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 ...
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 ...
Perspective: Computer simulations of long time dynamics
Energy Technology Data Exchange (ETDEWEB)
Elber, Ron [Department of Chemistry, The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712 (United States)
2016-02-14
Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.
Computer simulation of confined liquid crystal dynamics
Webster, R E
2001-01-01
are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results...
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.
Computer simulation of multiple dynamic photorefractive gratings
DEFF Research Database (Denmark)
Buchhave, Preben
1998-01-01
The benefits of a direct visualization of space-charge grating buildup are described. The visualization is carried out by a simple repetitive computer program, which simulates the basic processes in the band-transport model and displays the result graphically or in the form of numerical data. The....... The simulation sheds light on issues that are not amenable to analytical solutions, such as the spectral content of the wave forms, cross talk in three-beam interaction, and the range of applications of the band-transport model. (C) 1998 Optical Society of America....
Osmosis : a molecular dynamics computer simulation study
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
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.
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...
Improved Pyrolysis Micro reactor Design via Computational Fluid Dynamics Simulations
2017-05-23
NUMBER (Include area code) 23 May 2017 Briefing Charts 25 April 2017 - 23 May 2017 Improved Pyrolysis Micro-reactor Design via Computational Fluid... PYROLYSIS MICRO-REACTOR DESIGN VIA COMPUTATIONAL FLUID DYNAMICS SIMULATIONS Ghanshyam L. Vaghjiani* DISTRIBUTION A: Approved for public release...Approved for public release, distribution unlimited. PA Clearance 17247 Chen-Source (>240 references from SciFinder as of 5/1/17): Flash pyrolysis
Dynamic computer simulation of the Fort St. Vrain steam turbines
Energy Technology Data Exchange (ETDEWEB)
Conklin, J.C.
1983-01-01
A computer simulation is described for the dynamic response of the Fort St. Vrain nuclear reactor regenerative intermediate- and low-pressure steam turbines. The fundamental computer-modeling assumptions for the turbines and feedwater heaters are developed. A turbine heat balance specifying steam and feedwater conditions at a given generator load and the volumes of the feedwater heaters are all that are necessary as descriptive input parameters. Actual plant data for a generator load reduction from 100 to 50% power (which occurred as part of a plant transient on November 9, 1981) are compared with computer-generated predictions, with reasonably good agreement.
Dynamic Factor Method of Computing Dynamic Mathematical Model for System Simulation
Institute of Scientific and Technical Information of China (English)
老大中; 吴娟; 杨策; 蒋滋康
2003-01-01
The computational methods of a typical dynamic mathematical model that can describe the differential element and the inertial element for the system simulation are researched. The stability of numerical solutions of the dynamic mathematical model is researched. By means of theoretical analysis, the error formulas, the error sign criteria and the error relationship criterion of the implicit Euler method and the trapezoidal method are given, the dynamic factor affecting the computational accuracy has been found, the formula and the methods of computing the dynamic factor are given. The computational accuracy of the dynamic mathematical model like this can be improved by use of the dynamic factor.
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.
Insights from molecular dynamics simulations for computational protein design.
Childers, Matthew Carter; Daggett, Valerie
2017-02-01
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
Using Soft Computing Technologies for the Simulation of LCAC Dynamics
2011-09-01
real-time, time-domain predictions of the vehicle’s dynamics as a function of the control signals given by the driver. Results are presented...free- running LCAC model, faster-than-real-time simulation, soft computing technology 1.0 INTRODUCTION The Maneuvering and Control Division (MCD...like all hovercraft , rides on a cushion of air. The air is supplied to the cushion by four centrifugal fans driven by the craft’s gas turbine
The very local Hubble flow: computer simulations of dynamical history
Chernin, A D; Valtonen, M J; Dolgachev, V P; Domozhilova, L M; Makarov, D I
2003-01-01
The phenomenon of the very local ($\\le3$ Mpc) Hubble flow is studied on the basis of the data of recent precision observations. A set of computer simulations is performed to trace the trajectories of the flow galaxies back in time to the epoch of the formation of the Local Group. It is found that the `initial conditions' of the flow are drastically different from the linear velocity-distance relation. The simulations enable also to recognize the major trends of the flow evolution and identify the dynamical role of universal antigravity produced by cosmic vacuum.
Computational Fluid Dynamics and Building Energy Performance Simulation
DEFF Research Database (Denmark)
Nielsen, Peter V.; Tryggvason, Tryggvi
An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...... simulation program requires a detailed description of the energy flow in the air movement which can be obtained by a CFD program. The paper describes an energy consumption calculation in a large building, where the building energy simulation program is modified by CFD predictions of the flow between three...... program and a building energy performance simulation program will improve both the energy consumption data and the prediction of thermal comfort and air quality in a selected area of the building....
Computer simulation of methanol exchange dynamics around cations and anions
Energy Technology Data Exchange (ETDEWEB)
Roy, Santanu; Dang, Liem X.
2016-03-03
In this paper, we present the first computer simulation of methanol exchange dynamics between the first and second solvation shells around different cations and anions. After water, methanol is the most frequently used solvent for ions. Methanol has different structural and dynamical properties than water, so its ion solvation process is different. To this end, we performed molecular dynamics simulations using polarizable potential models to describe methanol-methanol and ion-methanol interactions. In particular, we computed methanol exchange rates by employing the transition state theory, the Impey-Madden-McDonald method, the reactive flux approach, and the Grote-Hynes theory. We observed that methanol exchange occurs at a nanosecond time scale for Na+ and at a picosecond time scale for other ions. We also observed a trend in which, for like charges, the exchange rate is slower for smaller ions because they are more strongly bound to methanol. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.
Lightweight computational steering of very large scale molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Beazley, D.M. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Computer Science; Lomdahl, P.S. [Los Alamos National Lab., NM (United States)
1996-09-01
We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.
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.
Numerical simulation of landfill aeration using computational fluid dynamics.
Fytanidis, Dimitrios K; Voudrias, Evangelos A
2014-04-01
The present study is an application of Computational Fluid Dynamics (CFD) to the numerical simulation of landfill aeration systems. Specifically, the CFD algorithms provided by the commercial solver ANSYS Fluent 14.0, combined with an in-house source code developed to modify the main solver, were used. The unsaturated multiphase flow of air and liquid phases and the biochemical processes for aerobic biodegradation of the organic fraction of municipal solid waste were simulated taking into consideration their temporal and spatial evolution, as well as complex effects, such as oxygen mass transfer across phases, unsaturated flow effects (capillary suction and unsaturated hydraulic conductivity), temperature variations due to biochemical processes and environmental correction factors for the applied kinetics (Monod and 1st order kinetics). The developed model results were compared with literature experimental data. Also, pilot scale simulations and sensitivity analysis were implemented. Moreover, simulation results of a hypothetical single aeration well were shown, while its zone of influence was estimated using both the pressure and oxygen distribution. Finally, a case study was simulated for a hypothetical landfill aeration system. Both a static (steadily positive or negative relative pressure with time) and a hybrid (following a square wave pattern of positive and negative values of relative pressure with time) scenarios for the aeration wells were examined. The results showed that the present model is capable of simulating landfill aeration and the obtained results were in good agreement with corresponding previous experimental and numerical investigations.
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems.
Chiu, Matt; Herbordt, Martin C
2010-11-01
The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. In one part of the study, we systematically explore the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, and various other optimizations. We examine simplifications and find that some have little effect on simulation quality. In the other part, we present the first FPGA study of the filtering of particle pairs with nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA's resources. Overall, we find that, for an Altera Stratix-III EP3ES260, 8 force pipelines running at nearly 200 MHz can fit on the FPGA, and that they can perform at 95% efficiency. This results in an 80-fold per core speed-up for the short-range force, which is likely to make FPGAs highly competitive for MD.
Simulating Smoke Filling in Big Halls by Computational Fluid Dynamics
Directory of Open Access Journals (Sweden)
W. K. Chow
2011-01-01
Full Text Available Many tall halls of big space volume were built and, to be built in many construction projects in the Far East, particularly Mainland China, Hong Kong, and Taiwan. Smoke is identified to be the key hazard to handle. Consequently, smoke exhaust systems are specified in the fire code in those areas. An update on applying Computational Fluid Dynamics (CFD in smoke exhaust design will be presented in this paper. Key points to note in CFD simulations on smoke filling due to a fire in a big hall will be discussed. Mathematical aspects concerning of discretization of partial differential equations and algorithms for solving the velocity-pressure linked equations are briefly outlined. Results predicted by CFD with different free boundary conditions are compared with those on room fire tests. Standards on grid size, relaxation factors, convergence criteria, and false diffusion should be set up for numerical experiments with CFD.
DYNAMICS OF DETECTED FIRE FACTORS IN CLOSED COMPARTMENT: COMPUTER SIMULATION
Directory of Open Access Journals (Sweden)
V. V. Nevdakh
2015-01-01
Full Text Available Computer simulation of the initial fire stages in closed compartment with the volume of ≈ 60 m3 and with a burner on a floor and 2 m above floor have been carried using FDS software. Fires with different t 2 –power low heat release rates have been modeled. Fires which growth times to reach 1055 kW were 100 s and 500 s have been considered as fast and slow fires respectively. Dynamics of heat release rates and detected fire factors such as spatial distributions of air temperature, smoke obscuration and variations of indoor pressure have been studied. It has been obtained that dynamics of heat release rates of the initial fire stages in closed compartment consists of two stages. During the first stage the heat release rate is proportional to mass burning rate and flaming occurs only above a burner. At the second stage dynamics of heat release rates has a form of irregular in amplitude and duration pulsations, which are caused by self-ignition in the smoke layer. The compartment air volume may be layered with respect to the height and every layer has its oven temperature, smoke obscuration, self-ignition areas have been shown. The layer thickness, gradients of temperature and obscuration depend on a fire growth rate and on a burner height above floor have been concluded. The spatial distributions of air temperature and pressure variation have the opposite gradients on a height have been obtained. Maximal pressure variation and its gradient occurs under the fast fire with a burner on a floor have been obtained too.
The Computer Simulation of Liquids by Molecular Dynamics.
Smith, W.
1987-01-01
Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)
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...
Computational Fluid Dynamics Simulation of Fluidized Bed Polymerization Reactors
Energy Technology Data Exchange (ETDEWEB)
Fan, Rong [Iowa State Univ., Ames, IA (United States)
2006-01-01
Fluidized beds (FB) reactors are widely used in the polymerization industry due to their superior heat- and mass-transfer characteristics. Nevertheless, problems associated with local overheating of polymer particles and excessive agglomeration leading to FB reactors defluidization still persist and limit the range of operating temperatures that can be safely achieved in plant-scale reactors. Many people have been worked on the modeling of FB polymerization reactors, and quite a few models are available in the open literature, such as the well-mixed model developed by McAuley, Talbot, and Harris (1994), the constant bubble size model (Choi and Ray, 1985) and the heterogeneous three phase model (Fernandes and Lona, 2002). Most these research works focus on the kinetic aspects, but from industrial viewpoint, the behavior of FB reactors should be modeled by considering the particle and fluid dynamics in the reactor. Computational fluid dynamics (CFD) is a powerful tool for understanding the effect of fluid dynamics on chemical reactor performance. For single-phase flows, CFD models for turbulent reacting flows are now well understood and routinely applied to investigate complex flows with detailed chemistry. For multiphase flows, the state-of-the-art in CFD models is changing rapidly and it is now possible to predict reasonably well the flow characteristics of gas-solid FB reactors with mono-dispersed, non-cohesive solids. This thesis is organized into seven chapters. In Chapter 2, an overview of fluidized bed polymerization reactors is given, and a simplified two-site kinetic mechanism are discussed. Some basic theories used in our work are given in detail in Chapter 3. First, the governing equations and other constitutive equations for the multi-fluid model are summarized, and the kinetic theory for describing the solid stress tensor is discussed. The detailed derivation of DQMOM for the population balance equation is given as the second section. In this section
Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E
2016-01-01
. 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...... 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...... rate, different dehydrated structures were observed. Removing all water molecules immediately and removing water relatively fast (10 water molecules/10 ps) resulted in an amorphous system, whereas relatively slow computational dehydration (3 water molecules/10 ps) resulted in a crystalline anhydrate...
Introducing Computational Fluid Dynamics Simulation into Olfactory Display
Ishida, Hiroshi; Yoshida, Hitoshi; Nakamoto, Takamichi
An olfactory display is a device that delivers various odors to the user's nose. It can be used to add special effects to movies and games by releasing odors relevant to the scenes shown on the screen. In order to provide high-presence olfactory stimuli to the users, the display must be able to generate realistic odors with appropriate concentrations in a timely manner together with visual and audio playbacks. In this paper, we propose to use computational fluid dynamics (CFD) simulations in conjunction with the olfactory display. Odor molecules released from their source are transported mainly by turbulent flow, and their behavior can be extremely complicated even in a simple indoor environment. In the proposed system, a CFD solver is employed to calculate the airflow field and the odor dispersal in the given environment. An odor blender is used to generate the odor with the concentration determined based on the calculated odor distribution. Experimental results on presenting odor stimuli synchronously with movie clips show the effectiveness of the proposed system.
Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
Directory of Open Access Journals (Sweden)
Eric Paquet
2015-01-01
Full Text Available Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods.
Computational Fluid Dynamics Simulation of Dual Bell Nozzle Film Cooling
Braman, Kalen; Garcia, Christian; Ruf, Joseph; Bui, Trong
2015-01-01
Marshall Space Flight Center (MSFC) and Armstrong Flight Research Center (AFRC) are working together to advance the technology readiness level (TRL) of the dual bell nozzle concept. Dual bell nozzles are a form of altitude compensating nozzle that consists of two connecting bell contours. At low altitude the nozzle flows fully in the first, relatively lower area ratio, nozzle. The nozzle flow separates from the wall at the inflection point which joins the two bell contours. This relatively low expansion results in higher nozzle efficiency during the low altitude portion of the launch. As ambient pressure decreases with increasing altitude, the nozzle flow will expand to fill the relatively large area ratio second nozzle. The larger area ratio of the second bell enables higher Isp during the high altitude and vacuum portions of the launch. Despite a long history of theoretical consideration and promise towards improving rocket performance, dual bell nozzles have yet to be developed for practical use and have seen only limited testing. One barrier to use of dual bell nozzles is the lack of control over the nozzle flow transition from the first bell to the second bell during operation. A method that this team is pursuing to enhance the controllability of the nozzle flow transition is manipulation of the film coolant that is injected near the inflection between the two bell contours. Computational fluid dynamics (CFD) analysis is being run to assess the degree of control over nozzle flow transition generated via manipulation of the film injection. A cold flow dual bell nozzle, without film coolant, was tested over a range of simulated altitudes in 2004 in MSFC's nozzle test facility. Both NASA centers have performed a series of simulations of that dual bell to validate their computational models. Those CFD results are compared to the experimental results within this paper. MSFC then proceeded to add film injection to the CFD grid of the dual bell nozzle. A series of
Neutron Scattering and Computer Simulation Studies of Ice Dynamics
Institute of Scientific and Technical Information of China (English)
DONG Shunle; YU Xinsheng
2002-01-01
In this article we describe a range of simulations (lattice dynamics and molecular dynamics) of the inelastic inco-herent neutron scattering spectra of ices (normal ice, ice Ⅱ and ice Ⅷ ). These simulations use a variety of different inter-molecular potentials from simple classic pair-wise (rigid and non-rigid molecule) potentials to sophisticated polarisable poten-tials. It was found that MCY makes stretching and bending interactions too weak while others do them well. We demon-strate that in order to reproduce the measured neutron spectrum, greater anisotropy (or orientational variation) is requiredthan these potentials presently provide.
Reveal protein dynamics by combining computer simulation and neutron scattering
Hong, Liang; Smith, Jeremy; CenterMolecular Biophysics Team
2014-03-01
Protein carries out most functions in living things on the earth through characteristic modulation of its three-dimensional structure over time. Understanding the microscopic nature of the protein internal motion and its connection to the function and structure of the biomolecule is a central topic in biophysics, and of great practical importance for drug design, study of diseases, and the development of renewable energy, etc. Under physiological conditions, protein exhibits a complex dynamics landscape, i.e., a variety of diffusive and conformational motions occur on similar time and length scales. This variety renders difficult the derivation of a simplified description of protein internal motions in terms of a small number of distinct, additive components. This difficulty is overcome by our work using a combined approach of Molecular Dynamics (MD) simulations and the Neutron Scattering experiments. Our approach enables distinct protein motions to be characterized separately, furnishing an in-depth understanding of the connection between protein structure, dynamics and function.
Comparative Implementation of High Performance Computing for Power System Dynamic Simulations
Energy Technology Data Exchange (ETDEWEB)
Jin, Shuangshuang; Huang, Zhenyu; Diao, Ruisheng; Wu, Di; Chen, Yousu
2017-05-01
Dynamic simulation for transient stability assessment is one of the most important, but intensive, computations for power system planning and operation. Present commercial software is mainly designed for sequential computation to run a single simulation, which is very time consuming with a single processer. The application of High Performance Computing (HPC) to dynamic simulations is very promising in accelerating the computing process by parallelizing its kernel algorithms while maintaining the same level of computation accuracy. This paper describes the comparative implementation of four parallel dynamic simulation schemes in two state-of-the-art HPC environments: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP). These implementations serve to match the application with dedicated multi-processor computing hardware and maximize the utilization and benefits of HPC during the development process.
Computational Fluid Dynamics Simulation of Multiphase Flow in Structured Packings
Directory of Open Access Journals (Sweden)
Saeed Shojaee
2012-01-01
Full Text Available A volume of fluid multiphase flow model was used to investigate the effective area and the created liquid film in the structured packings. The computational results revealed that the gas and liquid flow rates play significant roles in the effective interfacial area of the packing. In particular, the effective area increases as the flow rates of both phases increase. Numerical results were compared with the Brunazzi and SRP models, and a good agreement between them was found. Attention was given to the process of liquid film formation in both two-dimensional (2D and three-dimensional (3D models. The current study revealed that computational fluid dynamics (CFD can be used as an effective tool to provide information on the details of gas and liquid flows in complex packing geometries.
Computer simulation of some dynamical properties of the Lorentz gas
Joslin, C. G.; Egelstaff, P. A.
1989-07-01
We carried out molecular dynamics simulations of a Lorentz gas, consisting of a lone hydrogen molecule moving in a sea of stationary argon atoms. A Lennard-Jones form was assumed for the H2-Ar potential. The calculations were performed at a reduced temperature K * = kT/ɛH 2-Ar = 4.64 and at reduced densities ρ *= ρ Arσ{Ar/3} in the range 0.074-0.414. The placement of Ar atoms was assumed to be random rather than dictated by equilibrium considerations. We followed the trajectories of many H2 molecules, each of which is assigned in turn a velocity given by the Maxwell-Boltzmann distribution at the temperature of the simulation. Solving the equations of motion classically, we obtained the translational part of the incoherent dynamic structure factor for the H2 molecule, S tr( q, ω). This was convoluted with the rotational structure factor S rot( q, ω) calculated assuming unhindered rotation to obtain the total structure factor S( q, ω). Our results agree well with experimental data on this function obtained by Egelstaff et al. At the highest density ( ρ *=0.414) we studied the dependence of S( q, ω) on system size (number of Ar atoms), number of H2 molecules for which trajectories are generated, and the length of time over which these trajectories are followed.
Molecular dynamics computer simulation of permeation in solids
Energy Technology Data Exchange (ETDEWEB)
Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M. [Sandia National Labs., Albuquerque, NM (United States)
1997-12-31
In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.
Institute of Scientific and Technical Information of China (English)
Tianwei TAN; Peiyong QIN
2010-01-01
@@ This special issue of Frontiers of Chemical Engineering in China is dedicated to the topic of Computational Fluid Dynamics (CFD) and Molecular Simulation. It features a selection of some of the best papers presented at the Symposium on CFD and Molecular Simulation, which was held in Beijing, China, on 22-23 May 2009.
Numerical Simulation of Bird Flight Using Both CFD and Computational Flight Dynamics
Ueno, Yosuke; Nakamura, Yoshiaki
A numerical simulation method taking into account both aerodynamics and flight dynamics has been developed to simulate the flight of a low speed flying object, where it undergoes unsteady deformation. This method can also be applied to simulate the unsteady motion of small vehicles such as micro air vehicles (MAV). In the present study, we take up a bird and demonstrate its flight in the air. In particular the effect of fluid forces on the bird's flying motion is examined in detail, based on CFD×CFD: Computational Fluid Dynamics (CFD) and Computational Flight Dynamics. It is found from simulated results that this bird can generate lift and thrust enough to fly by flapping its wing. In addition, it can make a level flight by adjusting its oscillation frequency. Thus, the present method is promising to study the aerodynamics and flight dynamics of a moving object with its shape morphing.
Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.
2004-01-01
A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.
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
Angelikopoulos, Panagiotis; Papadimitriou, Costas; Koumoutsakos, Petros
2012-10-01
We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures. Furthermore, adaptive surrogate models are proposed in order to reduce the computational cost associated with the large number of MD model runs. The effectiveness and computational efficiency of the proposed Bayesian framework is demonstrated in MD simulations of liquid and gaseous argon.
Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs
Institute of Scientific and Technical Information of China (English)
CHEN Fei-Guo; GE Wei; LI Jing-Hai
2009-01-01
Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20-60 fold speedup over that of one core of the Intel Xeon 5430 CPU was achieved, reaching up to 150 Gflopa. MD simulation of cavity flow and particle-bubble interaction in liquid was implemented on multiple GPUs using a message passing interface (MPI). Up to 200 GPUs were tested on a special network topology, which achieves good scalability. The capability of GPU clusters for large-scale molecular dynamics simulation of meso-scale flow behavior was, therefore, uncovered.
Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20-60 fold speedup over that of one core of the Intel Xeon 5430 CPU was achieved, reaching up to 150 Gflops. MD simulation of cavity flow and particle-bubble interaction in liquid was implemented on multiple GPUs using a message passing interface (MPI). Up to 200 GPUs were tested on a special network topology, which achieves good scalability. The capability of GPU clusters for large-scale molecular dynamics simulation of meso-scale flow behavior was, therefore, uncovered.
Advanced Computation Dynamics Simulation of Protective Structures Research
2013-02-01
workmanship, water- cement ratio, and curing conditions. Most of these parameters are not fixed and are determined in the field by the mason. Also, bond usually...type Portland or Mortar Cement (psi) Masonry cement (psi) M or S N M or S N Normal to bed joint Ungrouted 33 25 20 12 Fully Grouted 86 84 81 77...multi-wythe walls that were fully grouted and had a brick veneer filled with a foam insulated cavity. He simulated the grout and CMU with a single
Roccatano, Danilo
2015-07-01
The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions.
