposition and clearance, while being adaptable for age, ethnicity,...
A Report on the Research and Development of Instructional Simulation.
West, Charles K.; And Others
The purpose of this report is to communicate findings on current knowledge of simulation design, development, and evaluation. Research on this project was guided by questions posed by the Defense Systems Management College in Fort Belvoir, Virginia. These questions fall into three categories: the constituents of good instructional simulations, the…
Games and Simulations in Online Learning: Research and Development Frameworks
Gibson, David; Aldrich, Clark; Prensky, Marc
2007-01-01
Games and Simulations in Online Learning: Research and Development Frameworks examines the potential of games and simulations in online learning, and how the future could look as developers learn to use the emerging capabilities of the Semantic Web. It presents a general understanding of how the Semantic Web will impact education and how games and…
International Nuclear Information System (INIS)
Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.
2011-01-01
Highlights: → Molecular Dynamics codes implemented on GPUs have achieved two-order of magnitude computational accelerations. → Brownian Dynamics and Dissipative Particle Dynamics simulations require a large number of random numbers per time step. → We introduce a method for generating small batches of pseudorandom numbers distributed over many threads of calculations. → With this method, Dissipative Particle Dynamics is implemented on a GPU device without requiring thread-to-thread communication. - Abstract: Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.
Cooperative research in space geodesy and crustal dynamics
1994-01-01
This research grant, which covered the period of July 1991 to August 1994, was concerned with a variety of topics within the geodesy and crustal dynamics fields. The specific topics of this grant included satellite tracking and gravity field determinations and crustal dynamics (this concentrated of space geodetic site stability for VLBI sites). Summaries of the specific research projects are included along with a list of publications and presentations supported by this research grant.
International Nuclear Information System (INIS)
Su, Mingze; Zhao, Haibo; Ma, Jinchen
2015-01-01
Highlights: • CFD simulation of a 5 kW_t_h CLC reactor of coal was conducted. • Gas leakage, flow pattern and combustion efficiency of the reactor was analyzed. • Optimal condition was achieved based on operation characteristics understanding. - Abstract: A dual circulation fluidized bed system is widely accepted for chemical looping combustion (CLC) for enriching CO_2 from the utilization of fossil fuels. Due to the limitations of the measurement, the details of multiphase reactive flows in the interconnected fluidized bed reactors are difficult to obtain. Computational Fluid Dynamics (CFD) simulation provides a promising method to understand the hydrodynamics, chemical reaction, and heat and mass transfers in CLC reactors, which are very important for the rational design, optimal operation, and scaling-up of the CLC system. In this work, a 5 kW_t_h coal-fired CLC dual circulation fluidized bed system, which was developed by our research group, was first simulated for understanding gas leakage, flow pattern and combustion efficiency. The simulation results achieved good agreement with the experimental measurements, which validates the simulation model. Subsequently, to improve the combustion efficiency, a new operation condition was simulated by increasing the reactor temperature and decreasing the coal feeding. An improvement in the combustion efficiency was attained, and the simulation results for the new operation condition were also validated by the experimental measurements in the same CLC combustor. All of the above processes demonstrated the validity and usefulness of the simulation results to improve the CLC reactor operation.
Hybrid neuro-heuristic methodology for simulation and control of dynamic systems over time interval.
Woźniak, Marcin; Połap, Dawid
2017-09-01
Simulation and positioning are very important aspects of computer aided engineering. To process these two, we can apply traditional methods or intelligent techniques. The difference between them is in the way they process information. In the first case, to simulate an object in a particular state of action, we need to perform an entire process to read values of parameters. It is not very convenient for objects for which simulation takes a long time, i.e. when mathematical calculations are complicated. In the second case, an intelligent solution can efficiently help on devoted way of simulation, which enables us to simulate the object only in a situation that is necessary for a development process. We would like to present research results on developed intelligent simulation and control model of electric drive engine vehicle. For a dedicated simulation method based on intelligent computation, where evolutionary strategy is simulating the states of the dynamic model, an intelligent system based on devoted neural network is introduced to control co-working modules while motion is in time interval. Presented experimental results show implemented solution in situation when a vehicle transports things over area with many obstacles, what provokes sudden changes in stability that may lead to destruction of load. Therefore, applied neural network controller prevents the load from destruction by positioning characteristics like pressure, acceleration, and stiffness voltage to absorb the adverse changes of the ground. Copyright © 2017 Elsevier Ltd. All rights reserved.
Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica
2012-10-09
NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.