Computational simulations of thermally activated magnetisation dynamics at high frequencies
Hannay, J D
2001-01-01
short time scale breakdown of the Arrhenius-Neel law for a single magnetic moment is demonstrated and explained in terms of the dynamics of the precessional motion. The variation in response as a function of the damping parameter is found to be an important factor determining the remanent magnetisation for a given pulse width. The effects of interactions between moments are described, including the apparent increase in effective damping. It is shown that interactions between grains can be described in terms of thermally excited spin waves. The most important device for today's large scale information storage is the magnetic hard disk drive. This is because it can store vast amounts of data and also provides the fastest way of accessing this valuable information. A current state of the art commercially available hard disk has data rates in excess of 1 GHz which means the magnetic bits are required to reverse in less than one nanosecond. The areal density is greater than 10 Gbits/in sup 2 which requires extreme...
An investigation into computer simulation of the dynamic response of a gas turbine engine
Hendricks, Todd B
1997-01-01
Transient performance of gas turbines has a strong bearing on output and component life. For this reason, several articles have been written on the dynamic simulation of gas turbine systems in electrical generation, cogeneration, and marine applications. These models provide a basis for this present work. This paper describes a mathematical and computer model that was developed to investigate the dynamic response of a simple (no reheat, regeneration, or other auxiliary equipment) single-shaft...
Use of computational fluid dynamics simulations for design of a pretreatment screw conveyor reactor.
Berson, R Eric; Hanley, Thomas R
2005-01-01
Computational fluid dynamics simulations were employed to compare performance of various designs of a pretreatment screw conveyor reactor. The reactor consisted of a vertical screw used to create cross flow between the upward conveying solids and the downward flow of acid. Simulations were performed with the original screw design and a modified design in which the upper flights of the screw were removed. Results of the simulations show visually that the modified design provided favorable plug flow behavior within the reactor. Pressure drop across the length of the reactor without the upper screws in place was predicted by the simulations to be 5 vs 40 kPa for the original design.
Petascale molecular dynamics simulation using the fast multipole method on K computer
Ohno, Yousuke
2014-10-01
In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
Transient Solid Dynamics Simulations on the Sandia/Intel Teraflop Computer
Energy Technology Data Exchange (ETDEWEB)
Attaway, S.; Brown, K.; Gardner, D.; Hendrickson, B. [Sandia National Labs., Albuquerque, NM (United States); Barragy, T. [Itel Corporation, Beaverton, OR (United States)
1997-12-31
Transient solid dynamics simulations are among the most widely used engineering calculations. Industrial applications include vehicle crashworthiness studies, metal forging, and powder compaction prior to sintering. These calculations are also critical to defense applications including safety studies and weapons simulations. The practical importance of these calculations and their computational intensiveness make them natural candidates for parallelization. This has proved to be difficult, and existing implementations fail to scale to more than a few dozen processors. In this paper we describe our parallelization of PRONTO, Sandia`s transient solid dynamics code, via a novel algorithmic approach that utilizes multiple decompositions for different key segments of the computations, including the material contact calculation. This latter calculation is notoriously difficult to perform well in parallel, because it involves dynamically changing geometry, global searches for elements in contact, and unstructured communications among the compute nodes. Our approach scales to at least 3600 compute nodes of the Sandia/Intel Teraflop computer (the largest set of nodes to which we have had access to date) on problems involving millions of finite elements. On this machine we can simulate models using more than ten- million elements in a few tenths of a second per timestep, and solve problems more than 3000 times faster than a single processor Cray Jedi.
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.
Lin, Yi-Chung; Haftka, Raphael T; Queipo, Nestor V; Fregly, Benjamin J
2009-04-01
Computational speed is a major limiting factor for performing design sensitivity and optimization studies of total knee replacements. Much of this limitation arises from extensive geometry calculations required by contact analyses. This study presents a novel surrogate contact modeling approach to address this limitation. The approach involves fitting contact forces from a computationally expensive contact model (e.g., a finite element model) as a function of the relative pose between the contacting bodies. Because contact forces are much more sensitive to displacements in some directions than others, standard surrogate sampling and modeling techniques do not work well, necessitating the development of special techniques for contact problems. We present a computational evaluation and practical application of the approach using dynamic wear simulation of a total knee replacement constrained to planar motion in a Stanmore machine. The sample points needed for surrogate model fitting were generated by an elastic foundation (EF) contact model. For the computational evaluation, we performed nine different dynamic wear simulations with both the surrogate contact model and the EF contact model. In all cases, the surrogate contact model accurately reproduced the contact force, motion, and wear volume results from the EF model, with computation time being reduced from 13 min to 13 s. For the practical application, we performed a series of Monte Carlo analyses to determine the sensitivity of predicted wear volume to Stanmore machine setup issues. Wear volume was highly sensitive to small variations in motion and load inputs, especially femoral flexion angle, but not to small variations in component placements. Computational speed was reduced from an estimated 230 h to 4 h per analysis. Surrogate contact modeling can significantly improve the computational speed of dynamic contact and wear simulations of total knee replacements and is appropriate for use in design sensitivity
Directory of Open Access Journals (Sweden)
J. M. Ruiz-Avilés
2012-01-01
Full Text Available In the context of Long-Term Evolution (LTE, the next generation mobile telecommunication network, femtocells are low-power base stations that efficiently provide coverage and capacity indoors. This paper presents a computationally efficient dynamic system-level LTE simulator for enterprise femtocell scenarios. The simulator includes specific mobility and traffic and propagation models for indoor environments. A physical layer abstraction is performed to predict link-layer performance with low computational cost. At link layer, two important functions are included to increase network capacity: Link Adaptation and Dynamic Scheduling. At network layer, other Radio Resource Management functionalities, such as Admission Control and Mobility Management, are also included. The resulting tool can be used to test and validate optimization algorithms in the context of Self-Organizing Networks (SON.
High-throughput all-atom molecular dynamics simulations using distributed computing.
Buch, I; Harvey, M J; Giorgino, T; Anderson, D P; De Fabritiis, G
2010-03-22
Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.
Fersht, Alan R
2002-10-29
There are proposals to overcome the current incompatibilities between the time scales of protein folding and molecular dynamics simulation by using a large number of short simulations of only tens of nanoseconds (distributed computing). According to the principles of first-order kinetic processes, a sufficiently large number of short simulations will include, de facto, a small number of long time scale events that have proceeded to completion. But protein folding is not an elementary kinetic step: folding has a series of early conformational steps that lead to lag phases at the beginning of the kinetics. The presence of these lag phases can bias short simulations toward selecting minor pathways that have fewer or faster lag steps and so miss the major folding pathways. Attempts to circumvent the lags by using loosely coupled parallel simulations that search for first-order transitions are also problematic because of the difficulty of detecting transitions in molecular dynamics simulations. Nevertheless, the procedure of using parallel independent simulations is perfectly valid and quite feasible once the time scale of simulation proceeds past the lag phases into a single exponential region.
Institute of Scientific and Technical Information of China (English)
WANG Yu; HE Pingting; YE Hong; XIN Zhihong
2007-01-01
Instantaneous flow field and temperature field of the two-phase fluid are measured by particle image velocimetry (PIV) and steady state method during the state of onflow. A turbulent two-phase fluid model of stirred bioreactor with punched impeller is established by the computational fluid dynamics (CFD), using a rotating coordinate system and sliding mesh to describe the relative motion between impeller and baffles. The simulation and experiment results of flow and temperature field prove their warps are less than 10% and the mathematic model can well simulate the fields, which will also provide the study on optimized-design and scale-up of bioreactors with reference value.
Ivancic, B.; Riedmann, H.; Frey, M.; Knab, O.; Karl, S.; Hannemann, K.
2016-07-01
The paper summarizes technical results and first highlights of the cooperation between DLR and Airbus Defence and Space (DS) within the work package "CFD Modeling of Combustion Chamber Processes" conducted in the frame of the Propulsion 2020 Project. Within the addressed work package, DLR Göttingen and Airbus DS Ottobrunn have identified several test cases where adequate test data are available and which can be used for proper validation of the computational fluid dynamics (CFD) tools. In this paper, the first test case, the Penn State chamber (RCM1), is discussed. Presenting the simulation results from three different tools, it is shown that the test case can be computed properly with steady-state Reynolds-averaged Navier-Stokes (RANS) approaches. The achieved simulation results reproduce the measured wall heat flux as an important validation parameter very well but also reveal some inconsistencies in the test data which are addressed in this paper.
COMPUTATIONAL FLUID DYNAMICS (CFD) SIMULATIONS OF DRAG REDUCTION WITH PERIODIC MICRO-STRUCTURED WALL
Institute of Scientific and Technical Information of China (English)
LI Gang; ZHOU Ming; WU Bo; YE Xia; CAI Lan
2008-01-01
Computational fluid dynamics(CFD) simulations are adopted to investigate rectangular microchannel flows with various periodic micro-structured wall by introducing velocity slip boundary condition at low Reynolds number. The purpose of the current study is to numerically find out the effects of periodic micro-structured wall on the flow resistance in rectangular microchannel with the different spacings between microridges ranging from 15 to 60 μm. The simulative results indicate that pressure drop with different spacing between microridges increases linearly with flow velocity and decreases monotonically with slip velocity; Pressure drop reduction also increases with the spacing between microridges at the same condition of slip velocity and flow velocity. The results of numerical simulation are compared with theoretical predictions and experimental results in the literatures. It is found that there is qualitative agreement between them.
Tang, William
2013-04-01
Advanced computing is generally recognized to be an increasingly vital tool for accelerating progress in scientific research in the 21st Century. The imperative is to translate the combination of the rapid advances in super-computing power together with the emergence of effective new algorithms and computational methodologies to help enable corresponding increases in the physics fidelity and the performance of the scientific codes used to model complex physical systems. If properly validated against experimental measurements and verified with mathematical tests and computational benchmarks, these codes can provide more reliable predictive capability for the behavior of complex systems, including fusion energy relevant high temperature plasmas. The magnetic fusion energy research community has made excellent progress in developing advanced codes for which computer run-time and problem size scale very well with the number of processors on massively parallel supercomputers. A good example is the effective usage of the full power of modern leadership class computational platforms from the terascale to the petascale and beyond to produce nonlinear particle-in-cell simulations which have accelerated progress in understanding the nature of plasma turbulence in magnetically-confined high temperature plasmas. Illustrative results provide great encouragement for being able to include increasingly realistic dynamics in extreme-scale computing campaigns to enable predictive simulations with unprecedented physics fidelity. Some illustrative examples will be presented of the algorithmic progress from the magnetic fusion energy sciences area in dealing with low memory per core extreme scale computing challenges for the current top 3 supercomputers worldwide. These include advanced CPU systems (such as the IBM-Blue-Gene-Q system and the Fujitsu K Machine) as well as the GPU-CPU hybrid system (Titan).
Energy Technology Data Exchange (ETDEWEB)
Ko, Soon Heum [Linkoeping University, Linkoeping (Sweden); Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel [Louisiana State University, Baton Rouge (United States); Jha, Shantenu [Rutgers University, Piscataway (United States)
2014-01-15
Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.
Cyclo-lib: a database of computational molecular dynamics simulations of cyclodextrins.
Mixcoha, Edgar; Rosende, Roberto; Garcia-Fandino, Rebeca; Piñeiro, Ángel
2016-11-01
Cyclodextrins (CDs) are amongst the most versatile/multi-functional molecules used in molecular research and chemical applications. They are natural cyclic oligosaccharides typically employed to encapsulate hydrophobic groups in their central cavity. This allows solubilizing, protecting or reducing the toxicity of a large variety of different molecules including drugs, dyes and surfactant agents. In spite of their great potential, atomic level information of these molecules, which is key for their function, is really scarce. Computational Molecular Dynamics (MD) simulations have the potential to efficiently fill this gap, providing structural-dynamic information at atomic level in time scales ranging from ps to μs. Cyclo-lib is a database with a publicly accessible web-interface containing structural and dynamic analysis obtained from computational MD simulation trajectories (250 ns long) of native and modified CDs in explicit water molecules. Cyclo-lib currently includes 70 CDs typically employed for fundamental and industrial research. Tools for comparative analysis between different CDs, as well as to restrict the analysis to specific time-segments within the trajectories are also available. Cyclo-lib provides atomic resolution information aimed to complement experimental results performed with the same molecules. The database is freely available under http://cyclo-lib.mduse.com/ CONTACT: Angel.Pineiro@usc.es. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Stovern, Michael; Felix, Omar; Csavina, Janae; Rine, Kyle P.; Russell, MacKenzie R.; Jones, Robert M.; King, Matt; Betterton, Eric A.; Sáez, A. Eduardo
2014-09-01
Mining operations are potential sources of airborne particulate metal and metalloid contaminants through both direct smelter emissions and wind erosion of mine tailings. The warmer, drier conditions predicted for the Southwestern US by climate models may make contaminated atmospheric dust and aerosols increasingly important, due to potential deleterious effects on human health and ecology. Dust emissions and dispersion of dust and aerosol from the Iron King Mine tailings in Dewey-Humboldt, Arizona, a Superfund site, are currently being investigated through in situ field measurements and computational fluid dynamics modeling. These tailings are heavily contaminated with lead and arsenic. Using a computational fluid dynamics model, we model dust transport from the mine tailings to the surrounding region. The model includes gaseous plume dispersion to simulate the transport of the fine aerosols, while individual particle transport is used to track the trajectories of larger particles and to monitor their deposition locations. In order to improve the accuracy of the dust transport simulations, both regional topographical features and local weather patterns have been incorporated into the model simulations. Results show that local topography and wind velocity profiles are the major factors that control deposition.
Stovern, Michael; Felix, Omar; Csavina, Janae; Rine, Kyle P.; Russell, MacKenzie R.; Jones, Robert M.; King, Matt; Betterton, Eric A.; Sáez, A. Eduardo
2014-01-01
Mining operations are potential sources of airborne particulate metal and metalloid contaminants through both direct smelter emissions and wind erosion of mine tailings. The warmer, drier conditions predicted for the Southwestern US by climate models may make contaminated atmospheric dust and aerosols increasingly important, due to potential deleterious effects on human health and ecology. Dust emissions and dispersion of dust and aerosol from the Iron King Mine tailings in Dewey-Humboldt, Arizona, a Superfund site, are currently being investigated through in situ field measurements and computational fluid dynamics modeling. These tailings are heavily contaminated with lead and arsenic. Using a computational fluid dynamics model, we model dust transport from the mine tailings to the surrounding region. The model includes gaseous plume dispersion to simulate the transport of the fine aerosols, while individual particle transport is used to track the trajectories of larger particles and to monitor their deposition locations. In order to improve the accuracy of the dust transport simulations, both regional topographical features and local weather patterns have been incorporated into the model simulations. Results show that local topography and wind velocity profiles are the major factors that control deposition. PMID:25621085
Machine learning from computer simulations with applications in rail vehicle dynamics
Taheri, Mehdi; Ahmadian, Mehdi
2016-05-01
The application of stochastic modelling for learning the behaviour of a multibody dynamics (MBD) models is investigated. Post-processing data from a simulation run are used to train the stochastic model that estimates the relationship between model inputs (suspension relative displacement and velocity) and the output (sum of suspension forces). The stochastic model can be used to reduce the computational burden of the MBD model by replacing a computationally expensive subsystem in the model (suspension subsystem). With minor changes, the stochastic modelling technique is able to learn the behaviour of a physical system and integrate its behaviour within MBD models. The technique is highly advantageous for MBD models where real-time simulations are necessary, or with models that have a large number of repeated substructures, e.g. modelling a train with a large number of railcars. The fact that the training data are acquired prior to the development of the stochastic model discards the conventional sampling plan strategies like Latin Hypercube sampling plans where simulations are performed using the inputs dictated by the sampling plan. Since the sampling plan greatly influences the overall accuracy and efficiency of the stochastic predictions, a sampling plan suitable for the process is developed where the most space-filling subset of the acquired data with ? number of sample points that best describes the dynamic behaviour of the system under study is selected as the training data. Results indicated that the stochastic modelling technique is effective in improving the computational efficiency of the MBD model without compromising the accuracy of the predictions, although the improvements in the computational efficiency of the technique could not be quantified due to the inefficiencies associated with transferring the data between multiple software packages (SIMPACK, SIMULINK).
Final Project Report: Data Locality Enhancement of Dynamic Simulations for Exascale Computing
Energy Technology Data Exchange (ETDEWEB)
Shen, Xipeng [North Carolina State Univ., Raleigh, NC (United States)
2016-04-27
The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future manycore systems, alleviating the memory performance issues for exascale computing. In the first three years, the PI and his group have achieves some significant progress towards the goal, producing a set of novel techniques for improving the memory performance and data locality in manycore systems, yielding 18 conference and workshop papers and 4 journal papers and graduating 6 Ph.Ds. This report summarizes the research results of this project through that period.
DEFF Research Database (Denmark)
Gruber, M.F.; Johnson, C.J.; Tang, C.Y.;
2011-01-01
Forward osmosis is an osmotically driven membrane separation process that relies on the utilization of a large osmotic pressure differential generated across a semi-permeable membrane. In recent years forward osmosis has shown great promise in the areas of wastewater treatment, seawater...... the understanding of membrane systems, models that can accurately encapsulate all significant physical processes occurring in the systems are required. The present study demonstrates a computational fluid dynamics (CFD) model capable of simulating forward osmosis systems with asymmetric membranes. The model...
Computational Simulation of Dynamic Response of Vehicle Tatra T815 and the Ground
Vlček, Jozef; Valašková, Veronika
2016-10-01
The effect of a moving load represents the actual problem which is analysed in engineering practice. The response of the vehicle and its dynamic effect on the pavement can be analysed by experimental or computational ways. The aim of this paper was to perform computer simulations of a vehicle-ground interaction. For this purpose, a half-part model of heavy lorry Tatra 815 and ground was modelled in computational programmes ADINA and PLAXIS based on FEM methods, utilizing analytical approaches. Two procedures were then selected for further calculations. The first one is based on the simplification of the stiffer pavement layers to the beam element supported by the springs simulating the subgrade layers using Winkler-Pasternak theory of elastic half-space. Modulus of subgrade reaction was determined in the standard programme trough the simulation of a plate load test. Second approach considers a multi-layered ground system with layers of different thicknesses and material properties. For comparison of outputs of both approaches, the same input values were used for every calculation procedure. Crucial parameter for the simulations was the velocity of the passing vehicle with regard to the ground response to the impulse of the pass. Lower velocities result in almost static response of the pavement, but higher velocities induce response that can be better described by the dynamic theory. For small deformations, an elastic material model seems to be sufficient to define the ground response to the moving load, but for larger deformations advanced material models for the ground environment would be more reliable.
Energy Technology Data Exchange (ETDEWEB)
Jardini, Andre L.; Bineli, Aulus R.R.; Viadana, Adriana M.; Maciel, Maria Regina Wolf; Maciel Filho, Rubens [State University of Campinas (UNICAMP), SP (Brazil). School of Chemical Engineering; Medina, Lilian C.; Gomes, Alexandre de O. [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Barros, Ricardo S. [University Foundation Jose Bonifacio (FUJB), Rio de Janeiro, RJ (Brazil)
2008-07-01
In this paper, the design of microreactor with microfluidics channels has been carried out in Computer Aided Design Software (CAD) and constructed in rapid prototyping system to be used in chemical reaction processing of the heavy oil fractions. The flow pattern properties of microreactor (fluid dynamics, mixing behavior) have been considered through CFD (computational fluid dynamics) simulations. CFD calculations are also used to study the design and specification of new microreactor developments. The potential advantages of using a microreactor include better control of reaction conditions, improved safety and portability. A more detailed crude assay of the raw national oil, whose importance was evidenced by PETROBRAS/CENPES allows establishing the optimum strategies and processing conditions, aiming at a maximum utilization of the heavy oil fractions, towards valuable products. These residues are able to be processed in microreactor, in which conventional process like as hydrotreating, catalytic and thermal cracking may be carried out in a much more intensified fashion. The whole process development involves a prior thermal study to define the possible operating conditions for a particular task, the microreactor design through computational fluid dynamics and construction using rapid prototyping. This gives high flexibility for process development, shorter time, and costumer/task oriented process/product development. (author)
Energy Technology Data Exchange (ETDEWEB)
Mays, Brian [AREVA Federal Services, Lynchburg, VA (United States); Jackson, R. Brian [TerraPower, Bellevue, WA (United States)
2017-03-08
The project, Toward a Longer Life Core: Thermal Hydraulic CFD Simulations and Experimental Investigation of Deformed Fuel Assemblies, DOE Project code DE-NE0008321, was a verification and validation project for flow and heat transfer through wire wrapped simulated liquid metal fuel assemblies that included both experiments and computational fluid dynamics simulations of those experiments. This project was a two year collaboration between AREVA, TerraPower, Argonne National Laboratory and Texas A&M University. Experiments were performed by AREVA and Texas A&M University. Numerical simulations of these experiments were performed by TerraPower and Argonne National Lab. Project management was performed by AREVA Federal Services. The first of a kind project resulted in the production of both local point temperature measurements and local flow mixing experiment data paired with numerical simulation benchmarking of the experiments. The project experiments included the largest wire-wrapped pin assembly Mass Index of Refraction (MIR) experiment in the world, the first known wire-wrapped assembly experiment with deformed duct geometries and the largest numerical simulations ever produced for wire-wrapped bundles.
Meng, Yilin; Dashti, Danial Sabri; Roitberg, Adrian E
2011-09-13
Alchemical free energy calculations play a very important role in the field of molecular modeling. Efforts have been made to improve the accuracy and precision of those calculations. One of the efforts is to employ a Hamiltonian replica exchange molecular dynamics (H-REMD) method to enhance conformational sampling. In this paper, we demonstrated that HREMD method not only improves convergence in alchemical free energy calculations but also can be used to compute free energy differences directly via the Free Energy Perturbation (FEP)algorithm. We show a direct mapping between the H-REMD and the usual FEP equations, which are then used directly to compute free energies. The H-REMD alchemical free energy calculation (Replica exchange Free Energy Perturbation, REFEP) was tested on predicting the pK(a) value of the buried Asp26 in thioredoxin. We compare the results of REFEP with TI and regular FEP simulations. REFEP calculations converged faster than those from TI and regular FEP simulations. The final predicted pK(a) value from the H-REMD simulation was also very accurate, only 0.4 pK(a) unit above the experimental value. Utilizing the REFEP algorithm significantly improves conformational sampling, and this in turn improves the convergence of alchemical free energy simulations.
Afjeh, Abdollah A.; Reed, John A.
2003-01-01
The following reports are presented on this project:A first year progress report on: Development of a Dynamically Configurable,Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; A second year progress report on: Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; An Extensible, Interchangeable and Sharable Database Model for Improving Multidisciplinary Aircraft Design; Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration; and Improving the Aircraft Design Process Using Web-based Modeling and Simulation.
HIGH-FIDELITY SIMULATION-DRIVEN MODEL DEVELOPMENT FOR COARSE-GRAINED COMPUTATIONAL FLUID DYNAMICS
Energy Technology Data Exchange (ETDEWEB)
Hanna, Botros N.; Dinh, Nam T.; Bolotnov, Igor A.
2016-06-01
Nuclear reactor safety analysis requires identifying various credible accident scenarios and determining their consequences. For a full-scale nuclear power plant system behavior, it is impossible to obtain sufficient experimental data for a broad range of risk-significant accident scenarios. In single-phase flow convective problems, Direct Numerical Simulation (DNS) and Large Eddy Simulation (LES) can provide us with high fidelity results when physical data are unavailable. However, these methods are computationally expensive and cannot be afforded for simulation of long transient scenarios in nuclear accidents despite extraordinary advances in high performance scientific computing over the past decades. The major issue is the inability to make the transient computation parallel, thus making number of time steps required in high-fidelity methods unaffordable for long transients. In this work, we propose to apply a high fidelity simulation-driven approach to model sub-grid scale (SGS) effect in Coarse Grained Computational Fluid Dynamics CG-CFD. This approach aims to develop a statistical surrogate model instead of the deterministic SGS model. We chose to start with a turbulent natural convection case with volumetric heating in a horizontal fluid layer with a rigid, insulated lower boundary and isothermal (cold) upper boundary. This scenario of unstable stratification is relevant to turbulent natural convection in a molten corium pool during a severe nuclear reactor accident, as well as in containment mixing and passive cooling. The presented approach demonstrates how to create a correction for the CG-CFD solution by modifying the energy balance equation. A global correction for the temperature equation proves to achieve a significant improvement to the prediction of steady state temperature distribution through the fluid layer.
Cotes-Ruiz, Iván Tomás; Prado, Rocío P; García-Galán, Sebastián; Muñoz-Expósito, José Enrique; Ruiz-Reyes, Nicolás
2017-01-01
Nowadays, the growing computational capabilities of Cloud systems rely on the reduction of the consumed power of their data centers to make them sustainable and economically profitable. The efficient management of computing resources is at the heart of any energy-aware data center and of special relevance is the adaptation of its performance to workload. Intensive computing applications in diverse areas of science generate complex workload called workflows, whose successful management in terms of energy saving is still at its beginning. WorkflowSim is currently one of the most advanced simulators for research on workflows processing, offering advanced features such as task clustering and failure policies. In this work, an expected power-aware extension of WorkflowSim is presented. This new tool integrates a power model based on a computing-plus-communication design to allow the optimization of new management strategies in energy saving considering computing, reconfiguration and networks costs as well as quality of service, and it incorporates the preeminent strategy for on host energy saving: Dynamic Voltage Frequency Scaling (DVFS). The simulator is designed to be consistent in different real scenarios and to include a wide repertory of DVFS governors. Results showing the validity of the simulator in terms of resources utilization, frequency and voltage scaling, power, energy and time saving are presented. Also, results achieved by the intra-host DVFS strategy with different governors are compared to those of the data center using a recent and successful DVFS-based inter-host scheduling strategy as overlapped mechanism to the DVFS intra-host technique.
Institute of Scientific and Technical Information of China (English)
Jun LI; Ying-wei KANG; Guang-yi CAO; Xin-jian ZHU; Heng-yong TU; Jian LI
2008-01-01
A detailed mathematical model of a direct internal reforming solid oxide fuel cell (DIR-SOFC) incorporating with simulation of chemical and physical processes in the fuel cell is presented. The model is developed based on the reforming and electrochemical reaction mechanisms, mass and energy conservation, and heat transfer. A computational fluid dynamics (CFD) method is used for solving the complicated multiple partial differential equations (PDEs) to obtain the numerical approximations.The resulting distributions of chemical species concentrations, temperature and current density in a cross-flow DIR-SOFC are given and analyzed in detail. Further, the influence between distributions of chemical species concentrations, temperature and current density during the simulation is illustrated and discussed. The heat and mass transfer, and the kinetics of reforming and electrochemical reactions have significant effects on the parameter distributions within the cell. The results show the particularchar acteristics of the DIR-SOFC among fuel cells, and can aid in stack design and control.
MOLOCH computer code for molecular-dynamics simulation of processes in condensed matter
Directory of Open Access Journals (Sweden)
Derbenev I.V.
2011-01-01
Full Text Available Theoretical and experimental investigation into properties of condensed matter is one of the mainstreams in RFNC-VNIITF scientific activity. The method of molecular dynamics (MD is an innovative method of theoretical materials science. Modern supercomputers allow the direct simulation of collective effects in multibillion atom sample, making it possible to model physical processes on the atomistic level, including material response to dynamic load, radiation damage, influence of defects and alloying additions upon material mechanical properties, or aging of actinides. During past ten years, the computer code MOLOCH has been developed at RFNC-VNIITF. It is a parallel code suitable for massive parallel computing. Modern programming techniques were used to make the code almost 100% efficient. Practically all instruments required for modelling were implemented in the code: a potential builder for different materials, simulation of physical processes in arbitrary 3D geometry, and calculated data processing. A set of tests was developed to analyse algorithms efficiency. It can be used to compare codes with different MD implementation between each other.
MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations.
Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto
2014-08-06
We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(-1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.
Wendell, David C; Samyn, Margaret M; Cava, Joseph R; Ellwein, Laura M; Krolikowski, Mary M; Gandy, Kimberly L; Pelech, Andrew N; Shadden, Shawn C; LaDisa, John F
2013-06-01
Computational fluid dynamics (CFD) simulations quantifying thoracic aortic flow patterns have not included disturbances from the aortic valve (AoV). 80% of patients with aortic coarctation (CoA) have a bicuspid aortic valve (BAV) which may cause adverse flow patterns contributing to morbidity. Our objectives were to develop a method to account for the AoV in CFD simulations, and quantify its impact on local hemodynamics. The method developed facilitates segmentation of the AoV, spatiotemporal interpolation of segments, and anatomic positioning of segments at the CFD model inlet. The AoV was included in CFD model examples of a normal (tricuspid AoV) and a post-surgical CoA patient (BAV). Velocity, turbulent kinetic energy (TKE), time-averaged wall shear stress (TAWSS), and oscillatory shear index (OSI) results were compared to equivalent simulations using a plug inlet profile. The plug inlet greatly underestimated TKE for both examples. TAWSS differences extended throughout the thoracic aorta for the CoA BAV, but were limited to the arch for the normal example. OSI differences existed mainly in the ascending aorta for both cases. The impact of AoV can now be included with CFD simulations to identify regions of deleterious hemodynamics thereby advancing simulations of the thoracic aorta one step closer to reality. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
K. Kiriamiti
2010-02-01
Full Text Available Stirred tanks are typically used in many reactions. The quality of mixing generated by the impellers can be determined using either experimental and simulation methods, or both methods. The experimental techniques have evolved from traditional approaches, such as the application of hot-wire anemometry, to more modern ones like laser Doppler velocimetry (LDV. Similarly, computational fluid dynamics (CFD simulation techniques have attracted a lot of attention in recent years in the study of the hydrodynamics in stirred tanks, compared to the empirical modelling approach. Studies have shown that the LDV technique can provide very detailed information on the spatio-temporal variations in a tank, but the method is costly. For this reason, CFD simulation techniques may be employed to provide such data at a lower cost. In recent years, both integrated experimental and CFD approaches have been used to determine flow field and to design various systems. Both CFD and LDV data reveal the existence of flow maldistribution caused by system design features, and these in turn show that the configurations that have, over the years, been regarded as standard may not provide the optimal operating conditions with regards to the system homogeneity and power consumption. The current trends in CFD studies point towards an increasing application of more refined grids, such as in large eddy simulation, to capture turbulent structures at microscales. This trend will further improve the quality of the simulation results for processes such as precipitation, in which micromixing and reaction kinetics are important.
Reagan, Andrew J; Dubief, Yves; Dodds, Peter Sheridan; Danforth, Christopher M
2016-01-01
A thermal convection loop is a annular chamber filled with water, heated on the bottom half and cooled on the top half. With sufficiently large forcing of heat, the direction of fluid flow in the loop oscillates chaotically, dynamics analogous to the Earth's weather. As is the case for state-of-the-art weather models, we only observe the statistics over a small region of state space, making prediction difficult. To overcome this challenge, data assimilation (DA) methods, and specifically ensemble methods, use the computational model itself to estimate the uncertainty of the model to optimally combine these observations into an initial condition for predicting the future state. Here, we build and verify four distinct DA methods, and then, we perform a twin model experiment with the computational fluid dynamics simulation of the loop using the Ensemble Transform Kalman Filter (ETKF) to assimilate observations and predict flow reversals. We show that using adaptively shaped localized covariance outperforms static localized covariance with the ETKF, and allows for the use of less observations in predicting flow reversals. We also show that a Dynamic Mode Decomposition (DMD) of the temperature and velocity fields recovers the low dimensional system underlying reversals, finding specific modes which together are predictive of reversal direction.
Directory of Open Access Journals (Sweden)
Andrew J Reagan
Full Text Available A thermal convection loop is a annular chamber filled with water, heated on the bottom half and cooled on the top half. With sufficiently large forcing of heat, the direction of fluid flow in the loop oscillates chaotically, dynamics analogous to the Earth's weather. As is the case for state-of-the-art weather models, we only observe the statistics over a small region of state space, making prediction difficult. To overcome this challenge, data assimilation (DA methods, and specifically ensemble methods, use the computational model itself to estimate the uncertainty of the model to optimally combine these observations into an initial condition for predicting the future state. Here, we build and verify four distinct DA methods, and then, we perform a twin model experiment with the computational fluid dynamics simulation of the loop using the Ensemble Transform Kalman Filter (ETKF to assimilate observations and predict flow reversals. We show that using adaptively shaped localized covariance outperforms static localized covariance with the ETKF, and allows for the use of less observations in predicting flow reversals. We also show that a Dynamic Mode Decomposition (DMD of the temperature and velocity fields recovers the low dimensional system underlying reversals, finding specific modes which together are predictive of reversal direction.
Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes.
Soares, Thereza A; Vanni, Stefano; Milano, Giuseppe; Cascella, Michele
2017-08-03
Cellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries of the cells, they are involved in a wide range of biological functions, associated with both their structural and the dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel-liquid phase transitions, change of aggregation structure, formation of microtubules, or rupture into vesicles. All of these processes are dependent on a delicate interplay between intermolecular forces, molecular crowding, and entropy, and their understanding requires approaches that are able to capture and rationalize the details of all of the involved interactions. Molecular dynamics-based computational models at atom-level resolution are, in principle, the best way to perform such investigations. Unfortunately, the relevant spatial and time dimensionalities involved in membrane remodeling phenomena would require computational costs that are today unaffordable on a routinely basis. Such hurdles can be removed by coarse-graining the representations of the individual molecular components of the systems. This procedure anyway reduces the possibility of describing the chemical variations in the lipid mixtures composing biological membranes. New hybrid particle field multiscale approaches offer today a promising alternative to the more traditional particle-based simulations methods. By combining chemically distinguishable molecular representations with mesoscale-based computationally affordable potentials, they appear as one of the most promising ways to keep an accurate description of the chemical complexity of biological membranes and, at the same time, cover the required scales to describe remodeling events.
Isaacs, Kristin K; Schlesinger, R B; Martonen, Ted B
2006-01-01
Simulation of the dynamics and disposition of inhaled particles within human lungs is an invaluable tool in both the development of inhaled pharmacologic drugs and the risk assessment of environmental particulate matter (PM). The goal of the present focused study was to assess the utility of three-dimensional computational fluid dynamics (CFD) models in studying the local deposition patterns of PM in respiratory airways. CFD models were validated using data from published experimental studies in human lung casts. The ability of CFD to appropriately simulate trends in deposition patterns due to changing ventilatory conditions was specifically addressed. CFD simulations of airflow and particle motion were performed in a model of the trachea and main bronchi using Fluent Inc.'s FIDAP CFD software. Particle diameters of 8 microm were considered for input flow rates of 15 and 60 L/min. CFD was able to reproduce the observed spatial heterogeneities of deposition within the modeled bifurcations, and correctly predicted the "hot-spots" of particle deposition on carinal ridges. The CFD methods also predicted observed differences in deposition for high-versus-low flow rates. CFD models may provide an efficient means of studying the complex effects of airway geometry, particle characteristics, and ventilatory parameters on particle deposition and therefore aid in the design of human subject experiments.
Zhou, Hongyu; Gong, Peiyun; Du, Xuesen; Wang, Meng
2015-02-01
This paper aims to analyze the impact of splenic vein thrombosis (SVT) on the hemodynamic parameters in hepatic portal vein system. Based on computed tomography (CT) images of a patient with portal hypertension and commercial software MIMICS, the patient's portal venous system model was reconstructed. Color Doppler ultrasound method was used to measure the blood flow velocity in portal vein system and then the blood flow velocities were used as the inlet boundary conditions of simulation. By using the computational fluid dynamics (CFD) method, we simulated the changes of hemodynamic parameters in portal venous system with and without splenic vein thrombosis and analyzed the influence of physiological processes. The simulation results reproduced the blood flow process in portal venous system and the results showed that the splenic vein thrombosis caused serious impacts on hemodynamics. When blood flowed through the thrombosis, blood pressure reduced, flow velocity and wall shear stress increased. Flow resistance increased, blood flow velocity slowed down, the pressure gradient and wall shear stress distribution were more uniform in portal vein. The blood supply to liver decreased. Splenic vein thrombosis led to the possibility of forming new thrombosis in portal vein and surroundings.
Dietterich, Hannah; Lev, Einat; Chen, Jiangzhi; Richardson, Jacob A.; Cashman, Katharine V.
2017-01-01
Numerical simulations of lava flow emplacement are valuable for assessing lava flow hazards, forecasting active flows, designing flow mitigation measures, interpreting past eruptions, and understanding the controls on lava flow behavior. Existing lava flow models vary in simplifying assumptions, physics, dimensionality, and the degree to which they have been validated against analytical solutions, experiments, and natural observations. In order to assess existing models and guide the development of new codes, we conduct a benchmarking study of computational fluid dynamics (CFD) models for lava flow emplacement, including VolcFlow, OpenFOAM, FLOW-3D, COMSOL, and MOLASSES. We model viscous, cooling, and solidifying flows over horizontal planes, sloping surfaces, and into topographic obstacles. We compare model results to physical observations made during well-controlled analogue and molten basalt experiments, and to analytical theory when available. Overall, the models accurately simulate viscous flow with some variability in flow thickness where flows intersect obstacles. OpenFOAM, COMSOL, and FLOW-3D can each reproduce experimental measurements of cooling viscous flows, and OpenFOAM and FLOW-3D simulations with temperature-dependent rheology match results from molten basalt experiments. We assess the goodness-of-fit of the simulation results and the computational cost. Our results guide the selection of numerical simulation codes for different applications, including inferring emplacement conditions of past lava flows, modeling the temporal evolution of ongoing flows during eruption, and probabilistic assessment of lava flow hazard prior to eruption. Finally, we outline potential experiments and desired key observational data from future flows that would extend existing benchmarking data sets.
Energy Technology Data Exchange (ETDEWEB)
Hassan, Ashraf Aly [U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 W. Martin Luther King Drive, Cincinnati, OH 45268 (United States); Li, Zhen [School of Energy, Environmental, Biological, and Medical Engineering, Environmental Engineering Program, University of Cincinnati, Cincinnati, OH (United States); Sahle-Demessie, Endalkachew, E-mail: sahle-demessie.endalkachew@epa.gov [U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 W. Martin Luther King Drive, Cincinnati, OH 45268 (United States); Sorial, George A. [School of Energy, Environmental, Biological, and Medical Engineering, Environmental Engineering Program, University of Cincinnati, Cincinnati, OH (United States)
2013-01-15
Highlights: ► Breakthrough curves used to study fate of NPs in slow sand filters (SSF). ► CFD simulate transport, attachment/detachment of NPs in SSFs. ► CFD predicted spatial and temporal changes for transient concentrations of NPs. ► CFD predicts low concentrations and steady NP influx would not be retained by SSFs. ► Pulse input is retained with outlet concentration of 0.2% of the inlet. -- Abstract: Experimental and computational investigation of the transport parameters of nanoparticles (NPs) flowing through porous media has been made. This work intends to develop a simulation applicable to the transport and retention of NPs in saturated porous media for investigating the effect of process conditions and operating parameters such, as ion strength, and filtration efficiency. Experimental data obtained from tracer and nano-ceria, CeO{sub 2}, breakthrough studies were used to characterize dispersion of nanoparticle with the flow and their interaction with sand packed columns with different heights. Nanoparticle transport and concentration dynamics were solved using the Eulerian computational fluid dynamics (CFD) solver ANSYS/FLUENT{sup ®} based on a scaled down flow model. A numerical study using the Navier–Stokes equation with second order interaction terms was used to simulate the process. Parameters were estimated by fitting tracer, experimental NP transport data, and interaction of NP with the sand media. The model considers different concentrations of steady state inflow of NPs and different amounts of spike concentrations. Results suggest that steady state flow of dispersant-coated NPs would not be retained by a sand filter, while spike concentrations could be dampened effectively. Unlike analytical solutions, the CFD allows estimating flow profiles for structures with complex irregular geometry and uneven packing.
Chen, Gaoqiang; Feng, Zhili; Zhu, Yucan; Shi, Qingyu
2016-09-01
For better application of numerical simulation in optimization and design of friction stir welding (FSW), this paper presents a new frictional boundary condition at the tool/workpiece interface for computational fluid dynamics (CFD) modeling of FSW. The proposed boundary condition is based on an implementation of the Coulomb friction model. Using the new boundary condition, the CFD simulation yields non-uniform distribution of contact state over the tool/workpiece interface, as validated by the experimental weld macrostructure. It is found that interfacial sticking state is present over large area at the tool-workpiece interface, while significant interfacial sliding occurs at the shoulder periphery, the lower part of pin side, and the periphery of pin bottom. Due to the interfacial sticking, a rotating flow zone is found under the shoulder, in which fast circular motion occurs. The diameter of the rotating flow zone is smaller than the shoulder diameter, which is attributed to the presence of the interfacial sliding at the shoulder periphery. For the simulated welding condition, the heat generation due to friction and plastic deformation makes up 54.4 and 45.6% of the total heat generation rate, respectively. The simulated temperature field is validated by the good agreement to the experimental measurements.
Institute of Scientific and Technical Information of China (English)
Zhuo-dong ZHANG; Ralf WIELAND; Matthias REICHE; Roger FUNK; Carsten HOFFMANN; Yong LI; Michael SOMMER
2012-01-01
To provide physically based wind modelling for wind erosion research at regional scale,a 3D computational fluid dynamics (CFD) wind model was developed.The model was programmed in C language based on the Navier-Stokes equations,and it is freely available as open source.Integrated with the spatial analysis and modelling tool (SAMT),the wind model has convenient input preparation and powerful output visualization.To validate the wind model,a series of experiments was conducted in a wind tunnel.A blocking inflow experiment was designed to test the performance of the model on simulation of basic fluid processes.A round obstacle experiment was designed to check if the model could simulate the influences of the obstacle on wind field.Results show that measured and simulated wind fields have high correlations,and the wind model can simulate both the basic processes of the wind and the influences of the obstacle on the wind field.These results show the high reliability of the wind model.A digital elevation model (DEM) of an area (3800 m long and 1700 m wide) in the Xilingele grassland in Inner Mongolia (autonomous region,China) was applied to the model,and a 3D wind field has been successfully generated.The clear implementation of the model and the adequate validation by wind tunnel experiments laid a solid foundation for the prediction and assessment of wind erosion at regional scale.
Landazuri, Andrea C.
This dissertation focuses on aerosol transport modeling in occupational environments and mining sites in Arizona using computational fluid dynamics (CFD). The impacts of human exposure in both environments are explored with the emphasis on turbulence, wind speed, wind direction and particle sizes. Final emissions simulations involved the digitalization process of available elevation contour plots of one of the mining sites to account for realistic topographical features. The digital elevation map (DEM) of one of the sites was imported to COMSOL MULTIPHYSICSRTM for subsequent turbulence and particle simulations. Simulation results that include realistic topography show considerable deviations of wind direction. Inter-element correlation results using metal and metalloid size resolved concentration data using a Micro-Orifice Uniform Deposit Impactor (MOUDI) under given wind speeds and directions provided guidance on groups of metals that coexist throughout mining activities. Groups between Fe-Mg, Cr-Fe, Al-Sc, Sc-Fe, and Mg-Al are strongly correlated for unrestricted wind directions and speeds, suggesting that the source may be of soil origin (e.g. ore and tailings); also, groups of elements where Cu is present, in the coarse fraction range, may come from mechanical action mining activities and saltation phenomenon. Besides, MOUDI data under low wind speeds (processed in the smelter site, whereas the source of elements associated to Pb in the coarse fraction is of different origin. CFD simulation results will not only provide realistic and quantifiable information in terms of potential deleterious effects, but also that the application of CFD represents an important contribution to actual dispersion modeling studies; therefore, Computational Fluid Dynamics can be used as a source apportionment tool to identify areas that have an effect over specific sampling points and susceptible regions under certain meteorological conditions, and these conclusions can be supported
Kozelkov, A. S.; Kurulin, V. V.; Lashkin, S. V.; Shagaliev, R. M.; Yalozo, A. V.
2016-08-01
Two main issues of the efficient usage of computational fluid dynamics (CFD) in industrial applications—simulation of turbulence and speedup of computations—are analyzed. Results of the investigation of potentials of the eddy-resolving approaches to turbulence simulation in industrial applications with the use of arbitrary unstructured grids are presented. Algorithms for speeding up the scalable high-performance computations based on multigrid technologies are proposed.
Dietterich, H. R.; Lev, E.; Chen, J.; Cashman, K. V.; Honor, C.
2015-12-01
Recent eruptions in Hawai'i, Iceland, and Cape Verde highlight the need for improved lava flow models for forecasting and hazard assessment. Existing models used for lava flow simulation range in assumptions, complexity, and the degree to which they have been validated against analytical solutions, experiments, and natural observations. In order to assess the capabilities of existing models and test the development of new codes, we conduct a benchmarking study of computational fluid dynamics models for lava flows, including VolcFlow, OpenFOAM, Flow3D, and COMSOL. Using new benchmark scenarios defined in Cordonnier et al. (2015) as a guide, we model Newtonian, Herschel-Bulkley and cooling flows over inclined planes, obstacles, and digital elevation models with a wide range of source conditions. Results are compared to analytical theory, analogue and molten basalt experiments, and measurements from natural lava flows. Our study highlights the strengths and weakness of each code, including accuracy and computational costs, and provides insights regarding code selection. We apply the best-fit codes to simulate the lava flows in Harrat Rahat, a predominately mafic volcanic field in Saudi Arabia. Input parameters are assembled from rheology and volume measurements of past flows using geochemistry, crystallinity, and present-day lidar and photogrammetric digital elevation models. With these data, we use our verified models to reconstruct historic and prehistoric events, in order to assess the hazards posed by lava flows for Harrat Rahat.