Dynamic stack testing and HiL simulation
Energy Technology Data Exchange (ETDEWEB)
Randolf, G. [GRandalytics, Honolulu, HI (United States)
2009-07-01
The applications for fuel cell and stack deployment have changed rapidly over the years, from stationary backup supplies to highly dynamic automotive power systems. As a result, testing must keep up in order to ensure mature products of high quality. A new breed of stack test stations has been designed, based on a newly developed single cell, high dynamic hardware-in-the-loop (HiL) simulator in order to meet the growing demand of realistic fuel cell testing scenarios for aviation and automotive industries. The paper described and illustrated the test station architecture and outline of communication nodes. The paper also described the voltage monitor and presented schematics of voltage monitoring modules. The basic requirements of the architecture that were presented included low latency; flexible communication with simulation targets and other data input/output nodes; scalability to various stack sizes; and, safety and reliability. It was concluded that first tests with the voltage monitoring system not only confirmed the design, high throughput and signal quality, but also suggested another application, namely a stack impedance spectrometer for each individual cell. 1 ref., 3 figs.
Lattice gas simulations of dynamical geometry in two dimensions.
Klales, Anna; Cianci, Donato; Needell, Zachary; Meyer, David A; Love, Peter J
2010-10-01
We present a hydrodynamic lattice gas model for two-dimensional flows on curved surfaces with dynamical geometry. This model is an extension to two dimensions of the dynamical geometry lattice gas model previously studied in one dimension. We expand upon a variation of the two-dimensional flat space Frisch-Hasslacher-Pomeau (FHP) model created by Frisch [Phys. Rev. Lett. 56, 1505 (1986)] and independently by Wolfram, and modified by Boghosian [Philos. Trans. R. Soc. London, Ser. A 360, 333 (2002)]. We define a hydrodynamic lattice gas model on an arbitrary triangulation whose flat space limit is the FHP model. Rules that change the geometry are constructed using the Pachner moves, which alter the triangulation but not the topology. We present results on the growth of the number of triangles as a function of time. Simulations show that the number of triangles grows with time as t(1/3), in agreement with a mean-field prediction. We also present preliminary results on the distribution of curvature for a typical triangulation in these simulations.
Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.
Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W
2011-09-22
Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.
Dynamic Simulation of Random Packing of Polydispersive Fine Particles
Ferraz, Carlos Handrey Araujo; Marques, Samuel Apolinário
2018-02-01
In this paper, we perform molecular dynamic (MD) simulations to study the two-dimensional packing process of both monosized and random size particles with radii ranging from 1.0 to 7.0 μm. The initial positions as well as the radii of five thousand fine particles were defined inside a rectangular box by using a random number generator. Both the translational and rotational movements of each particle were considered in the simulations. In order to deal with interacting fine particles, we take into account both the contact forces and the long-range dispersive forces. We account for normal and static/sliding tangential friction forces between particles and between particle and wall by means of a linear model approach, while the long-range dispersive forces are computed by using a Lennard-Jones-like potential. The packing processes were studied assuming different long-range interaction strengths. We carry out statistical calculations of the different quantities studied such as packing density, mean coordination number, kinetic energy, and radial distribution function as the system evolves over time. We find that the long-range dispersive forces can strongly influence the packing process dynamics as they might form large particle clusters, depending on the intensity of the long-range interaction strength.
Directory of Open Access Journals (Sweden)
Kei Moritsugu
Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.
Review of research on simulation engineering in FY2007
International Nuclear Information System (INIS)
2009-02-01
Research on simulation engineering for nuclear applications, based on the plan for meeting the mid-term goal of the Japan Atomic Energy Agency', has been performed at Center for Computational Science and e-Systems, Japan Atomic Energy Agency (CCSE/JAEA). CCSE established the committee consisting outside experts and authorities which does research evaluation and advices for the assistance of the research and development. This report summarizes the result of the evaluation by the committee on the research on simulation engineering performed at CCSE/JAEA in FY2007. (author)
Review of research on simulation engineering in FY2008
International Nuclear Information System (INIS)
2010-02-01
Research on simulation engineering for nuclear applications, based on 'the plan for meeting the mid-term goal of the Japan Atomic Energy Agency', has been performed at Center for Computational Science and e-Systems, Japan Atomic Energy Agency (CCSE/JAEA). CCSE established the committee consisting outside experts and authorities which does research evaluation and advices for the assistance of the research and development. This report summarizes the result of the evaluation by the committee on the research on simulation engineering performed at CCSE/JAEA in FY2008. (author)
Vlasov simulations of electron hole dynamics in inhomogeneous magnetic field
Kuzichev, Ilya; Vasko, Ivan; Agapitov, Oleksiy; Mozer, Forrest; Artemyev, Anton
2017-04-01
Electron holes (EHs) or phase space vortices are solitary electrostatic waves existing due to electrons trapped within EH electrostatic potential. Since the first direct observation [1], EHs have been widely observed in the Earth's magnetosphere: in reconnecting current sheets [2], injection fronts [3], auroral region [4], and many other space plasma systems. EHs have typical spatial scales up to tens of Debye lengths, electric field amplitudes up to hundreds of mV/m and propagate along magnetic field lines with velocities of about electron thermal velocity [5]. The role of EHs in energy dissipation and supporting of large-scale potential drops is under active investigation. The accurate interpretation of spacecraft observations requires understanding of EH evolution in inhomogeneous plasma. The critical role of plasma density gradients in EH evolution was demonstrated in [6] using PIC simulations. Interestingly, up to date no studies have addressed a role of magnetic field gradients in EH evolution. In this report, we use 1.5D gyrokinetic Vlasov code to demonstrate the critical role of magnetic field gradients in EH dynamics. We show that EHs propagating into stronger (weaker) magnetic field are decelerated (accelerated) with deceleration (acceleration) rate dependent on the magnetic field gradient. Remarkably, the reflection points of decelerating EHs are independent of the average magnetic field gradient in the system and depend only on the EH parameters. EHs are decelerated (accelerated) faster than would follow from the "quasi-particle" concept assuming that EH is decelerated (accelerated) entirely due to the mirror force acting on electrons trapped within EH. We demonstrate that EH propagation in inhomogeneous magnetic fields results in development of a net potential drop along an EH, which depends on the magnetic field gradient. The revealed features will be helpful for interpreting spacecraft observations and results of advanced particle simulations. In
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.