Computational Fluid Dynamics Simulation Study of Active Power Control in Wind Plants
Energy Technology Data Exchange (ETDEWEB)
Fleming, Paul; Aho, Jake; Gebraad, Pieter; Pao, Lucy; Zhang, Yingchen
2016-08-01
This paper presents an analysis performed on a wind plant's ability to provide active power control services using a high-fidelity computational fluid dynamics-based wind plant simulator. This approach allows examination of the impact on wind turbine wake interactions within a wind plant on performance of the wind plant controller. The paper investigates several control methods for improving performance in waked conditions. One method uses wind plant wake controls, an active field of research in which wind turbine control systems are coordinated to account for their wakes, to improve the overall performance. Results demonstrate the challenge of providing active power control in waked conditions but also the potential methods for improving this performance.
Computer simulation study of surface wave dynamics at the crystal--melt interface
Benet, Jorge; Sanz, Eduardo
2014-01-01
We study, by means of computer simulations, the crystal-melt interface of three different systems: hard-spheres, Lennard Jones and the TIP4P/2005 water model. In particular, we focus on the dynamics of surface waves. We observe that the processes involved in the relaxation of surface waves are characterized by distinct time scales: a slow one related to the continuous recrystallization and melting, that is governed by capillary forces; and a fast one which we suggest to be due to a combination of processes that quickly cause small perturbations to the shape of the interface (like e. g. Rayleigh waves, subdiffusion, or attachment/detachment of particles to/from the crystal). The relaxation of surface waves becomes dominated by the slow process as the wavelength increases. Moreover, we see that the slow relaxation is not influenced by the details of the microscopic dynamics. In a time scale characteristic for the diffusion of the liquid phase, the relaxation dynamics of the crystal-melt interface of water is ar...
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
Hopkins, Paul; Fortini, Andrea; Archer, Andrew J; Schmidt, Matthias
2010-12-14
We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the "self " component having only one particle, the "distinct" component consisting of all the other particles, and using DDFT to calculate the time evolution of the density profiles for the two components. We apply this approach to a bulk fluid of Brownian hard spheres and compare to results for the van Hove function and the intermediate scattering function from Brownian dynamics computer simulations. We find good agreement at low and intermediate densities using the very simple Ramakrishnan-Yussouff [Phys. Rev. B 19, 2775 (1979)] approximation for the excess free energy functional. Since the DDFT is based on the equilibrium Helmholtz free energy functional, we can probe a free energy landscape that underlies the dynamics. Within the mean-field approximation we find that as the particle density increases, this landscape develops a minimum, while an exact treatment of a model confined situation shows that for an ergodic fluid this landscape should be monotonic. We discuss possible implications for slow, glassy, and arrested dynamics at high densities.
Computational fluid dynamics (CFD) simulations of aerosol in a U-shaped steam generator tube
Longmire, Pamela
To quantify primary side aerosol retention, an Eulerian/Lagrangian approach was used to investigate aerosol transport in a compressible, turbulent, adiabatic, internal, wall-bounded flow. The ARTIST experimental project (Phase I) served as the physical model replicated for numerical simulation. Realizable k-epsilon and standard k-o turbulence models were selected from the computational fluid dynamics (CFD) code, FLUENT, to provide the Eulerian description of the gaseous phase. Flow field simulation results exhibited: (a) onset of weak secondary flow accelerated at bend entrance towards the inner wall; (b) flow separation zone development on the convex wall that persisted from the point of onset; (c) centrifugal force concentrated high velocity flow in the direction of the concave wall; (d) formation of vortices throughout the flow domain resulted from rotational (Dean-type) flow; (e) weakened secondary flow assisted the formation of twin vortices in the outflow cross section; and (f) perturbations induced by the bend influenced flow recovery several pipe diameters upstream of the bend. These observations were consistent with those of previous investigators. The Lagrangian discrete random walk model, with and without turbulent dispersion, simulated the dispersed phase behavior, incorrectly. Accurate deposition predictions in wall-bounded flow require modification of the Eddy Impaction Model (EIM). Thus, to circumvent shortcomings of the EIM, the Lagrangian time scale was changed to a wall function and the root-mean-square (RMS) fluctuating velocities were modified to account for the strong anisotropic nature of flow in the immediate vicinity of the wall (boundary layer). Subsequent computed trajectories suggest a precision that ranges from 0.1% to 0.7%, statistical sampling error. The aerodynamic mass median diameter (AMMD) at the inlet (5.5 mum) was consistent with the ARTIST experimental findings. The geometric standard deviation (GSD) varied depending on the
Fan, De-Qiu; Sohn, H. Y.; Mohassab, Yousef; Elzohiery, Mohamed
2016-08-01
A three-dimensional computational fluid dynamics (CFD) model was developed to study the hydrogen reduction of magnetite concentrate particles in a laboratory flash reactor representing a novel flash ironmaking process. The model was used to simulate the fluid flow, heat transfer, and chemical reactions involved. The governing equations for the gas phase were solved in the Eulerian frame of reference while the particles were tracked in the Lagrangian framework. The change in the particle mass was related to the chemical reaction and the particle temperature was calculated by taking into consideration the heat of reaction, convection, and radiation. The stochastic trajectory model was used to describe particle dispersion due to turbulence. Partial combustion of H2 by O2 injected through a non-premixed burner was also simulated in this study. The partial combustion mechanism used in this model consisted of seven chemical reactions involving six species. The temperature profiles and reduction degrees obtained from the simulations satisfactorily agreed with the experimental measurements.
Fan, De-Qiu; Sohn, H. Y.; Mohassab, Yousef; Elzohiery, Mohamed
2016-12-01
A three-dimensional computational fluid dynamics (CFD) model was developed to study the hydrogen reduction of magnetite concentrate particles in a laboratory flash reactor representing a novel flash ironmaking process. The model was used to simulate the fluid flow, heat transfer, and chemical reactions involved. The governing equations for the gas phase were solved in the Eulerian frame of reference while the particles were tracked in the Lagrangian framework. The change in the particle mass was related to the chemical reaction and the particle temperature was calculated by taking into consideration the heat of reaction, convection, and radiation. The stochastic trajectory model was used to describe particle dispersion due to turbulence. Partial combustion of H2 by O2 injected through a non-premixed burner was also simulated in this study. The partial combustion mechanism used in this model consisted of seven chemical reactions involving six species. The temperature profiles and reduction degrees obtained from the simulations satisfactorily agreed with the experimental measurements.
Computational Fluid Dynamics Simulation of Oxygen Seepage in Coal Mine Goaf with Gas Drainage
Directory of Open Access Journals (Sweden)
Guo-Qing Shi
2015-01-01
Full Text Available Mine fires mainly arise from spontaneous combustion of coal seams and are a global issue that has attracted increasing public attention. Particularly in china, the closure of coal workfaces because of spontaneous combustion has contributed to substantial economic loss. To reduce the occurrence of mine fires, the spontaneous coal combustion underground needs to be studied. In this paper, a computational fluid dynamics (CFD model was developed for coal spontaneous combustion under goaf gas drainage conditions. The CFD model was used to simulate the distribution of oxygen in the goaf at the workface in a fully mechanized cave mine. The goaf was treated as an anisotropic medium, and the effects of methane drainage and oxygen consumption on spontaneous combustion were considered. The simulation results matched observational data from a field study, which indicates CFD simulation is suitable for research on the distribution of oxygen in coalmines. The results also indicated that near the workface spontaneous combustion was more likely to take place in the upper part of the goaf than near the bottom, while further from workface the risk of spontaneous combustion was greater in the lower part of the goaf. These results can be used to develop firefighting approaches for coalmines.
Yeh, In-Chul
1999-10-01
This dissertation investigates the structural and dynamical properties of aqueous solutions in clusters, in bulk, and at interfaces using molecular dynamics computer simulations. First, the photodetachment spectra of Cl- (H 2O)n (n = 2,3,...15) clusters have been calculated. The dependence of the spectra on the variations in the temperature of the clusters, the potential parameter for the postejected ion, and the type of the potential (pair-wise non-polarizable vs. many-body polarizable) has been investigated. Next, I have compared structural and dynamical properties of bulk water calculated by the simple point charge (SPC) and extended simple point charge (SPC/E) models. Tetrahedral network in SPC water is found to be weaker than those in SPC/E water due to smaller point charges, resulting in a larger self-diffusion coefficient. As a model interfacial system, I discuss the structure of water next to metal surfaces: Pt(100) and Pt(111). The two dimensional Ewald summation technique has been used for the calculation of long range Coulombic forces. Water next to an uncharged metallic surface is perturbed to a distance of 1 nm. Next to the charged surface water is reorienting and when the external field is strong, undergoes a layering transition. The dielectric constant of water as a function of electric fields has been also calculated. Simulations of water between walls and bulk water have been done to confirm the macroscopic nature of the dielectric constant. Calculated dielectric constants have been compared with those obtained by a theoretical prediction and a recent simulation study. Distance dependent density profiles of water near charged Ag(111) surfaces have been calculated and compared with experimental profiles. The effect of ionic screening is accounted for by an exponetially decaying electric field. Finally, I propose a modification in the three dimensional Ewald summation technique for calculations of long-range Coulombic forces for systems with a slab
Computational lfuid dynamics simulation of intracranial aneurysms - comparing size and shape
Institute of Scientific and Technical Information of China (English)
Zifeng Yang; Hongtao Yu; George P Huang; Ryan Schwieterman; Bryan Ludwig
2015-01-01
Objective:To study the hemodynamics of an anatomic internal carotid artery aneurysm derived from a patient-specific model and then manipulate into two phantom morphologies: one growing uniformly by size and the other changing shape unevenly. Methods: The computational model of the saccular, internal carotid artery, aneurysm was constructed from 3D rotational, digitally subtracted, catheter angiography images. Computational fluid dynamics simulations were performed under pulsatile cardiac flow conditions. Velocity vectors, streamlines, pressure, and wall shear stress (WSS) and its variance distributions were quantitatively visualized. Results: The maximum pressure andWSS from the time-averaged distribution on the inside saccular surface of the original case are 415.38 and 17.61 Pa. In contrast, the bi-lobed shape gives rise to higher peak values of pressure (461.00 Pa) andWSS (33.20 Pa) on the saccular dome. Conversely, the evenly enlarged aneurysm actually results in a slightly lower peak pressure (399.58 Pa) and drastically decreasedWSS (9.81 Pa). Conclusions:The current study indicates that the size of the aneurysm should not be the only determining factor for the rupture risk consideration, the irregularity of the aneurysm shape and the corresponding aberrant hemodynamics might be a more important factor to consider for risk assessment.
Huang, Weidong; Li, Kun; Wang, Gan; Wang, Yingzhe
2013-11-01
In this article, we present a newly designed inverse umbrella surface aerator, and tested its performance in driving flow of an oxidation ditch. Results show that it has a better performance in driving the oxidation ditch than the original one with higher average velocity and more uniform flow field. We also present a computational fluid dynamics model for predicting the flow field in an oxidation ditch driven by a surface aerator. The improved momentum source term approach to simulate the flow field of the oxidation ditch driven by an inverse umbrella surface aerator was developed and validated through experiments. Four kinds of turbulent models were investigated with the approach, including the standard k-ɛ model, RNG k-ɛ model, realizable k-ɛ model, and Reynolds stress model, and the predicted data were compared with those calculated with the multiple rotating reference frame approach (MRF) and sliding mesh approach (SM). Results of the momentum source term approach are in good agreement with the experimental data, and its prediction accuracy is better than MRF, close to SM. It is also found that the momentum source term approach has lower computational expenses, is simpler to preprocess, and is easier to use.
Computational Fluid Dynamics (CFD) Simulations of Jet Mixing in Tanks of Different Scales
Breisacher, Kevin; Moder, Jeffrey
2010-01-01
For long-duration in-space storage of cryogenic propellants, an axial jet mixer is one concept for controlling tank pressure and reducing thermal stratification. Extensive ground-test data from the 1960s to the present exist for tank diameters of 10 ft or less. The design of axial jet mixers for tanks on the order of 30 ft diameter, such as those planned for the Ares V Earth Departure Stage (EDS) LH2 tank, will require scaling of available experimental data from much smaller tanks, as well designing for microgravity effects. This study will assess the ability for Computational Fluid Dynamics (CFD) to handle a change of scale of this magnitude by performing simulations of existing ground-based axial jet mixing experiments at two tank sizes differing by a factor of ten. Simulations of several axial jet configurations for an Ares V scale EDS LH2 tank during low Earth orbit (LEO) coast are evaluated and selected results are also presented. Data from jet mixing experiments performed in the 1960s by General Dynamics with water at two tank sizes (1 and 10 ft diameter) are used to evaluate CFD accuracy. Jet nozzle diameters ranged from 0.032 to 0.25 in. for the 1 ft diameter tank experiments and from 0.625 to 0.875 in. for the 10 ft diameter tank experiments. Thermally stratified layers were created in both tanks prior to turning on the jet mixer. Jet mixer efficiency was determined by monitoring the temperatures on thermocouple rakes in the tanks to time when the stratified layer was mixed out. Dye was frequently injected into the stratified tank and its penetration recorded. There were no velocities or turbulence quantities available in the experimental data. A commercially available, time accurate, multi-dimensional CFD code with free surface tracking (FLOW-3D from Flow Science, Inc.) is used for the simulations presented. Comparisons are made between computed temperatures at various axial locations in the tank at different times and those observed experimentally. The
Computational fluid dynamics simulation of an earth-air heat exchanger for ventilation system
Raczkowski, Andrzej; Suchorab, Zbigniew; Czechowska-Kosacka, Aneta
2017-07-01
Directive 2010/31/EU (EPBD Recast) obligates European Union members to improve energetic performance of the buildings. One of the crucial standards of energy-saving buildings are the passive houses, which are characterized by annual maximum space heating below 15 kWh/(m2.a) and the use of the specific primary energy for all domestic applications (also heating, hot water production and electricity) below 120 kWh/(m2.a). To achieve this standard there should be applied the solutions based on ground energy acquisition. One of them is the earth-air heat exchanger (EAHC) for ventilation systems. The article presents numerical simulations conducted by solving partial differential equations for three dimensional heat transfer. For the simulations it was applied Computational Fluid Dynamics (CFD) technique. The efficiency of EAHC was considered under different values of external temperature during the winter period (from -24 to -8 °C). Obtained results prove linear correlation with calculations of EAHC according to standards of the Polish National Energy Conservation Agency (NAPE). The slope of regression between outlet temperatures calculated with CFD model and NAPE standards, equals 0.59 which means, that according the CFD model, the efficiency of the exchanger is lower.
Directory of Open Access Journals (Sweden)
S. Sugiharto1
2013-04-01
Full Text Available Multiphase flow modeling presents great challenges due to its extreme importance in various industrial and environmental applications. In the present study, prediction of separation length of multiphase flow is examined experimentally by injection of two kinds of iodine-based radiotracer solutions into a hydrocarbon transport pipeline (HCT having an inner diameter of 24 in (60,96 m. The main components of fluids in the pipeline are water 95%, crude oil 3% and gas 2%. A radiotracing experiment was carried out at the segment of pipe which is located far from branch points with assumptions that stratified flows in such segment were achieved. Two radiation detectors located at 80 and 100 m from injection point were used to generate residence time distribution (RTD curve resulting from injection of radiotracer solutions. Multiphase computational fluid dynamics (CFD simulations using Eulerian-Eulerian control volume and commercial CFD package Fluent 6.2 were employed to simulate separation length of multiphase flow. The results of study shows that the flow velocity of water is higher than the flow rate of crude oil in water-dominated system despite the higher density of water than the density of the crude oil. The separation length in multiphase flow predicted by Fluent mixture model is approximately 20 m, measured from injection point. This result confirms that the placement of the first radiation detector at the distance 80 m from the injection point was correct
Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E
Energy Technology Data Exchange (ETDEWEB)
Kumar, Ambuj [Bioinformatics Division, School of Bio Sciences and Technology, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu (India); Purohit, Rituraj, E-mail: riturajpurohit@gmail.com [Bioinformatics Division, School of Bio Sciences and Technology, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu (India)
2012-10-15
Aneuploidy and chromosomal instability (CIN) are hallmarks of most solid tumors. Mutations in centroemere proteins have been observed in promoting aneuploidy and tumorigenesis. Recent studies reported that Centromere-associated protein-E (CENP-E) is involved in inducing cancers. In this study we investigated the pathogenic effect of 132 nsSNPs reported in CENP-E using computational platform. Y63H point mutation found to be associated with cancer using SIFT, Polyphen, PhD-SNP, MutPred, CanPredict and Dr. Cancer tools. Further we investigated the binding affinity of ATP molecule to the CENP-E motor domain. Complementarity scores obtained from docking studies showed significant loss in ATP binding affinity of mutant structure. Molecular dynamics simulation was carried to examine the structural consequences of Y63H mutation. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R{sub g}), solvent accessibility surface area (SASA), energy value, hydrogen bond (NH Bond), eigenvector projection, trace of covariance matrix and atom density analysis results showed notable loss in stability for mutant structure. Y63H mutation was also shown to disrupt the native conformation of ATP binding region in CENP-E motor domain. Docking studies for remaining 18 mutations at 63rd residue position as well as other two computationally predicted disease associated mutations S22L and P69S were also carried to investigate their affect on ATP binding affinity of CENP-E motor domain. Our study provided a promising computational methodology to study the tumorigenic consequences of nsSNPs that have not been characterized and clear clue to the wet lab scientist.
Energy Technology Data Exchange (ETDEWEB)
Masse, B.
2001-07-01
By modifying the runner at the blade trailing edge in the draft tube elbow Hydro-Quebec was able to improve the efficiency of hydropower turbines and through computational fluid dynamic (CFD) simulations achieve revenue gains of between $200,000 and $500,000 per year for each of twelve turbines at one of its plants. The revenue gains were made possible by these modifications, validated by simulations. Power output was raised by 7.8 MW and weighted turbine efficiency by 1.6 per cent. The FIDAP CFD code from Fluent Incorporated, Lebanon, New Hampshire, was used as one of the modeling and analysis tools. This software package uses the finite element approach, and has the advantage of using non-structured grids which provide greater flexibility in modeling the complex and irregular geometries involved in hydropower turbines. The presence of a large eddy in the draft tube elbow was discovered and considered to be the cause of the less than expected hydraulic efficiency of the twelve identical hydro turbines. Water flow between the runner and the draft tube was improved by modification of the runner outlet and the design of a new trailing edge. Significant increase in efficiency at all operating conditions was the result which was confirmed by parametric study on the draft tube flow. This application of CFD simulations provides an excellent illustration of how CFD can identify hydropower problems and help develop alternatives to improve machine performance. The revenue gains resulting from the modifications to reduce the eddy in the runner and the draft tube elbow have been validated in one turbine and the design changes are in the process of being implemented on the other eleven turbines for a combined potential revenue gain in the order of $5 million per year. 3 figs.
Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.
2008-12-01
Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the
Computational fluid dynamics simulation and redesign of a screw conveyor reactor.
Wan, Yinkun; Hanley, Thomas R
2004-01-01
National Renewable Energy Laboratory (NREL) designed a shrinking-bed reactor to maintain a constant bulk packing density of cellulosic biomass. The high solid-to-liquid ratio in the pretreatment process allows a high sugar yield and avoids the need to flush large volumes of solution through the reactor. To scale up the shrinking-bed reactor, NREL investigated a pilot-scale screw conveyor reactor in which an interrupted flight between screws was employed to mimic the "shrinking-bed" effect. In the experiments with the screw conveyor reactor, overmixing and uneven flow occurred. These phenomena produce negative effects on biomass hydrolysis. The flow behavior inside the reactor was analyzed to allow redesign of the screw to achieve adequate mixing and even flow. In the present study, computational fluid dynamics (CFD) was utilized to simulate the fluid flow in the porous media, and a new screw design was proposed. CFD analysis performed on the redesigned reactor indicated that an even flow pattern was achieved.
Computational Fluid Dynamics Simulation of Liquid-Phase FCC Diesel Hydrotreating in Tubular Reactor
Institute of Scientific and Technical Information of China (English)
Li Hua; Liu Ningqiang; Zeng Zhiyu; Zou Ying; Wang Jiming
2015-01-01
The computational lfuid dynamics (CFD) code, FLUENT, was used to simulate the liquid-phase FCC diesel hy-drotreating tubular reactor with a ceramic membrane tube dispenser. The chemical reaction and reaction heat were added to the model by user-deifned function (UDF), showing the distribution of temperature and content of sulifdes, nitrides, bicyclic aromatics and monocyclic aromatics in different parts of the reaction bed. When the pressure was 6.5 MPa, the amount of mixing hydrogen was 0.84% (m), the space velocity was 2 h-1 and the inlet temperature was 633K, the temperature reached a maximum at a height of 0.15 m, and the range of radial temperature reached its maximum (2.5 K) at a height of 0.15 m. It indicated that the proper ratio of height to diameter of catalyst bed in the tubular reactor was 5-6. The increase of inlet temperature, the mixing hydrogen and the decrease of space velocity led to the decrease in the content of bicyclic aromatics, sulifdes and nitrides, and the increase in monocyclic aromatics content, while the high temperature increased. The results were in good agreement with experimental data, indicating to the high accuracy of the model.
Energy Technology Data Exchange (ETDEWEB)
Rzeznik, L., E-mail: rzeznik@lippmann.lu [University of Information Technology and Management, Sucharskiego 2, 35-225 Rzeszów (Poland); Postawa, Z. [Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków (Poland)
2014-05-01
Molecular dynamics computer simulations have been used to probe the role of the projectile composition on the emission efficiency and the sample damage. A benzene crystal was bombarded by 15 keV large heterogeneous noble gas clusters containing 2953 atoms. The projectiles used in this study are two-component clusters composed of Ne, Ar, and Kr atoms directed at 0° and 60° relative to the surface normal. It has been found that for normal incidence the total sputtering yield decreases with the projectile mass, whereas for 60° impact angle the yield increases with this quantity. For both 0° and 60° impact angles the observed sputtering yield for heterogeneous clusters cannot be calculated as a sum of sputtering yields obtained for homogeneous projectiles multiplied by the concentration of each component in the multi-component cluster. The difference in deposition scenarios of the primary kinetic energy is shown to be responsible for the observed behavior of the total sputtering yield.
Computational fluid dynamics simulation of laboratory scale reactor of fast pyrolysis fluidised bed
Amirmostafa Jourabchi, Seyed; Kiat Ng, Hoon; Gan, Suyin; Tan, Zhong Jian
2017-04-01
Euler-Eulerian two-fluid model (EE-TFM), among the computational fluid dynamics (CFD) techniques and module available on the market, have been chosen to study and obtain the operational parameters required for the fluidisation of different materials and different particle diameters of the fluidised bed model. In the present work, the effect of the material, namely stainless steel and sand with the respective diameters of 0.5 and 1 mm have been investigated with the aid of ANSYS FLUENT 15. From the simulation, it has found that the minimum required superficial velocity of the driving gas for fluidisation of steel beads are 70 cm/s and 140 cm/s respectively for diameter of 0.5 and 1.0 mm. On the other hand, the minimum required superficial velocities to fluidise the less dense sand beads are 30 cm/s and 70 cm/s for particle diameter of 0.5 and 1.0 mm respectively. The results show that the minimum fluidisation velocity increases as the density of the particle material increases; while it also increases, when the particle diameter increases. It is concluded that the drag force required to fluidise the specific solid bead material is proportional to both the density and the diameter of the particle chosen.
Numerical Simulation of Mixing in a Micro-well Scale Bioreactor by Computational Fluid Dynamics
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
The introduction of the multi-well plate miniaturisation technology with its associated automated dispensers, readers and integrated systems coupled with advances in life sciences has a propelling effect on the rate at which new potential drug molecules are discovered. The translation of these discoveries to real outcome now demands parallel approaches which allow large numbers of process options to be rapidly assessed. The engineering challenges in achieving this provide the motivation for the proposed work. In this work we used computational fluid dynamics(CFD) analysis to study flow conditions in a gas-liquid contactor which has the potential to be used as a fermenter on a multi-well format. The bioreactor had a working volume of 6.5 mL with the major dimensions equal to those of a single well of a 24-well plate. The 6.5 mL bioreactor was mechanically agitated and aerated by a single sparger placed beneath the bottom impeller. Detailed numerical procedure for solving the governing flow equations is given. The CFD results are combined with population balance equations to establish the size of the bubbles and their distribution in the bioreactor, Power curves with and without aeration are provided based on the simulated results.
An imaging-based computational model for simulating angiogenesis and tumour oxygenation dynamics
Adhikarla, Vikram; Jeraj, Robert
2016-05-01
Tumour growth, angiogenesis and oxygenation vary substantially among tumours and significantly impact their treatment outcome. Imaging provides a unique means of investigating these tumour-specific characteristics. Here we propose a computational model to simulate tumour-specific oxygenation changes based on the molecular imaging data. Tumour oxygenation in the model is reflected by the perfused vessel density. Tumour growth depends on its doubling time (T d) and the imaged proliferation. Perfused vessel density recruitment rate depends on the perfused vessel density around the tumour (sMVDtissue) and the maximum VEGF concentration for complete vessel dysfunctionality (VEGFmax). The model parameters were benchmarked to reproduce the dynamics of tumour oxygenation over its entire lifecycle, which is the most challenging test. Tumour oxygenation dynamics were quantified using the peak pO2 (pO2peak) and the time to peak pO2 (t peak). Sensitivity of tumour oxygenation to model parameters was assessed by changing each parameter by 20%. t peak was found to be more sensitive to tumour cell line related doubling time (~30%) as compared to tissue vasculature density (~10%). On the other hand, pO2peak was found to be similarly influenced by the above tumour- and vasculature-associated parameters (~30-40%). Interestingly, both pO2peak and t peak were only marginally affected by VEGFmax (~5%). The development of a poorly oxygenated (hypoxic) core with tumour growth increased VEGF accumulation, thus disrupting the vessel perfusion as well as further increasing hypoxia with time. The model with its benchmarked parameters, is applied to hypoxia imaging data obtained using a [64Cu]Cu-ATSM PET scan of a mouse tumour and the temporal development of the vasculature and hypoxia maps are shown. The work underscores the importance of using tumour-specific input for analysing tumour evolution. An extended model incorporating therapeutic effects can serve as a powerful tool for analysing
Macqueron, Corentin
2014-01-01
The traditional sauna is studied from a thermal and fluid dynamics standpoint using the NIST's Fire Dynamics Simulator (FDS) software. Calculations are performed in order to determine temperature and velocity fields, heat flux, soot and steam cloud transport, etc. Results are discussed in order to assess the reliability of this new kind of utilization of the FDS fire safety engineering software.
Kalinichev, A. G.; Xu, X.; Kirkpatrick, R.
2006-12-01
Dissolved organic matter (DOM) is ubiquitous in soil and surface water and plays many important geochemical and environmental roles acting as a proton donor/acceptor and pH buffer and interacting with metal ions, minerals and organic species to form water-soluble and water-insoluble complexes of widely differing chemical and biological stabilities. There are strong correlations among the concentration of DOM and the speciation, solubility and toxicity of many trace metals in soil and water due to metal-DOM interaction. DOM can also significantly negatively affect the performance of nanofiltration and reverse osmosis membranes used industrially for water purification and desalination, being one of the major causes of a so-called `membrane bio- fouling'. The molecular scale mechanisms and dynamics of the DOM interactions with metals and membranes are, however, quite poorly understood. Methods of computational molecular modeling, combined with element- specific nuclear magnetic resonance (NMR) spectroscopy, can serve as highly effective tools to probe and quantify on a fundamental molecular level the DOM interactions with metal cations in aqueous solutions, and to develop predictive models of the molecular mechanisms responsible for the metal-DOM complexation in the environment. This paper presents the results of molecular dynamics (MD) computer simulations of the interaction of DOM with dissolved Na+, Cs+, Mg2+, and Ca2+. Na+ forms only very weak outer-sphere complexes with DOM. These results and the results of other recent molecular modeling efforts (e.g., Sutton et al., Environmental Toxicology and Chemistry, 24, 1902-1911, 2005), clearly indicate that both the structural and dynamic aspects of the cation-DOM complexation follow a simple trend in terms of the charge/size ratio for the ions. Due to the competition between ion hydration in bulk aqueous solution and adsorption of these cations by the negatively charged DOM functional groups (primarily carboxylate
Cao, Minsong; Stantz, Keith M.; Liang, Yun
2006-03-01
Initial animal study for quantifying myocardial physiology through contrast-enhanced dynamic x-ray CT suggested that beam hardening is one of the limiting factors for accurate regional physiology measurement. In this study, a series of simulations were performed to investigate its deterioration effects and two correction algorithms were adapted to evaluate for their efficiency in improving the measurements. The simulation tool consists of a module simulating data acquisition of a real polyenergetic scanner system and a heart phantom consisting of simple geometric objects representing ventricles and myocardium. Each phantom component was modeled with time-varying attenuation coefficients determined by ideal iodine contrast dynamic curves obtained from experimental data or simulation. A compartment model was used to generate the ideal myocardium contrast curve using physiological parameters consistent with measured values. Projection data of the phantom were simulated and reconstructed to produce a sequence of simulated CT images. Simulated contrast dynamic curves were fitted to the compartmental model and the resultant physiological parameters were compared with ideal values to estimate the errors induced by beam hardening artifacts. The simulations yielded similar deterioration patterns of contrast dynamic curves as observed in the initial study. Significant underestimation of left ventricle curves and corruption of regional myocardium curves result in systematic errors of regional perfusion up to approximately 24% and overestimates of fractional blood volume (f iv) up to 13%. The correction algorithms lead to significant improvement with errors of perfusion reduced to 7% and errors of f iv within 2% which shows promise for more robust myocardial physiology measurement.
Kinetic Energy-Based Temperature Computation in Non-Equilibrium Molecular Dynamics Simulation
Liu, Bin; Xu, Ran; He, Xiaoqiao
2009-01-01
The average kinetic energy is widely used to characterize temperature in molecular dynamics (MD) simulation. In this letter, the applicability of three types of average kinetic energy as measures of temperature is investigated, i.e., the total kinetic energy, kinetic energy without the centroid translation part, and thermal disturbance kinetic energy. Our MD simulations indicate that definitions of temperature based on the kinetic energy including rigid translational or rotational motion may ...
A 5D computational phantom for pharmacokinetic simulation studies in dynamic emission tomography
Kotasidis, Fotis A.; Tsoumpas, Charalampos; Polycarpou, Irene; Zaidi, Habib
2014-01-01
Introduction: Dynamic image acquisition protocols are increasingly used in emission tomography for drug development and clinical research. As such, there is a need for computational phantoms to accurately describe both the spatial and temporal distribution of radiotracers, also accounting for period
Grid computing and biomolecular simulation.
Woods, Christopher J; Ng, Muan Hong; Johnston, Steven; Murdock, Stuart E; Wu, Bing; Tai, Kaihsu; Fangohr, Hans; Jeffreys, Paul; Cox, Simon; Frey, Jeremy G; Sansom, Mark S P; Essex, Jonathan W
2005-08-15
Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.
Weingart, Robert
This thesis is about the validation of a computational fluid dynamics simulation of a ground vehicle by means of a low-budget coast-down test. The vehicle is built to the standards of the 2014 Formula SAE rules. It is equipped with large wings in the front and rear of the car; the vertical loads on the tires are measured by specifically calibrated shock potentiometers. The coast-down test was performed on a runway of a local airport and is used to determine vehicle specific coefficients such as drag, downforce, aerodynamic balance, and rolling resistance for different aerodynamic setups. The test results are then compared to the respective simulated results. The drag deviates about 5% from the simulated to the measured results. The downforce numbers show a deviation up to 18% respectively. Moreover, a sensitivity analysis of inlet velocities, ride heights, and pitch angles was performed with the help of the computational simulation.
Observation of dynamical precursors of the isotropic-nematic transition by computer simulation
Allen, M.P.; Frenkel, D.
1987-01-01
We present the results of the first molecular-dynamics simulations of a molecular liquid, namely a system of prolate hard ellipsoids of revolution, near the isotropic-nematic liquid-crystal phase transition. Collective rotational motion in the isotropic phase slows down on approach to the transition
Experimental and computational investigation of the transport parameters of nano particles flowing through porous media has been made. The objective of this work was to develop a simulation capability applicable to the transport and retention of nanoparticles (NPs) in saturated p...
Energy Technology Data Exchange (ETDEWEB)
Bertolotto, D.
2011-11-15
The current doctoral research is focused on the development and validation of a coupled computational tool, to combine the advantages of computational fluid dynamics (CFD) in analyzing complex flow fields and of state-of-the-art system codes employed for nuclear power plant (NPP) simulations. Such a tool can considerably enhance the analysis of NPP transient behavior, e.g. in the case of pressurized water reactor (PWR) accident scenarios such as Main Steam Line Break (MSLB) and boron dilution, in which strong coolant flow asymmetries and multi-dimensional mixing effects strongly influence the reactivity of the reactor core, as described in Chap. 1. To start with, a literature review on code coupling is presented in Chap. 2, together with the corresponding ongoing projects in the international community. Special reference is made to the framework in which this research has been carried out, i.e. the Paul Scherrer Institute's (PSI) project STARS (Steady-state and Transient Analysis Research for the Swiss reactors). In particular, the codes chosen for the coupling, i.e. the CFD code ANSYS CFX V11.0 and the system code US-NRC TRACE V5.0, are part of the STARS codes system. Their main features are also described in Chap. 2. The development of the coupled tool, named CFX/TRACE from the names of the two constitutive codes, has proven to be a complex and broad-based task, and therefore constraints had to be put on the target requirements, while keeping in mind a certain modularity to allow future extensions to be made with minimal efforts. After careful consideration, the coupling was defined to be on-line, parallel and with non-overlapping domains connected by an interface, which was developed through the Parallel Virtual Machines (PVM) software, as described in Chap. 3. Moreover, two numerical coupling schemes were implemented and tested: a sequential explicit scheme and a sequential semi-implicit scheme. Finally, it was decided that the coupling would be single
Directory of Open Access Journals (Sweden)
Heru Suhartanto
2011-07-01
Full Text Available One of application that needs high performance computing resources is molecular dynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular dynamics of Indonesian grown herbal compounds show sufficient speed up on 32 nodes Cluster computing environment. In order to obtain a reliable simulation, one usually needs to run the experiment on the scale of hundred nodes. But this is expensive to develop and maintain. Since the invention of Graphical Processing Units that is also useful for general programming, many applications have been developed to run on this. This paper reports our experiments that evaluate the performance of GROMACS that runs on two different environment, Cluster computing resources and GPU based PCs. We run the experiment on BRV-1 and REM2 compounds. Four different GPUs are installed on the same type of PCs of quad cores; they are Gefore GTS 250, GTX 465, GTX 470 and Quadro 4000. We build a cluster of 16 nodes based on these four quad cores PCs. The preliminary experiment shows that those run on GTX 470 is the best among the other type of GPUs and as well as the cluster computing resource. A speed up around 11 and 12 is gained, while the cost of computer with GPU is only about 25 percent that of Cluster we built.
Senapati, Sanjib; Berkowitz, Max L.
2003-01-01
We performed a molecular dynamics simulation on a system containing a water pool inside the reverse micelle made up of an assembly of phosphate fluorosurfactant molecules dissolved in supercritical carbon dioxide. The water molecules in the first solvation shell of the headgroup lose the water to water tetrahedral hydrogen bonded network but are strongly bonded to the surfactant headgroups. This change in inter-water hydrogen bonding in connection with the confined geometry of the reverse micelle slows down the translational and especially the rotational dynamics of water.
Dynamic computer simulations of electrophoresis: a versatile research and teaching tool.
Thormann, Wolfgang; Breadmore, Michael C; Caslavska, Jitka; Mosher, Richard A
2010-03-01
Software is available, which 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. These dynamic models are based upon equations derived from the transport concepts such as electromigration, diffusion, electroosmosis and imposed hydrodynamic buffer flow that are applied to user-specified initial distributions of analytes and electrolytes. They are able to predict the evolution of electrolyte systems together with associated properties such as pH and conductivity profiles and are as such the most versatile tool to explore the fundamentals of electrokinetic separations and analyses. In addition to revealing the detailed mechanisms of fundamental phenomena that occur in electrophoretic separations, dynamic simulations are useful for educational purposes. This review includes a list of current high-resolution simulators, information on how a simulation is performed, simulation examples for zone electrophoresis, ITP, IEF and EKC and a comprehensive discussion of the applications and achievements.
DEFF Research Database (Denmark)
Rømer, Daniel; Johansen, Per; Pedersen, Henrik C.
2013-01-01
A fast rotating 1500 rpm radial piston digital displacement motor connected to a 350 bar high pressure manifold is simulated by means of transient 3D CFD analysis of a single pressure chamber. The analysis includes dynamic piston and valve movement, influencing the boundaries of the fluid domain....
Tsirkunov, Yu. M.; Romanyuk, D. A.
2016-07-01
A dusty gas flow through two, moving and immovable, cascades of airfoils (blades) is studied numerically. In the mathematical model of two-phase gas-particle flow, the carrier gas is treated as a continuum and it is described by the Navier-Stokes equations (pseudo-DNS (direct numerical simulation) approach) or the Reynolds averaged Navier-Stokes (RANS) equations (unsteady RANS approach) with the Menter k-ω shear stress transport (SST) turbulence model. The governing equations in both cases are solved by computational fluid dynamics (CFD) methods. The dispersed phase is treated as a discrete set of solid particles, the behavior of which is described by the generalized kinetic Boltzmann equation. The effects of gas-particle interaction, interparticle collisions, and particle scattering in particle-blade collisions are taken into account. The direct simulation Monte Carlo (DSMC) method is used for computational simulation of the dispersed phase flow. The effects of interparticle collisions and particle scattering are discussed.
COMPUTATIONAL TOOL FOR SIMULATION OF THE DYNAMIC RESPONSE OF VALVE TRAIN
Directory of Open Access Journals (Sweden)
Krešimir Osman
2014-03-01
Full Text Available This paper presents the development of the MOTORI 2004 computing tool that calculates the distance, speed and acceleration of a car engine valve train’s oscillating mass m, which is reduced to the valve axis. Distance diagrams, speed and accelerations are provided in dependence on the camshaft twist angle at a constant rotational speed in several consecutive revolutions. The computing tool implements a mathematical description and numerical solution for the motion of mass m of a valve gear dynamic model. Valve lift h is given numerically using a series of equidistant points in the period of one camshaft revolution. The variabilities of camshaft rotation and spring thread vibration as a result of cam lift harmonic excitation. The computing solutions were tested at valve opening points and in imaginary extreme operating conditions (soft/hard spring, low/high damping, low/high rotational speed and increased clearance.
Institute of Scientific and Technical Information of China (English)
Zhang Shanyuan; Lei Jianping; Zhao Longmao; Cheng Guoqiang; Lu Guoyun
2000-01-01
This article reports an experimental investigation on the axial impact buckling of thin metallic cylindrical shells fully filled with water. Low velocity impact tests are carried out by DHR-9401 drop hammer rig. The whole process of dynamic buckling is simulated using LS-DYNA computer code. The consistency between experimental observation and numerical simulation is quite satisfactory. The investigation indicates that quite high internal hydrodynamic pressure occurs inside the shell during the impact process. Under the combined action of the high internal pressure and axial compression plastic buckling occurs easily in the thin walled shells and buckling modes take on regular and axisymmetric wrinkles.
Slater, John W.; Saunders, John D.
2010-01-01
Methods of computational fluid dynamics were applied to simulate the aerodynamics within the turbine flowpath of a turbine-based combined-cycle propulsion system during inlet mode transition at Mach 4. Inlet mode transition involved the rotation of a splitter cowl to close the turbine flowpath to allow the full operation of a parallel dual-mode ramjet/scramjet flowpath. Steady-state simulations were performed at splitter cowl positions of 0deg, -2deg, -4deg, and -5.7deg, at which the turbine flowpath was closed half way. The simulations satisfied one objective of providing a greater understanding of the flow during inlet mode transition. Comparisons of the simulation results with wind-tunnel test data addressed another objective of assessing the applicability of the simulation methods for simulating inlet mode transition. The simulations showed that inlet mode transition could occur in a stable manner and that accurate modeling of the interactions among the shock waves, boundary layers, and porous bleed regions was critical for evaluating the inlet static and total pressures, bleed flow rates, and bleed plenum pressures. The simulations compared well with some of the wind-tunnel data, but uncertainties in both the windtunnel data and simulations prevented a formal evaluation of the accuracy of the simulation methods.
Dynamical Simulation of Probabilities
Zak, Michail
1996-01-01
It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-Lipschitz dynamics, without utilization of any man-made devices(such as random number generators). Self-orgainizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed. Special attention was focused upon coupled stochastic processes, defined in terms of conditional probabilities, for which joint probability does not exist. Simulations of quantum probabilities are also discussed.
Computational fluid dynamics simulation and geometric design of hydraulic turbine draft tube
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JB Sosa
2015-10-01
Full Text Available Any hydraulic reaction turbine is installed with a draft tube that impacts widely the entire turbine performance, on which its functions are as follows: drive the flux in appropriate manner after it releases its energy to the runner; recover the suction head by a suction effect; and improve the dynamic energy in the runner outlet. All these functions are strongly linked to the geometric definition of the draft tube. This article proposes a geometric parametrization and analysis of a Francis turbine draft tube. Based on the parametric definition, geometric changes in the draft tube are proposed and the turbine performance is modeled by computational fluid dynamics; the boundary conditions are set by measurements performed in a hydroelectric power plant. This modeling allows us to see the influence of the draft tube shape on the entire turbine performance. The numerical analysis is based on the steady-state solution of the turbine component flows for different guide vanes opening and multiple modified draft tubes. The computational fluid dynamics predictions are validated using hydroelectric plant measurements. The prediction of the turbine performance is successful and it is linked to the draft tube geometric features; therefore, it is possible to obtain a draft tube parameter value that results in a desired turbine performance.
Computational fluid dynamics simulations of blood flow regularized by 3D phase contrast MRI
DEFF Research Database (Denmark)
Rispoli, Vinicius C; Nielsen, Jon; Nayak, Krishna S
2015-01-01
approach in regularizing 3D flow fields is evaluated. METHODS: The proposed algorithm incorporates both a Newtonian fluid physics model and a linear PC-MRI signal model. The model equations are solved numerically using a modified CFD algorithm. The numerical solution corresponds to the optimal solution......BACKGROUND: Phase contrast magnetic resonance imaging (PC-MRI) is used clinically for quantitative assessment of cardiovascular flow and function, as it is capable of providing directly-measured 3D velocity maps. Alternatively, vascular flow can be estimated from model-based computation fluid...... dynamics (CFD) calculations. CFD provides arbitrarily high resolution, but its accuracy hinges on model assumptions, while velocity fields measured with PC-MRI generally do not satisfy the equations of fluid dynamics, provide limited resolution, and suffer from partial volume effects. The purpose...
Computational fluid dynamic applications
Energy Technology Data Exchange (ETDEWEB)
Chang, S.-L.; Lottes, S. A.; Zhou, C. Q.
2000-04-03
The rapid advancement of computational capability including speed and memory size has prompted the wide use of computational fluid dynamics (CFD) codes to simulate complex flow systems. CFD simulations are used to study the operating problems encountered in system, to evaluate the impacts of operation/design parameters on the performance of a system, and to investigate novel design concepts. CFD codes are generally developed based on the conservation laws of mass, momentum, and energy that govern the characteristics of a flow. The governing equations are simplified and discretized for a selected computational grid system. Numerical methods are selected to simplify and calculate approximate flow properties. For turbulent, reacting, and multiphase flow systems the complex processes relating to these aspects of the flow, i.e., turbulent diffusion, combustion kinetics, interfacial drag and heat and mass transfer, etc., are described in mathematical models, based on a combination of fundamental physics and empirical data, that are incorporated into the code. CFD simulation has been applied to a large variety of practical and industrial scale flow systems.
Gain in computational efficiency by vectorization in the dynamic simulation of multi-body systems
Amirouche, F. M. L.; Shareef, N. H.
1991-01-01
An improved technique for the identification and extraction of the exact quantities associated with the degrees of freedom at the element as well as the flexible body level is presented. It is implemented in the dynamic equations of motions based on the recursive formulation of Kane et al. (1987) and presented in a matrix form, integrating the concepts of strain energy, the finite-element approach, modal analysis, and reduction of equations. This technique eliminates the CPU intensive matrix multiplication operations in the code's hot spots for the dynamic simulation of the interconnected rigid and flexible bodies. A study of a simple robot with flexible links is presented by comparing the execution times on a scalar machine and a vector-processor with and without vector options. Performance figures demonstrating the substantial gains achieved by the technique are plotted.