Yoo, Jejoong; Aksimentiev, Aleksei
2013-12-10
The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.
Statistical properties of dynamical systems – Simulation and abstract computation
International Nuclear Information System (INIS)
Galatolo, Stefano; Hoyrup, Mathieu; Rojas, Cristóbal
2012-01-01
Highlights: ► A survey on results about computation and computability on the statistical properties of dynamical systems. ► Computability and non-computability results for invariant measures. ► A short proof for the computability of the convergence speed of ergodic averages. ► A kind of “constructive” version of the pointwise ergodic theorem. - Abstract: We survey an area of recent development, relating dynamics to theoretical computer science. We discuss some aspects of the theoretical simulation and computation of the long term behavior of dynamical systems. We will focus on the statistical limiting behavior and invariant measures. We present a general method allowing the algorithmic approximation at any given accuracy of invariant measures. The method can be applied in many interesting cases, as we shall explain. On the other hand, we exhibit some examples where the algorithmic approximation of invariant measures is not possible. We also explain how it is possible to compute the speed of convergence of ergodic averages (when the system is known exactly) and how this entails the computation of arbitrarily good approximations of points of the space having typical statistical behaviour (a sort of constructive version of the pointwise ergodic theorem).
Molecular dynamics simulation of electron trapping in the sapphire lattice
International Nuclear Information System (INIS)
Rambaut, C.; Oh, K.H.; Fayeulle, S.; Kohanoff, J.
1995-10-01
Energy storage and release in dielectric materials can be described on the basis of the charge trapping mechanism. Most phenomenological aspects have been recently rationalized in terms of the space charge mode. Dynamical aspects are studied here by performing Molecular Dynamics simulations. We show that an excess electron introduced into the sapphire lattice (α -Al 2 O 3 ) can be trapped only at a limited number of sites. The energy gained by allowing the electron to localize in these sites is of the order of 4-5 eV, in good agreement with the results of the space charge model. Displacements of the neighboring ions due to the implanted charge are shown to be localized in a small region of about 5 A. Detrapping is observed at 250 K. The ionic displacements turn out to play an important role in modifying the potential landscape by lowering, in a dynamical way, the barriers that cause localization at low temperature. (author). 18 refs, 7 figs, 2 tabs
Probing into frictional contact dynamics by ultrasound and electrical simulations
Directory of Open Access Journals (Sweden)
Changshan Jin
2014-12-01
Full Text Available Friction arises in the interface of friction pair, and therefore, it is difficult to detect it. Ultrasonic means, as a NDT, is the correct alternative. This paper introduces a means of detecting dynamic contact and an interpretation of behaviors of dry friction. It has been determined that frictional surfaces have a specific property of dynamic response hardening (DRH. Dynamic response forces and oscillation arise during static–kinetic transition process. While the contact zone of sliding surfaces appears “hard” in motion, it appears “soft” at rest. Consequently, a separation of the surfaces occurs and the real area of contact is decreased as sliding velocity increases. This is the cause of F–v descent phenomenon. When the friction comes to a rest, the remaining process of DRH and micro-oscillation do not disappear instantaneously, instead they gradually return to their original static position. The contact area, therefore, is increased by rest period (F–T ascent characteristics. Based on analogies between a solid unit (η–m–k and an R-L-C circuit, the DRH is demonstrated by electrical simulations.