Li, Yang
2014-07-07
The recruitment dynamics of lipids in the biomembrane is believed to play an important role in a variety of cellular processes. In this work, we investigate the nanoparticle-induced recruitment dynamics of lipids in the heterogeneous phospholipid bilayers of distearoyl-phosphatidylcholine (DSPC) and dioleoyl-phosphatidylglycerol (DOPG) via coarse-grained molecular dynamics simulations. Three dynamic modes of individual charged DOPG lipid molecules have been taken into account in the recruitment process: lateral diffusion, protrusions, and flip-flops. Based on analysis of the mobility pattern of lipids, structural variations in the membrane as well as activation energy of the structure of lipid eyelids characterized by the potential of mean force, we have concluded that the electrostatic attraction of nanoparticles plays a crucial role in the recruitment process of lipids in phospholipid bilayers. These studies are consistent with experimental observations and to some extent give insight into the origin of some cellular processes such as signaling, formation of lipid rafts, and endocytosis.
Méndez-Morales, Trinidad; Carrete, Jesús; García, Manuel; Cabeza, Oscar; Gallego, Luis J; Varela, Luis M
2011-12-29
In this work, extensive molecular dynamics simulations of the dynamics of mixtures of ionic liquids (ILs) composed of the cation 1-hexyl-3-methylimidazolium and several anions of different hydrophobicity degrees (Cl(-), BF(4)(-), PF(6)(-)) with alcohols of different chain lengths (methanol and ethanol) are reported. We evaluated the influence of the nature of the anion, the length of the molecular chain of the alcohol, and the alcohol concentration on some dynamical properties of the mixtures, such as self-diffusion coefficients of all the species, mean square displacements (with an analysis of both ballistic and diffusive regimes), and velocity autocorrelation functions of alcohol molecules. The diffusivity of the mixtures was found to be highly dependent on the nature of the anion since the interaction between chloride and alcohols is greater than that with fluorinated anions and leads to slower dynamics. Additionally, our results show that self-diffusion coefficients increase with alcohol concentration. On the other hand, a subdiffusive regime over thousands of picoseconds was detected at intermediate times through analysis of the center-of-mass mean square displacements of alcohol molecules, a region that becomes narrower as alcohol concentration increases. Finally, the study of the role of the anion and of solvent concentration on velocity autocorrelation functions reflects an increase in mean collision times as the amount of alcohol increases until the value of pure alcohols is reached. These collision times are smaller in mixtures with halogenated ILs. © 2011 American Chemical Society
Directory of Open Access Journals (Sweden)
Massimiliano eMeli
2016-05-01
Full Text Available Herein we investigate the molecular bases of DNA polymerase I conformational dynamics that underlie the replication fidelity of the enzyme. Such fidelity is determined by conformational changes that promote the rejection of incorrect nucleotides before the chemical ligation step. We report a comprehensive atomic resolution study of wild type and mutant enzymes in different bound states and starting from different crystal structures, using extensive molecular dynamics (MD simulations that cover a total timespan of ~ 5 microseconds. The resulting trajectories are examined via a combination of novel methods of internal dynamics and energetics analysis, aimed to reveal the principal molecular determinants for the (destabilization of a certain conformational state. Our results show that the presence of fidelity-decreasing mutations or the binding of incorrect nucleotides in ternary complexes tend to favor transitions from closed towards open structures, passing through an ensemble of semi-closed intermediates. The latter ensemble includes the experimentally observed ajar conformation which, consistent with previous experimental observations, emerges as a molecular checkpoint for the selection of the correct nucleotide to incorporate. We discuss the implications of our results for the understanding of the relationships between the structure, dynamics and function of DNA polymerase I at the atomistic level.
Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code
Energy Technology Data Exchange (ETDEWEB)
Schiffgens, J.O.; Graves, N.J.; Oster, C.A.
1980-04-01
This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.
Control of convergence in a computational fluid dynamic simulation using fuzzy logic
Institute of Scientific and Technical Information of China (English)
刘训良; 陶文铨; 郑平; 何雅玲; 王秋旺
2002-01-01
A fuzzy control method was used to accelerate iteration convergence in numerical fluid dynamic simulation using SIMPLER algorithm. The residual ratio of momentum or energy equation between two successive iterations was used as the input variable. A fuzzy logic algorithm was developed in order to obtain the relative increment of the under-relaxation factor and its new value was then used for the next iteration. The algorithm was tested by four benchmark problems. In all cases considered, when the fuzzy control logic was used, convergence was achieved with nearly the minimum number of iterations, showing the feasibility of the proposed method.
Sen, Seema; Lake, Markus; Kroppen, Norman; Farber, Peter; Wilden, Johannes; Schaaf, Peter
2017-02-01
This study describes the self-propagating exothermic reaction in Ti/Al reactive multilayer foils by using experiments and computational fluid dynamics simulation. The Ti/Al foils with different molar ratios of 1Ti/1Al, 1Ti/2Al and 1Ti/3Al were fabricated by magnetron sputtering method. Microstructural characteristics of the unreacted and reacted foils were analyzed by using electronic and atomic force microscopes. After an electrical ignition, the influence of ignition potentials on reaction propagation has been experimentally investigated. The reaction front propagates with a velocity of minimum 0.68 ± 0.4 m/s and maximum 2.57 ± 0.6 m/s depending on the input ignition potentials and the chemical compositions. Here, the 1Ti/3Al reactive foil exhibits both steady state and unsteady wavelike reaction propagation. Moreover, the numerical computational fluid dynamics (CFD) simulation shows the time dependent temperature flow and atomic mixing in a nanoscale reaction zone. The CFD simulation also indicates the potentiality for simulating exothermic reaction in the nanoscale Ti/Al foil.
Directory of Open Access Journals (Sweden)
G. SANTOS
2008-05-01
Full Text Available To develop and to evaluate the efficiency of a software able to simulate a virtual patient at different stages of addition was the main goal and challenge of this work. We developed the software in Borland™ Delphi 5® programming language. Techniques of artificial intelligence, neuronal networks and expert systems, were responsible for modeling the neurobiological structures and mechanisms of the interaction with the drugs used. Dynamical simulation and hypermedia were designed to increase the software’s interactivity which was able to show graphical information from virtual instrumentation and from realistic functional magnetic resonance imaging display. Early, the program was designed to be used by undergraduate students to improve their neurophysiologic learn, based not only in an interaction of membrane receptors with drugs, but in such a large behavioral simulation. The experimental manipulation of the software was accomplished by: i creating a virtual patient from a normal mood to a behavioral addiction, increasing gradatively: alcohol, opiate or cocaine doses. ii designing an approach to treat the patient, to get total or partial remission of behavioral disorder by combining psychopharmacology and psychotherapy. Integration of dynamic simulation with hypermedia and artificial intelligence has been able to point out behavioral details as tolerance, sensitization and level of addiction to drugs of abuse and so on, turned into a potentially useful tool in the development of teaching activities on several ways, such as education as well clinical skills, in which it could assist patients, families and health care to improve and test their knowledge and skills about different faces supported by drugs dependency. Those features are currently under investigation.
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S. Saha
2016-04-01
Full Text Available Combustion instability in solid propellant rocket motor is numerically simulated by implementing propellant response function with quasi steady homogeneous one dimensional formulation. The convolution integral of propellant response with pressure history is implemented through a user defined function in commercial computational fluid dynamics software. The methodology is validated against literature reported motor test and other simulation results. Computed amplitude of pressure fluctuations compare closely with the literarture data. The growth rate of pressure oscillations of a cylindrical grain solid rocket motor is determined for different response functions at the fundamental longitudinal frequency. It is observed that for response function more than a critical value, the motor exhibits exponential growth rate of pressure oscillations.
Simulation of quantum computers
De Raedt, H; Michielsen, K; Hams, AH; Miyashita, S; Saito, K; Landau, DP; Lewis, SP; Schuttler, HB
2001-01-01
We describe a simulation approach to study the functioning of Quantum Computer hardware. The latter is modeled by a collection of interacting spin-1/2 objects. The time evolution of this spin system maps one-to-one to a quantum program carried out by the Quantum Computer. Our simulation software con
Computational Fluid Dynamic Simulation of Flow in Abrasive Water Jet Machining
Venugopal, S.; Sathish, S.; Jothi Prakash, V. M.; Gopalakrishnan, T.
2017-03-01
Abrasive water jet cutting is one of the most recently developed non-traditional manufacturing technologies. In this machining, the abrasives are mixed with suspended liquid to form semi liquid mixture. The general nature of flow through the machining, results in fleeting wear of the nozzle which decrease the cutting performance. The inlet pressure of the abrasive water suspension has main effect on the major destruction characteristics of the inner surface of the nozzle. The aim of the project is to analyze the effect of inlet pressure on wall shear and exit kinetic energy. The analysis could be carried out by changing the taper angle of the nozzle, so as to obtain optimized process parameters for minimum nozzle wear. The two phase flow analysis would be carried by using computational fluid dynamics tool CFX. It is also used to analyze the flow characteristics of abrasive water jet machining on the inner surface of the nozzle. The availability of optimized process parameters of abrasive water jet machining (AWJM) is limited to water and experimental test can be cost prohibitive. In this case, Computational fluid dynamics analysis would provide better results.
Directory of Open Access Journals (Sweden)
Yang Zeqing
2013-07-01
Full Text Available In order to design the feed system of high speed Computer Numerical Control (CNC lathe, the static and dynamic characteristics of feed system driven by linear motor in high speed CNC lathe were analyzed. The slide board was taking as the main moving part of the feed system, and the guide rail was the main support component of the linear motor feed system. The mechanical structure static stiffness of feed system is researched through the slide board statics analysis. The simulation results show that the maximum deformation of the slide board occurs in the middle of the slide board where the linear motor is placed. The linear motor feed system control model was established based on analysis of high-speed linear feed system control principle, and the linear motor feed system transfer function was established, and servo dynamic stiffness factors were analyzed. The control parameters of the servo system and actuating mechanism parameters of feed system on the effect of the linear motor servo dynamic stiffness were analyzed using MATLAB software. The simulation results show that the position loop proportional gain, speed loop proportional gain and speed loop integral response time are the biggest influence factors on servo dynamic stiffness. The displacement response is reduced under the cutting interference force step inputting, the servo dynamic stiffness is increased, the number of system oscillation is also reduced, and the system tends to be stable.
DEFF Research Database (Denmark)
Nielsen, Peter Vilhelm
2003-01-01
An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution is introduced for improvement of the predictions of both the energy consumption and the indoor environment.The article describes a calculation...... of the energy consumption in a large building where the building energy simulation program is modified by CFD predictions of the flow between three zones that are connected by pressure and buoyancy-driven air flow through open areas. The two programs are interconnected in an iterative procedure. The article...... shows also an evaluation of the air quality in the main area of the buildings based on CFD predictions. It is demonstrated that an interconnection between a CFD program and a building energy performance simulation program will improve both the energy consumption data and the prediction of thermal...
Sajja, V S K; Kennedy, David J; Todd, Paul W; Hanley, Thomas R
2011-10-01
In the Quadrupole Magnetic Sorter (QMS) magnetic particles enter a vertical flow annulus and are separated from non-magnetic particles by radial deflection into an outer annulus where the purified magnetic particles are collected via a flow splitter. The purity of magnetically isolated particles in QMS is affected by the migration of nonmagnetic particles across transport lamina in the annular flow channel. Computational Fluid Dynamics (CFD) simulations were used to predict the flow patterns, pressure drop and nonspecific crossover in QMS flow channel for the isolation of pancreatic islets of Langerhans. Simulation results were compared with the experimental results to validate the CFD model. Results of the simulations were used to show that one design gives up to 10% less nonspecific crossover than another and this model can be used to optimise the flow channel design to achieve maximum purity of magnetic particles.
Computer Simulations on a Multidimensional Continuum:
DEFF Research Database (Denmark)
Girault, Isabelle; Pfeffer, Melanie; Chiocarriello, Augusto
2016-01-01
Computer simulations exist on a multidimensional continuum with other educational technologies including static animations, serious games, and virtual worlds. The act of defining simulations is context dependent. In our context of science education, we define simulations as algorithmic, dynamic...... with emphasis on simulations’ algorithmic, dynamic, and simple features. Defined as models, simulations can be computational or conceptual in nature and may reflect hypothetical or real events; such distinctions are addressed. Examples of programs that demonstrate the features of simulations emphasized in our...
Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume
2017-09-01
The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.
Directory of Open Access Journals (Sweden)
Paolo Maria Congedo
2016-11-01
Full Text Available Improving energy efficiency in buildings and promoting renewables are key objectives of European energy policies. Several technological measures are being developed to enhance the energy performance of buildings. Among these, geothermal systems present a huge potential to reduce energy consumption for mechanical ventilation and cooling, but their behavior depending on varying parameters, boundary and climatic conditions is not fully established. In this paper a horizontal air-ground heat exchanger (HAGHE system is studied by the development of a computational fluid dynamics (CFD model. Summer and winter conditions representative of the Mediterranean climate are analyzed to evaluate operation and thermal performance differences. A particular focus is given to humidity variations as this parameter has a major impact on indoor air quality and comfort. Results show the benefits that HAGHE systems can provide in reducing energy consumption in all seasons, in summer when free-cooling can be implemented avoiding post air treatment using heat pumps.
DYNAMIC COMPUTER SIMULATION OF CONCRETE ON DIFFERENT LEVELS OF THE MICROSTRUCTURE – PART 2
Directory of Open Access Journals (Sweden)
Piet Stroeven
2011-05-01
Full Text Available The establishment of an experimental basis for the dependence of a mechanical property on certain structural features (and the associated micro-mechanical properties would require extensive, cumbersome and complicated testing: mechanical testing for defining the very property, quantitative (section image analysis and stereological three-dimensional assessment of the relevant structural features. 'Realistic' simulation of material structure by computer would therefore offer an interesting alternative. This paper introduces the SPACE system (Software Package for the Assessment of Compositional Evolution as the most recent development in this field. It has been developed to assess the composition as well as configuration characteristics of dense random packing situations in opaque materials. This paper presents an introduction to the system and will thereupon highlight by means of illustrative examples of typical applications on different levels of the microstructure the system's capabilities. Although only a single application can be presented in this framework, they all concern areas of major engineering interest.
DYNAMIC COMPUTER SIMULATION OF CONCRETE ON DIFFERENT LEVELS OF THE MICROSTRUCTURE
Directory of Open Access Journals (Sweden)
Piet Stroeven
2011-05-01
Full Text Available The establishment of an experimental basis for the dependence of a mechanical property on certain structural features (and the associated micro-mechanical properties would require extensive, cumbersome and complicated testing: mechanical testing for defining the very property, quantitative (section image analysis and stereological three-dimensional assessment of the relevant structural features. 'Realistic' simulation of material structure by computer would therefore offer an interesting alternative. This paper introduces the SPACE system (Software Package for the Assessment of Compositional Evolution as the most recent development in this field. It has been developed to assess the composition as well as configuration characteristics of dense random packing situations in opaque materials. This paper presents an introduction to the system and will thereupon highlight by means of illustrative examples of typical applications on different levels of the microstructure the system's capabilities. Although only a single application can be presented in this framework, they all concern areas of major engineering interest.
Computational fluid dynamic simulations on liquid film behaviors at flooding in an inclined pipe☆
Institute of Scientific and Technical Information of China (English)
Jianye Chen; Yuan Tang; Wei Zhang; Yuchen Wang; Limin Qiu; Xiaobin Zhang
2015-01-01
The complex liquid film behaviors at flooding in an inclined pipe were investigated with computational fluid dynamic (CFD) approaches. The liquid film behaviors included the dynamic wave characteristics before flooding and the transition of flow pattern when flooding happened. The influences of the surface tension and liquid viscosity were specially analyzed. Comparisons of the calculated velocity at the onset of flooding with the available experimental results showed a good agreement. The calculations verify that the fluctuation frequency and the liquid film thickness are almost unaffected by the superficial gas velocity until the flooding is triggered due to the Kelvin–Helmholtz instability. When flooding triggered at the superficial liquid velocity larger than 0.15 m·s−1, the interfacial wave developed to slug flow, while it developed to entrainment flow when it was smaller than 0.08 m·s−1. The interfacial waves were more easily torn into tiny droplets with smaller surface tension, eventual y evolving into the mist flow. When the liquid viscosity increases, the liquid film has a thicker holdup with more intensive fluctuations, and more likely developed to the slug flow.
Structure and dynamics of Antarctic fish neuroglobin assessed by computer simulations.
Boron, Ignacio; Russo, Roberta; Boechi, Leonardo; Cheng, C-H Christina; di Prisco, Guido; Estrin, Darío A; Verde, Cinzia; Nadra, Alejandro D
2011-03-01
Neuroglobin (Ngb) is a heme protein, highly conserved along evolution, predominantly found in the nervous system. It is upregulated by hypoxia and ischemia and may have a neuroprotective role under hypoxic stress. Although many other roles have been proposed, the physiological function is still unclear. Antarctic icefishes lack hemoglobin and some species also lack myoglobin, but all have Ngb and thus may help the elucidation of Ngb function. We present the first theoretically derived structure of fish Ngb and describe its behavior using molecular dynamics simulations. Specifically, we sequenced and analyzed Ngbs from a colorless-blooded Antarctic icefish species Chaenocephalus aceratus and a related red-blooded species (Dissostichus mawsoni). Both fish Ngbs are 6-coordinated but have some peculiarities that differentiate them from mammalian counterparts: they have extensions in the N and C termini that can interact with the EF loop, and a gap in the alignment that changes the CD-region structure/dynamics that has been found to play a key role in human neuroglobin. Our results suggest that a single mutation between both fish Ngbs is responsible for significant difference in the behavior of the proteins. The functional role of these characteristics is discussed.
Campos, Marcelino; Llorens, Carlos; Sempere, José M; Futami, Ricardo; Rodriguez, Irene; Carrasco, Purificación; Capilla, Rafael; Latorre, Amparo; Coque, Teresa M; Moya, Andres; Baquero, Fernando
2015-08-05
Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered environments. The implementation of computable models with reciprocity within and between levels of biological organization (i.e. essential nesting) is central for studying antibiotic resistances. Antibiotic resistance is not just the result of antibiotic-driven selection but more properly the consequence of a complex hierarchy of processes shaping the ecology and evolution of the distinct subcellular, cellular and supra-cellular vehicles involved in the dissemination of resistance genes. Such a complex background motivated us to explore the P-system standards of membrane computing an innovative natural computing formalism that abstracts the notion of movement across membranes to simulate antibiotic resistance evolution processes across nested levels of micro- and macro-environmental organization in a given ecosystem. In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysis. The stochastic nature of the P-system model implemented in ARES explicitly links within and between host dynamics into a simulation, with
Feder, Jeffrey L; Nosil, Patrik; Flaxman, Samuel M
2014-01-01
Many hypotheses have been put forth to explain the origin and spread of inversions, and their significance for speciation. Several recent genic models have proposed that inversions promote speciation with gene flow due to the adaptive significance of the genes contained within them and because of the effects inversions have on suppressing recombination. However, the consequences of inversions for the dynamics of genome wide divergence across the speciation continuum remain unclear, an issue we examine here. We review a framework for the genomics of speciation involving the congealing of the genome into alternate adaptive states representing species ("genome wide congealing"). We then place inversions in this context as examples of how genetic hitchhiking can potentially hasten genome wide congealing. Specifically, we use simulation models to (i) examine the conditions under which inversions may speed genome congealing and (ii) quantify predicted magnitudes of these effects. Effects of inversions on promoting speciation were most common and pronounced when inversions were initially fixed between populations before secondary contact and adaptation involved many genes with small fitness effects. Further work is required on the role of underdominance and epistasis between a few loci of major effect within inversions. The results highlight five important aspects of the roles of inversions in speciation: (i) the geographic context of the origins and spread of inversions, (ii) the conditions under which inversions can facilitate divergence, (iii) the magnitude of that facilitation, (iv) the extent to which the buildup of divergence is likely to be biased within vs. outside of inversions, and (v) the dynamics of the appearance and disappearance of exceptional divergence within inversions. We conclude by discussing the empirical challenges in showing that inversions play a central role in facilitating speciation with gene flow.
Computational fluid dynamics (CFD) simulation of effect of baffles on separation in mixer settler
Institute of Scientific and Technical Information of China (English)
Mohsen Ostad Shabani; Ali Mazahery; Mehdi Alizadeh; Ali Asghar Tofigh; Mohammad Reza Rahimipour; Mansour Razavi; Alireza Kolahi
2012-01-01
The main ideas in the development of the solvent extraction mixer settler focused on achieving clean phase separation,minimizing the loss of the reagents and decreasing the surface area of the settlers.The role of baffles in a mechanically agitated vessel is to ensure even distribution,reduce settler turbulence,promote the stability of power drawn by the impeller and to prevent swirling and vortexing of liquid,thus,greatly improving the mixing of liquid.The insertion of the appropriate number of baffles clearly improves the extent of liquid mixing.However,excessive baffling would interrupt liquid mixing and lengthen the mixing time.Computational fluid dynamics (CFD) provides a tool for determining detailed information on fluid flow (hydrodynamics) which is necessary for modeling subprocesses in mixer settler.A total of 54 final CFD runs were carried out representing different combinations of variables like number of baffles,density and impeller speed.CFD data shows that amount of separation increases with increasing baffles number and decreasing impeller speed.
Debolt, Stephen Edward
Solvent effects were studied and described via molecular dynamics (MD) and free energy perturbation (FEP) simulations using the molecular mechanics program AMBER. The following specific topics were explored:. Polar solvents cause a blue shift of the rm nto pi^* transition band of simple alkyl carbonyl compounds. The ground- versus excited-state solvation effects responsible for the observed solvatochromism are described in terms of the molecular level details of solute-solvent interactions in several modeled solvents spanning the range from polar to nonpolar, including water, methanol, and carbon tetrachloride. The structure and dynamics of octanol media were studied to explore the question: "why is octanol/water media such a good biophase analog?". The formation of linear and cyclic polymers of hydrogen-bonded solvent molecules, micelle-like clusters, and the effects of saturating waters are described. Two small drug-sized molecules, benzene and phenol, were solvated in water-saturated octanol. The solute-solvent structure and dynamics were analysed. The difference in their partitioning free energies was calculated. MD and FEP calculations were adapted for parallel computation, increasing their "speed" or the time span accessible by a simulation. The non-cyclic polyether ionophore salinomycin was studied in methanol solvent via parallel FEP. The path of binding and release for a potassium ion was investigated by calculating the potential of mean force along the "exit vector".
Strange attractor simulated on a quantum computer
2002-01-01
We show that dissipative classical dynamics converging to a strange attractor can be simulated on a quantum computer. Such quantum computations allow to investigate efficiently the small scale structure of strange attractors, yielding new information inaccessible to classical computers. This opens new possibilities for quantum simulations of various dissipative processes in nature.
The Computational Fluid Dynamic Simulation of Fire Evacuation from the Student Dormitory
Directory of Open Access Journals (Sweden)
Teeranon Saelao
2012-01-01
Full Text Available Problem statement: The aim of this research is to investigate the fire evacuation problem from the student dormitory by using the Numerical method. The Fire Dynamics Simulator Software was used in the research with the evacuation function (FDS + Evac.. The problem under investigation concerns the building that has the open-air centre. The characteristics of the building are included with 5 floors, 2 open-air fire escape stairs located at 2 sides of the building. In addition, there is a single exit to the outside of the building and the sprinkler system is not installed inside the building. Approach: The simulation was designed to study the problem that has a source of fire occurring at the room closed to the open-air stair. The stairs will be severely affected by the smoke. The experimentation's are composed of 4 cases, which are (1 the first case assumes the true size of the door is 1 m (2 the second case assumes the true size of the door is 1 m and the smoke barrier is installed at the beam located before the stair entrance (3 the third case assumes the true size of the door is 2 m and (4 the fourth case assumes the true size of the door is 2 m and the smoke barrier is installed. Results: The results are shown that the escape time from the building with the 1 m door is 465 sec and the 2 m door is 265 sec. The time differentiation between the 1 m door and the 2 m door is 200 sec. The reason is the waiting occurred at the entrance if the smoke barrier is not installed. In this case, the smoke in the stairs without a smoke barrier installation has more than the smoke in case if the smoke barrier is installed. However, this research collected the data of the gas volume and found that the gas volume is not yet harmful to human life but the gas can be an obstacle to evacuation in the building that has an open-air centre. Conclusion: For safety reasons, the buildings user should improve the door size and install the smoke barrier at 2 sides of the
Simulating chemistry using quantum computers
Kassal, Ivan; Perdomo-Ortiz, Alejandro; Yung, Man-Hong; Aspuru-Guzik, Alán
2010-01-01
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on conventional computers, by mapping the quantum system to another, more controllable one. In this review, we discuss to what extent the ideas in quantum computation, now a well-established field, have been applied to chemical problems. We describe algorithms that achieve significant advantages for the electronic-structure problem, the simulation of chemical dynamics, protein folding, and other tasks. Although theory is still ahead of experiment, we outline recent advances that have led to the first chemical calculations on small quantum information processors.
Simulating chemistry using quantum computers.
Kassal, Ivan; Whitfield, James D; Perdomo-Ortiz, Alejandro; Yung, Man-Hong; Aspuru-Guzik, Alán
2011-01-01
The difficulty of simulating quantum systems, well known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on conventional computers, by mapping the quantum system to another, more controllable one. In this review, we discuss to what extent the ideas in quantum computation, now a well-established field, have been applied to chemical problems. We describe algorithms that achieve significant advantages for the electronic-structure problem, the simulation of chemical dynamics, protein folding, and other tasks. Although theory is still ahead of experiment, we outline recent advances that have led to the first chemical calculations on small quantum information processors.
Schlanstein, Peter C; Hesselmann, Felix; Jansen, Sebastian V; Gemsa, Jeannine; Kaufmann, Tim A; Klaas, Michael; Roggenkamp, Dorothee; Schröder, Wolfgang; Schmitz-Rode, Thomas; Steinseifer, Ulrich; Arens, Jutta
2015-09-01
Computational fluid dynamics (CFD) is used to simulate blood flow inside the fiber bundles of oxygenators. The results are interpreted in terms of flow distribution, e.g., stagnation and shunt areas. However, experimental measurements that provide such information on the local flow between the fibers are missing. A transparent model of an oxygenator was built to perform particle image velocimetry (PIV), to perform the experimental validation. The similitude theory was used to adjust the size of the PIV model to the minimal resolution of the PIV system used (scale factor 3.3). A standard flow of 80 mL/min was simulated with CFD for the real oxygenator and the equivalent flow of 711 mL/min, according to the similitude theory, was investigated with PIV. CFD predicts the global size of stagnation and shunt areas well, but underestimates the streamline length and changes in velocities due to the meandering flow around the real fibers in the PIV model. Symmetrical CFD simulation cannot consider asymmetries in the flow, due to manufacturing-related asymmetries in the fiber bundle. PIV could be useful for validation of CFD simulations; measurement quality however must be improved for a quantitative validation of CFD results and the investigation of flow effects such as tortuosity and anisotropic flow behavior.
Shuhaiber, Jeffrey H; Niehaus, Justin; Gottliebson, William; Abdallah, Shaaban
2013-08-01
The theoretical differences in energy losses as well as coronary flow with different band sizes for branch pulmonary arteries (PA) in hypoplastic left heart syndrome (HLHS) remain unknown. Our objective was to develop a computational fluid dynamic model (CFD) to determine the energy losses and pulmonary-to-systemic flow rates. This study was done for three different PA band sizes. Three-dimensional computer models of the hybrid procedure were constructed using the standard commercial CFD softwares Fluent and Gambit. The computer models were controlled for bilateral PA reduction to 25% (restrictive), 50% (intermediate) and 75% (loose) of the native branch pulmonary artery diameter. Velocity and pressure data were calculated throughout the heart geometry using the finite volume numerical method. Coronary flow was measured simultaneously with each model. Wall shear stress and the ratio of pulmonary-to-systemic volume flow rates were calculated. Computer simulations were compared at fixed points utilizing echocardiographic and catheter-based metric dimensions. Restricting the PA band to a 25% diameter demonstrated the greatest energy loss. The 25% banding model produced an energy loss of 16.76% systolic and 24.91% diastolic vs loose banding at 7.36% systolic and 17.90% diastolic. Also, restrictive PA bands had greater coronary flow compared with loose PA bands (50.2 vs 41.9 ml/min). Shear stress ranged from 3.75 Pascals with restrictive PA banding to 2.84 Pascals with loose banding. Intermediate PA banding at 50% diameter achieved a Qp/Qs (closest to 1) at 1.46 systolic and 0.66 diastolic compared with loose or restrictive banding without excess energy loss. CFD provides a unique platform to simulate pressure, shear stress as well as energy losses of the hybrid procedure. PA banding at 50% provided a balanced pulmonary and systemic circulation with adequate coronary flow but without extra energy losses incurred.
Directory of Open Access Journals (Sweden)
Elzubier A. Salih
2009-01-01
Full Text Available Problem statement: Earlier research on ohmic heating technique focused on viscous food and foods containing solid particles. In this study, use of ohmic heating on sterilization of guava juice is carried out. Computational fluid dynamics was used to model and simulate the system. Investigate the buoyancy effect on the CFD simulation of continuous ohmic heating systems of fluid foods. Approach: A two-dimensional model describing the flow, temperature and electric field distribution of non-Newtonian power law guava juice fluid in a cylindrical continuous ohmic heating cell was developed. The electrical conductivity, thermo physical and rheological properties of the fluid was temperature dependent. Numerical simulation was carried out using FLUENT 6.1 software package. A user defined functions available in FLUENT 6.1 was employed for the electric field equation. The heating cell used consisted of a cylindrical tube of diameter 0.05 m, height 0.50 m and having three collinear electrodes of 0.02 m width separated by a distance of 0.22 m. The sample was subjected to zero voltage at the top and bottom of electrodes while electrical potential of 90 volts (AC 50-60 Hz was set at the middle electrode. The inlet velocity is 0.003 m sec-1 and the temperature is in the range of 30-90°C. Results: Simulation was carried with and without buoyancy driven force effect. The ohmic heating was successfully simulated using CFD and the results showed that the buoyancy had a strong effect in temperature profiles and flow pattern of the collinear electrodes configuration ohmic heating. A more uniform velocity and temperature profiles were obtained with the buoyancy effect included. Conclusion: For accurate results, the inclusion of buoyancy effect into the CFD simulation is important.
Smolin, Nikolai; Winter, Roland
2008-01-24
It is now generally agreed that the hydration water and solvational properties play a crucial role in determining the dynamics and hence the functionality of proteins. We present molecular dynamics computer simulation studies on staphylococcal nuclease (SNase) at various temperatures and pressures as well as in different cosolvent solutions containing various concentrations of urea and glycerol. The aim is to provide a molecular level understanding of how different types of cosolvents (chaotropic and kosmotropic) as well as temperature and high hydrostatic pressure modify the structure and dynamics of the hydration water. Taken together, these three intrinsic thermodynamic variables, temperature, pressure, and chemical potential (or activity) of the solvent, are able to influence the stability and function of the protein by protein-solvent dynamic coupling in different ways. A detailed analysis of the structural and dynamical properties of the water and cosolvents at the protein surface (density profile, coordination numbers, hydrogen-bond distribution, average H-bond lifetimes (water-protein and water-water), and average residence time of water in the hydration shell) was carried out, and differences in the structural and dynamical properties of the hydration water in the presence of the different cosolvents and at temperatures between 300 and 400 K and pressures up to 5000 bar are discussed. Furthermore, the results obtained help understand various thermodynamic properties measured for the protein.
Computer Modeling and Simulation
Energy Technology Data Exchange (ETDEWEB)
Pronskikh, V. S. [Fermilab
2014-05-09
Verification and validation of computer codes and models used in simulation are two aspects of the scientific practice of high importance and have recently been discussed by philosophers of science. While verification is predominantly associated with the correctness of the way a model is represented by a computer code or algorithm, validation more often refers to model’s relation to the real world and its intended use. It has been argued that because complex simulations are generally not transparent to a practitioner, the Duhem problem can arise for verification and validation due to their entanglement; such an entanglement makes it impossible to distinguish whether a coding error or model’s general inadequacy to its target should be blamed in the case of the model failure. I argue that in order to disentangle verification and validation, a clear distinction between computer modeling (construction of mathematical computer models of elementary processes) and simulation (construction of models of composite objects and processes by means of numerical experimenting with them) needs to be made. Holding on to that distinction, I propose to relate verification (based on theoretical strategies such as inferences) to modeling and validation, which shares the common epistemology with experimentation, to simulation. To explain reasons of their intermittent entanglement I propose a weberian ideal-typical model of modeling and simulation as roles in practice. I suggest an approach to alleviate the Duhem problem for verification and validation generally applicable in practice and based on differences in epistemic strategies and scopes
Skripnyak, V. A.; Skripnyak, E. G.; Kozulin, A. A.; Skripnyak, V. V.; Korobenkov, M. V.
2009-12-01
Computer simulation is used to investigate the deformation and damage processes taking place in brittle porous oxide ceramics under intense dynamic loading. The pore structure is shown to substantially affect the size of the fragments and the strength of the materials. In porous ceramics subjected to shock loading, deformation is localized in mesoscopic bands having characteristic orientations along, across, and at ˜45° to the direction of propagation of the shock wave front. The localized-deformation bands may be transformed into macroscopic cracks. A method is proposed for a theoretical estimation of the effective elastic moduli of ceramics with pore structure without resorting to well-known hypotheses for the relation between elastic moduli and porosity of the materials.
Directory of Open Access Journals (Sweden)
Amelia eGreig
2015-01-01
Full Text Available Computational fluid dynamics (CFD simulations of a radio-frequency (13.56 MHz electro-thermal capacitively coupled plasma (CCP micro-thruster have been performed using the commercial CFD-ACE+ package. Standard operating conditions of a 10 W, 1.5 Torr argon discharge were used to compare with previously obtained experimental results for validation. Results show that the driving force behind plasma production within the thruster is ion-induced secondary electrons ejected from the surface of the discharge tube, accelerated through the sheath to electron temperatures up to 33.5 eV. The secondary electron coefficient was varied to determine the effect on the discharge, with results showing that full breakdown of the discharge did not occur for coefficients coefficients less than or equal to 0.01.
Siettos, C. I.; Pantelides, C. C.; Kevrekidis, I.G.
2003-01-01
We discuss computational superstructures that, using repeated, appropriately initialized short calls, enable temporal process simulators to perform alternative tasks such as fixed point computation, stability analysis and projective integration. We illustrate these concepts through the acceleration of a gPROMS-based Rapid Pressure Swing Adsorption simulation, and discuss their scope and possible extensions.
Shen, Fei; Tian, Libin; Yuan, Hairong; Pang, Yunzhi; Chen, Shulin; Zou, Dexun; Zhu, Baoning; Liu, Yanping; Li, Xiujin
2013-10-01
As a lignocellulose-based substrate for anaerobic digestion, rice straw is characterized by low density, high water absorbability, and poor fluidity. Its mixing performances in digestion are completely different from traditional substrates such as animal manures. Computational fluid dynamics (CFD) simulation was employed to investigate mixing performances and determine suitable stirring parameters for efficient biogas production from rice straw. The results from CFD simulation were applied in the anaerobic digestion tests to further investigate their reliability. The results indicated that the mixing performances could be improved by triple impellers with pitched blade, and complete mixing was easily achieved at the stirring rate of 80 rpm, as compared to 20-60 rpm. However, mixing could not be significantly improved when the stirring rate was further increased from 80 to 160 rpm. The simulation results agreed well with the experimental results. The determined mixing parameters could achieve the highest biogas yield of 370 mL (g TS)(-1) (729 mL (g TS(digested))(-1)) and 431 mL (g TS)(-1) (632 mL (g TS(digested))(-1)) with the shortest technical digestion time (T 80) of 46 days. The results obtained in this work could provide useful guides for the design and operation of biogas plants using rice straw as substrates.
Computer simulation of light scattering from dynamic inhomogeneities in live tissue
Priezzhev, Alexander V.; Fedoseev, Victor V.; Kudinov, Dmitry V.
1999-03-01
We describe the results of the study of light propagation and scattering in a model biological tissue comprising moving particles simulating blood perfusion. The study was performed by means of Monte Carlo simulation. The obtained dependencies of the total intensity and of the Doppler spectra of the backscattered light on the model parameters are analyzed. The CW and ultra-short pulse modes of sample probing and time gating of the detected signal are considered.
Moghani, Mahdy Malekzadeh; Khomami, Bamin
2017-02-01
The computational efficiency of Brownian dynamics (BD) simulation of the constrained model of a polymeric chain (bead-rod) with n beads and in the presence of hydrodynamic interaction (HI) is reduced to the order of n2 via an efficient algorithm which utilizes the conjugate-gradient (CG) method within a Picard iteration scheme. Moreover, the utility of the Barnes and Hut (BH) multipole method in BD simulation of polymeric solutions in the presence of HI, with regard to computational cost, scaling, and accuracy, is discussed. Overall, it is determined that this approach leads to a scaling of O (n1.2) . Furthermore, a stress algorithm is developed which accurately captures the transient stress growth in the startup of flow for the bead-rod model with HI and excluded volume (EV) interaction. Rheological properties of the chains up to n =350 in the presence of EV and HI are computed via the former algorithm. The result depicts qualitative differences in shear thinning behavior of the polymeric solutions in the intermediate values of the Weissenburg number (10
Computer Simulation of Dynamic Interactions Between Vehicle and Long Span Box Girder Bridges
Institute of Scientific and Technical Information of China (English)
Lei Gong; Moe S.Cheung
2008-01-01
Moving vehicle loads,associated with roadway traffic can induce significant dynamic effects on the structural behaviours of bridges,especially for long-span bridges.The main objective of current research is to study traffic induced dynamic responses of long-span box-girder bridges.The finite element method has been employed in this study to obtain a three-dimensional mathematical model for the bridge system.For vehicle-bridge dynamic interaction analysis,the vehicle is modeled as a more realistic three-axle,six-wheel system,and the corresponding dynamic interaction equations have been derived.The bridge-vehicle inter- action is affected by many factors.The current study has been focused on such factors as:vehicle speed, vehicle damping ratio,multiple traffic lanes,mass ratio of vehicle and bridge,and dynamic characteristics of bridge.Case studies have been conducted to investigate these factors by using several box girder bridge examples including Confederation Bridge,the longest box girder bridge in the world.
Computer simulation of liquid crystals
Energy Technology Data Exchange (ETDEWEB)
McBride, C.
1999-01-01
Molecular dynamics simulation performed on modern computer workstations provides a powerful tool for the investigation of the static and dynamic characteristics of liquid crystal phases. In this thesis molecular dynamics computer simulations have been performed for two model systems. Simulations of 4,4'-di-n-pentyl-bibicyclo[2.2.2]octane demonstrate the growth of a structurally ordered phase directly from an isotropic fluid. This is the first time that this has been achieved for an atomistic model. The results demonstrate a strong coupling between orientational ordering and molecular shape, but indicate that the coupling between molecular conformational changes and molecular reorientation is relatively weak. Simulations have also been performed for a hybrid Gay-Berne/Lennard-Jones model resulting in thermodynamically stable nematic and smectic phases. Frank elastic constants have been calculated for the nematic phase formed by the hybrid model through analysis of the fluctuations of the nematic director, giving results comparable with those found experimentally. Work presented in this thesis also describes the parameterization of the torsional potential of a fragment of a dimethyl siloxane polymer chain, disiloxane diol (HOMe[sub 2]Si)[sub 2]O, using ab initio quantum mechanical calculations. (author)
Computer simulation of liquid crystals
Energy Technology Data Exchange (ETDEWEB)
McBride, C
1999-09-01
Molecular dynamics simulation performed on modern computer workstations provides a powerful tool for the investigation of the static and dynamic characteristics of liquid crystal phases. In this thesis molecular dynamics computer simulations have been performed for two model systems. Simulations of 4,4`-di-n-pentyl-bibicyclo[2.2.2]octane demonstrate the growth of a structurally ordered phase directly from an isotropic fluid. This is the first time that this has been achieved for an atomistic model. The results demonstrate a strong coupling between orientational ordering and molecular shape, but indicate that the coupling between molecular conformational changes and molecular reorientation is relatively weak. Simulations have also been performed for a hybrid Gay-Berne/Lennard-Jones model resulting in thermodynamically stable nematic and smectic phases. Frank elastic constants have been calculated for the nematic phase formed by the hybrid model through analysis of the fluctuations of the nematic director, giving results comparable with those found experimentally. Work presented in this thesis also describes the parameterization of the torsional potential of a fragment of a dimethyl siloxane polymer chain, disiloxane diol (HOMe{sub 2}Si){sub 2}O, using ab initio quantum mechanical calculations. (author)
Preliminary Computational Fluid Dynamics (CFD) Simulation of EIIB Push Barge in Shallow Water
Beneš, Petr; Kollárik, Róbert
2011-12-01
This study presents preliminary CFD simulation of EIIb push barge in inland conditions using CFD software Ansys Fluent. The RANSE (Reynolds Averaged Navier-Stokes Equation) methods are used for the viscosity solution of turbulent flow around the ship hull. Different RANSE methods are used for the comparison of their results in ship resistance calculations, for selecting the appropriate and removing inappropriate methods. This study further familiarizes on the creation of geometrical model which considers exact water depth to vessel draft ratio in shallow water conditions, grid generation, setting mathematical model in Fluent and evaluation of the simulations results.
Matsumoto, Paul S.
2014-01-01
The article describes the use of Mathematica, a computer algebra system (CAS), in a high school chemistry course. Mathematica was used to generate a graph, where a slider controls the value of parameter(s) in the equation; thus, students can visualize the effect of the parameter(s) on the behavior of the system. Also, Mathematica can show the…
Directory of Open Access Journals (Sweden)
Xiao Hong
2013-08-01
Full Text Available Numerical simulation and experimental validation of a hypersonic flat plate and isothermal turning wall flow were conducted in the current study. The investigation was based on three kinds of grids (Grid1, Grid2 and Grid3 with laminar flow and three types of turbulence models (BL, SA and SST. Under the same initiation and different turbulence models, the convergence process of the friction drag coefficient CP and the Stanton number st of a hypersonic flat plate flow revealed four results. First, the flow turbulence effect in the BL model simulation was responsive to CP and st. Second, the SA and SST model simulations both reflected the development process of flow turbulence. Third, the flow turbulence effect in the SST model simulation did not gradually emerge until the laminar flow simulation was sufficient. Moreover, the SA model simulation did not exist on such obvious hysteresis. Fourth, by comparing CP and st of a hypersonic flat-plate laminar simulation under the three grids, the errors of the calculation results of Grid2 and Grid3 were small. In contrast, the error on Grid1 was large. By comparing CP and st of the BL model for the three grids, we found that the result of Grid3 was slightly better than the result of Grid2. The deviation between them basically remained within 10%. However, the result of Grid1 had a large deviation with oscillation. CP and st of the SA model for the three grids were then compared. A large difference was found only on the transition zone location between the result of Grid2 and Grid3. Nevertheless, the error and calculation of reference between them was maintained within 10%. Grid1 not only had a large deviation, but also had certain oscillation on the laminar flow area. Finally, CP and st of the SST model for the three grids were compared. There was a large difference only on the transition zone location between the result of Grid2 and Grid3, but the error between them was maintained within 10%. Grid1 had a
Computer simulation technology in inertial confinement (ICF)
Energy Technology Data Exchange (ETDEWEB)
Yabe, Takashi (Gunma Univ., Kiryu (Japan). Faculty of Engineering)
1994-12-01
Recent development of computational technologies in inertial confinement fusion (ICF) is reviewed with a special emphasis on hydrodynamic simulations. The CIP method developed for ICF simulations is one of the typical examples that are used in various fields of physics such as variety of computational fluid dynamics, astrophysics, laser applications, geophysics, and so on. (author).
Modeling and simulation of membrane separation process using computational fluid dynamics
Directory of Open Access Journals (Sweden)
Kambiz Tahvildari
2016-01-01
Full Text Available Separation of CO2 from air was simulated in this work. The considered process for removal of CO2 was a hollow-fiber membrane contactor and an aqueous solution of 2-amino-2-metyl-1-propanol (AMP as absorbent. The model was developed based on mass transfer as well as chemical reaction for CO2 and solvent in the contactor. The equations of model were solved using finite element method. Simulation results were compared with experimental data, and good agreement was observed. The results revealed that increasing solvent velocity enhances removal of CO2 in the hollow-fiber membrane contactor. Moreover, it was found that counter-current process mode is more favorable to achieve the highest separation efficiency.
Time-Accurate Computational Fluid Dynamics Simulation of a Pair of Moving Solid Rocket Boosters
Strutzenberg, Louise L.; Williams, Brandon R.
2011-01-01
Since the Columbia accident, the threat to the Shuttle launch vehicle from debris during the liftoff timeframe has been assessed by the Liftoff Debris Team at NASA/MSFC. In addition to engineering methods of analysis, CFD-generated flow fields during the liftoff timeframe have been used in conjunction with 3-DOF debris transport methods to predict the motion of liftoff debris. Early models made use of a quasi-steady flow field approximation with the vehicle positioned at a fixed location relative to the ground; however, a moving overset mesh capability has recently been developed for the Loci/CHEM CFD software which enables higher-fidelity simulation of the Shuttle transient plume startup and liftoff environment. The present work details the simulation of the launch pad and mobile launch platform (MLP) with truncated solid rocket boosters (SRBs) moving in a prescribed liftoff trajectory derived from Shuttle flight measurements. Using Loci/CHEM, time-accurate RANS and hybrid RANS/LES simulations were performed for the timeframe T0+0 to T0+3.5 seconds, which consists of SRB startup to a vehicle altitude of approximately 90 feet above the MLP. Analysis of the transient flowfield focuses on the evolution of the SRB plumes in the MLP plume holes and the flame trench, impingement on the flame deflector, and especially impingment on the MLP deck resulting in upward flow which is a transport mechanism for debris. The results show excellent qualitative agreement with the visual record from past Shuttle flights, and comparisons to pressure measurements in the flame trench and on the MLP provide confidence in these simulation capabilities.
Valenzuela, J. C.; Krasheninnikov, I.; Beg, F. N.; Wessel, F.; Rahman, H.; Ney, P.; Presura, R.; McKee, E.; Darling, T.; Covington, A.
2015-11-01
Previous experimental work on staged Z-pinches demonstrated that gas liners can efficiently couple energy and implode uniformly a target-plasma. A 1.5 MA, 1 μs current driver was used to implode a magnetized, Kr liner onto a D + target, producing 1010 neutrons per shot and providing clear evidence of enhanced pinch stability. Time-of-flight data suggest that primary and secondary neutrons were produced. MHD simulations show that in Zebra, a 1.5MA and 100ns rise-time current driver, high fusion gain can be attained when the optimum liner and plasma target conditions are used. In this work we present the design and optimization of a liner-on-target nozzle to be fielded in Zebra and demonstrate high fusion gain at 1 MA current level. The nozzle is composed of an annular high atomic number gas-puff and an on-axis plasma gun that will deliver the ionized deuterium target. The nozzle optimization was carried out using the computational fluid dynamics (CFD) code fluent and the MHD code Mach2. The CFD simulation produces density and temperature profiles, as a function of the nozzle shapes and gas conditions, which are then used in Mach2 to find the optimum plasma liner implosion-pinch conditions. Funded by the US Department of Energy, ARPA-E, Control Number 1184-1527.
Krujatz, Felix; Illing, Rico; Krautwer, Tobias; Liao, Jing; Helbig, Karsten; Goy, Katharina; Opitz, Jörg; Cuniberti, Gianaurelio; Bley, Thomas; Weber, Jost
2015-12-01
Externally illuminated photobioreactors (PBRs) are widely used in studies on the use of phototrophic microorganisms as sources of bioenergy and other photobiotechnology research. In this work, straightforward simulation techniques were used to describe effects of varying fluid flow conditions in a continuous hydrogen-producing PBR on the rate of photofermentative hydrogen production (rH2 ) by Rhodobacter sphaeroides DSM 158. A ZEMAX optical ray tracing simulation was performed to quantify the illumination intensity reaching the interior of the cylindrical PBR vessel. 24.2% of the emitted energy was lost through optical effects, or did not reach the PBR surface. In a dense culture of continuously producing bacteria during chemostatic cultivation, the illumination intensity became completely attenuated within the first centimeter of the PBR radius as described by an empirical three-parametric model implemented in Mathcad. The bacterial movement in chemostatic steady-state conditions was influenced by varying the fluid Reynolds number. The "Computational Fluid Dynamics" and "Particle Tracing" tools of COMSOL Multiphysics were used to visualize the fluid flow pattern and cellular trajectories through well-illuminated zones near the PBR periphery and dark zones in the center of the PBR. A moderate turbulence (Reynolds number = 12,600) and fluctuating illumination of 1.5 Hz were found to yield the highest continuous rH2 by R. sphaeroides DSM 158 (170.5 mL L(-1) h(-1) ) in this study.
Computer Simulation and Computabiblity of Biological Systems
Baianu, I C
2004-01-01
The ability to simulate a biological organism by employing a computer is related to the ability of the computer to calculate the behavior of such a dynamical system, or the "computability" of the system. However, the two questions of computability and simulation are not equivalent. Since the question of computability can be given a precise answer in terms of recursive functions, automata theory and dynamical systems, it will be appropriate to consider it first. The more elusive question of adequate simulation of biological systems by a computer will be then addressed and a possible connection between the two answers given will be considered as follows. A symbolic, algebraic-topological "quantum computer" (as introduced in Baianu, 1971b) is here suggested to provide one such potential means for adequate biological simulations based on QMV Quantum Logic and meta-Categorical Modeling as for example in a QMV-based, Quantum-Topos (Baianu and Glazebrook,2004.
Energy Technology Data Exchange (ETDEWEB)
L. BARTLEIN
2001-05-01
The objective of this report is to provide a methodology for utilization of the NIST FDS code to evaluate the effects of radiant and convective heating from single and multiple fire sources, on heat sensitive targets as Special Nuclear Materials (SNM), and High Explosives (HE). The presentation will demonstrate practical applications of the FDS computer program in fire hazards analysis, and illustrate the advantages over hand calculations for radiant heat and convective transfer and fire progression. The ''visualization'' of radiant and convective heat effects will be demonstrated as a tool for supporting conclusions of fire hazards analysis and TSR development.
Tronville, Paolo Maria
2013-01-01
One form of numerical simulation of flow and particle capture by air filter media sees gases as continuous fluids, influenced by the macro-properties viscosity, density, and pressure. The alternate approach treats gases as atoms or molecules in random motion, impacting their own kind and solid surfaces on a micro-scale. The appropriate form for analysis of flow through a given filter medium at a given operating condition depends on the gas condition and the Knudsen number (Kn) of the finest f...
Directory of Open Access Journals (Sweden)
O. V. Shavykin
2016-09-01
Full Text Available The Brownian dynamics method has been used to study the effect of the branching asymmetry on the local orientational mobility of segments and bonds in dendrimers in good solvent. “Coarse-grained” models of flexible dendrimers with different branching symmetry but with the same average segment length were considered. The frequency dependences of the rate of the spin-lattice relaxation nuclear magnetic resonance (NMR [1/T1H(H] for segments or bonds located at different distances from terminal monomers were calculated. After the exclusion of the contribution of the overall dendrimer rotation the position of the maxima of the frequency dependences [1/T1H(ωH] for different segments with the same length doesn’t depend on their location inside a dendrimer both for phantom models and for models with excluded volume interactions. This effect doesn’t depend also on the branching symmetry, but the position of the maximum [1/T1H(ωH] is determined by the segment length. For bonds inside segments the positions of the maximum [1/T1H(ωH] coincide for all models considered. Therefore, the obtained earlier conclusion about the weak influence of the excluded volume interactions on the local dynamics in the flexible symmetric dendrimers can be generalized for dendrimers with an asymmetric branching.
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].
A Unified Computational Method for Simulating Dynamic Behavior of Planing Vessels
Institute of Scientific and Technical Information of China (English)
Mohammad Saeed SEIF; Ebrahim JAHANBAKHSH; Roozbeh PANAHI; Mohammad Hossein KARIMI
2009-01-01
High speed planing hulls have complex hydrodynamic behaviors. The trim angle and drafts are very sensitive to speed and location of the center of gravity. Therefore, motion simulation for such vessels needs a strong coupling between rigid body motions and hydrodynamic analysis. In addition, free surface shoald be predicted with good accuracy for each time step. In this paper, velocity and pressure fields are coupled by use of the fractional step method. On the basis of in- tegration of the two-phase viscous flow induced stresses over the hull, acting loads (forces and moments) are calculated. With the strategy of boundary-fitted body-attached mesh and calculation of 6-DoF motions in each time step, time history of ship motions including displacements, speeds and accelerations are evaluated. For the demonstration of the software capabilities, circular cylinder slamming is simulated as a simple type of water slamming. Then, a high-speed planing catamaran is investigated in the case of steady forward motion. All of the results are in good concordance with experimen-tal data. The present toothed can be widely implemented in design as well as in the performance prediction of high-speed vessels.
Blazek, Jiri
2015-01-01
Computational Fluid Dynamics: Principles and Applications, Third Edition presents students, engineers, and scientists with all they need to gain a solid understanding of the numerical methods and principles underlying modern computation techniques in fluid dynamics. By providing complete coverage of the essential knowledge required in order to write codes or understand commercial codes, the book gives the reader an overview of fundamentals and solution strategies in the early chapters before moving on to cover the details of different solution techniques. This updated edition includes new
Gas Dynamics Equations: Computation
Chen, Gui-Qiang G
2012-01-01
Shock waves, vorticity waves, and entropy waves are fundamental discontinuity waves in nature and arise in supersonic or transonic gas flow, or from a very sudden release (explosion) of chemical, nuclear, electrical, radiation, or mechanical energy in a limited space. Tracking these discontinuities and their interactions, especially when and where new waves arise and interact in the motion of gases, is one of the main motivations for numerical computation for the gas dynamics equations. In this paper, we discuss some historic and recent developments, as well as mathematical challenges, in designing and formulating efficient numerical methods and algorithms to compute weak entropy solutions for the Euler equations for gas dynamics.
Demerdash, N. A. O.; Nehl, T. W.
1979-01-01
A description and user's guide of the computer program developed to simulate the dynamics of an electromechanical actuator for aerospace applications are presented. The effects of the stator phase currents on the permanent magnets of the rotor are examined. The voltage and current waveforms present in the power conditioner network during the motoring, regenerative braking, and plugging modes of operation are presented and discussed.
A Computer Model for the Simulation of Nonspherical Particle Dynamics in the Human Respiratory Tract
Directory of Open Access Journals (Sweden)
Robert Sturm
2012-01-01
Full Text Available In the study presented here deposition of spheres and nonspherical particles with various aspect ratios (0.01–100 in the human respiratory tract was theoretically modeled. Shape of the nonspherical particles was considered by the application of the latest aerodynamic diameter concepts. Particle deposition was predicted by using a stochastic model of the lung geometry and simulating particle transport trajectories according to the random-walk algorithm. Concerning fibers total deposition is significantly enhanced with respect to that of spheres for μm-sized particles, whereby at normal breathing conditions peripheral lung compartments serve as primary deposition targets. In the case of oblate disks, total deposition becomes mostly remarkable for submicron particles, with the bronchioli and alveoli being targeted to a high extent. Enhancement of the aerodynamic diameter and/or flow rate generally causes a displacement of deposition maxima from peripheral to more proximal lung regions. From these findings, it can be concluded that these particle classes may represent tremendous occupational hazards, especially if they are attached with radioactive elements or heavy metals.
Computational Fluid Dynamic Simulation on NACA 0026 Airfoil with V-Groove Riblets
Directory of Open Access Journals (Sweden)
M.I Ghazali
2016-08-01
Full Text Available The aims of this research is to look into the percentage drag reduction on a NACA 0026 airfoil with V-Groove riblets installed around at some locations around its surface. NACA 0026 is a symmetrical airfoil mostly used as turbine blade and aircraft wing. Research on drag reduction by using riblets on the surface was introduced by NASA Langley Research Centre in 1970s. There are many types of riblet designed in this research area such as V groove, segmented blade and continuous sawtooth. This research used NACA 0026 with external geometry 500 mm spans, 615 mm chord and 156 mm thickness. V-groove riblets with 1 mm pitch and 1 mm high and 30 mm width are attached at peak points of the airfoil profile. The CFD simulation used ANSYS Fluent to analyze the velocity, pressure gradient, turbulent kinetic energy and vortex development. The result shows the percentage in drag reduction compared to clean surface for the zero angle of attack is 11.8% and 300 angle of attack is 1.64%. By this condition the airfoil will have better motion performance in their applications.
Mirzaie, Sako; Chupani, Latifeh; Asadabadi, Ebrahim Barzegari; Shahverdi, Ahmad Reza; Jamalan, Mostafa
2013-01-01
Inhibition of aromatase (CYTP450) as a key enzyme in the estrogen biosynthesis could result in regression of estrogen-dependent tumors and even preventing the promotion of breast cancer. Although today potent steroid and non-steroid inhibitors of aromatase are available, isoflavanone derivatives as natural compounds with least side effects have been described as the candidate for a new generation of aromatase inhibitors. 2a as an isoflavanone derivative is the most potent inhibitor of aromatase, synthesized by Bonfield et al. (2012[7]). In our computational study, the mentioned compound was used as the template for virtual screening. Between 286 selected compounds with 70 % of structural similarity to 2a, 150 of them showed lower docking energy in comparison with 2a. Compound 2a_1 with 11.2 kcal/mol had the lowest docking energy. Interaction of 2a_1 with aromatase was further investigated and compared with 2a and androstenedione (ASD) as a natural substrate of aromatase, through 20 ns of molecular dynamic simulation. Analysis of trajectories showed, while ASD interacts with aromatase through hydrogen bonds and 2a just interacts via hydrophobic forces, 2a_1 not only accommodates in the hydrophobic active site of aromatase in a suitable manner but it also makes a stable coordination with iron atom of aromatase heme group via OB.
Bao, J.; Zhou, T.; Huang, M.; Hou, Z.; Perkins, W. A.; Harding, S.; Hammond, G. E.; Ren, H.; Thorne, P. D.; Suffield, S. R.; Zachara, J. M.
2016-12-01
Hyporheic exchange between river water and groundwater is an important mechanism for biogeochemical processes, such as carbon and nitrogen cycling, and biodegradation of organic contaminants, in the subsurface interaction zone. The relationship between river flow conditions and hyporheic exchanges therefore is of great interests to hydrologists, biogeochemists, and ecologists. However, quantifying relative influences of hydrostatic and hydrodynamic drivers on hyporheic exchanges is very challenging in large rivers due to accessibility and spatial coverage of measurements, and computational tools available for numerical experiments. In this study, we aim to demonstrate that a high resolution computational fluid dynamics (CFD) model that couples surface and subsurface flow and transport can be used to simulate hyporheic exchanges and the residence time of river water in the hypothetic zone. Base on the assumption that the hyporheic exchange does not affect the surface water flow condition due to its small magnitude compared to the velocity of river water, we developed a one way coupled surface and subsurface water flow model in a commercial CFD software STAR-CCM+, that connects the Reynolds-averaged Navier-Stokes (RANS) equation solver with a realizable two-layer turbulence model, a two-layer all y+ wall treatment, and the volume of fluid (VOF) method for tracking the free water-air interface as well as porous media flow in the subsurface domain. The model is applied to a 7-km long section of the Columbia River and validated against measurements from the acoustic Doppler current profiler (ADCP) in the surface water and hyporheic fluxes derived from a set of temperature profilers installed across the riverbed. The validated model is then employed to systematically investigate how hyporheic exchanges influenced by 1) riverbed properties such as the permeability and thickness of the alluvial layer; 2) surface water hydrodynamics due to channel geomorphological settings
Karmonik, Christof; Yen, Christopher; Gabriel, Edgar; Partovi, Sasan; Horner, Marc; Zhang, Yi J; Klucznik, Richard P; Diaz, Orlando; Grossman, Robert G
2013-11-01
Towards the translation of computational fluid dynamics (CFD) techniques into the clinical workflow, performance increases achieved with parallel multi-central processing unit (CPU) pulsatile CFD simulations in a patient-derived model of a bilobed posterior communicating artery aneurysm were evaluated while simultaneously monitoring changes in the accuracy of the solution. Simulations were performed using 2, 4, 6, 8, 10 and 12 processors. In addition, a baseline simulation was obtained with a dual-core dual CPU computer of similar computational power to clinical imaging workstations. Parallel performance indices including computation speed-up, efficiency (speed-up divided by number of processors), computational cost (computation time × number of processors) and accuracy (velocity at four distinct locations: proximal and distal to the aneurysm, in the aneurysm ostium and aneurysm dome) were determined from the simulations and compared. Total computation time decreased from 9 h 10 min (baseline) to 2 h 34 min (10 CPU). Speed-up relative to baseline increased from 1.35 (2 CPU) to 3.57 (maximum at 10 CPU) while efficiency decreased from 0.65 to 0.35 with increasing cost (33.013 to 92.535). Relative velocity component deviations were less than 0.0073% and larger for 12 CPU than for 2 CPU (0.004 ± 0.002%, not statistically significant, p=0.07). Without compromising accuracy, parallel multi-CPU simulation reduces computing time for the simulation of hemodynamics in a model of a cerebral aneurysm by up to a factor of 3.57 (10 CPUs) to 2 h 34 min compared with a workstation with computational power similar to clinical imaging workstations.
McCloud, Peter L.
2010-01-01
Thermal Protection System (TPS) Cavity Heating is predicted using Computational Fluid Dynamics (CFD) on unstructured grids for both simplified cavities and actual cavity geometries. Validation was performed using comparisons to wind tunnel experimental results and CFD predictions using structured grids. Full-scale predictions were made for simplified and actual geometry configurations on the Space Shuttle Orbiter in a mission support timeframe.
Toja-Silva, Francisco; Chen, Jia; Hachinger, Stephan
2017-04-01
Climate change, a societal challenge for the European Union, is affecting all regions in Europe and has a profound impact on society and environment. It is now clear that the present global warming period is due to the strong anthropogenic greenhouse gas (GHG) emission, occurring at an unprecedented rate. Therefore, the identification and control of the greenhouse gas sources has a great relevance. Since the GHG emissions from cities are the largest human contribution to climate change, the present investigation focuses on the urban environment. Bottom-up annual emission inventories are compiled for most countries. However, a rigorous approach requires to perform experimental measurements in order to verify the official estimates. Measurements of column-averaged dry-air mole fractions of GHG (XGHG) can be used for this. To comprehensively detect and quantify GHG emission sources, these punctual column data, however, have to be extended to the surrounding urban map, requiring a deep understanding of the gas transport. The resulting emission estimation will serve several practical purposes, e.g. the verification of official emission rates and the determination of trends in urban emissions. They will enable the administration to make targeted and economically efficient decisions about mitigation options, and help to stop unintentional and furtive releases. With this aim, this investigation presents a completely new approach to the analysis of the carbon dioxide (CO2) emissions from fossil fuel thermal power plants in urban environments by combining differential column measurements with computational fluid dynamics (CFD) simulations in order to deeply understand the experimental conditions. The case study is a natural gas-fueled cogeneration (combined heat and power, CHP) thermal power plant inside the city of Munich (Germany). The software used for the simulations (OpenFOAM) was modified in order to use the most advanced RANS turbulence modeling (i.e. Durbin) and
Computational Fluid Dynamics in Cardiovascular Disease
Lee, Byoung-kwon
2011-01-01
Computational fluid dynamics (CFD) is a mechanical engineering field for analyzing fluid flow, heat transfer, and associated phenomena, using computer-based simulation. CFD is a widely adopted methodology for solving complex problems in many modern engineering fields. The merit of CFD is developing new and improved devices and system designs, and optimization is conducted on existing equipment through computational simulations, resulting in enhanced efficiency and lower operating costs. Howev...
Simulations of Probabilities for Quantum Computing
Zak, M.
1996-01-01
It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-LIpschitz dynamics, without utilization of any man-made devices (such as random number generators). Self-organizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed.
Massively parallel quantum computer simulator
De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.
2007-01-01
We describe portable software to simulate universal quantum computers on massive parallel Computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray
Energy Technology Data Exchange (ETDEWEB)
Shimizu, Y.; Kasahara, H.; Seki, K.; Furukubo, K. (Mie Univ., Mie, (Japan). Faculty of Engineering Tokai Univ., Tokyo, (Japan). Faculty of Engineering Suzuki Motor Co. Ltd., Shizuoka, (Japan))
1990-04-25
The dynamic characteristics of a middle scale horizontal axis wind turbine controlled by a computer were theoretically analyzed with a dynamic model, comparing with field test results. In experiments, the three-blades wind turbine was used of 7.5m in rotor height above ground, 8.2m in rotor diameter and 8kW in rated output, and the rotation force of the turbine was analyzed by a local circulation mehtod. After the characteristics were simulated using the measured data of rotor revolution, blade pitch angle and wind velocity as initial values, based on a real control program, blade pitch angle control variables were calculated from the simulated data of rotor revolution and generation current, to estimate the dynamic characteristics theoretically. As a result, the theoretical values of generation power, current, rotor revolution and blade pitch angle control agreed roughly with measured values, and both time-integrated total powers agreed fairly with each other, indicating a favorable applicability to power estimation. 6 refs., 11 figs., 1 tab.
Farag, Mina Berty; Karmonik, Christof; Rengier, Fabian; Loebe, Matthias; Karck, Matthias; von Tengg-Kobligk, Hendrik; Ruhparwar, Arjang; Partovi, Sasan
2014-01-01
Many end-stage heart failure patients are not eligible to undergo heart transplantation due to organ shortage, and even those under consideration for transplantation might suffer long waiting periods. A better understanding of the hemodynamic impact of left ventricular assist devices (LVAD) on the cardiovascular system is therefore of great interest. Computational fluid dynamics (CFD) simulations give the opportunity to study the hemodynamics in this patient population using clinical imaging data such as computed tomographic angiography. This article reviews a recent study series involving patients with pulsatile and constant-flow LVAD devices in which CFD simulations were used to qualitatively and quantitatively assess blood flow dynamics in the thoracic aorta, demonstrating its potential to enhance the information available from medical imaging.
Energy Technology Data Exchange (ETDEWEB)
Abe, M.; Morisawa, M. [Musashi Institute of Technology, Tokyo (Japan); Sato, T. [Keio University, Tokyo (Japan); Kobayashi, K. [Molex-Japan Co. Ltd., Tokyo (Japan)
1997-10-01
The past study of safety at vehicle collision pays attention to phenomena within the short time from starting collision, and the behavior of rollover is studied separating from that at collision. Most simulations of traffic accident are two-dimensional simulations. Therefore, it is indispensable for vehicle design to the analyze three-dimensional and continuous behavior from crash till stopping. Accordingly, in this study, the three-dimensional behavior of two vehicles at collision was simulated by computer using dynamic models. Then, by comparison of the calculated results with real vehicles` collision test data, it was confirmed that dynamic model of this study was reliable. 10 refs., 6 figs., 3 tabs.
DEFF Research Database (Denmark)
Solov'yov, Ilia; Yakubovich, Alexander V.; Nikolaev, Pavel V.;
2012-01-01
We present a multipurpose computer code MesoBioNano Explorer (MBN Explorer). The package allows to model molecular systems of varied level of complexity. In particular, MBN Explorer is suited to compute system's energy, to optimize molecular structure as well as to consider the molecular and random...... walk dynamics. MBN Explorer allows to use a broad variety of interatomic potentials, to model different molecular systems, such as atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, composite systems, nanofractals, and so on. A distinct feature of the program, which makes...
Magoules, Frederic
2011-01-01
Exploring new variations of classical methods as well as recent approaches appearing in the field, Computational Fluid Dynamics demonstrates the extensive use of numerical techniques and mathematical models in fluid mechanics. It presents various numerical methods, including finite volume, finite difference, finite element, spectral, smoothed particle hydrodynamics (SPH), mixed-element-volume, and free surface flow.Taking a unified point of view, the book first introduces the basis of finite volume, weighted residual, and spectral approaches. The contributors present the SPH method, a novel ap
Essential Computational Fluid Dynamics
Zikanov, Oleg
2011-01-01
This book serves as a complete and self-contained introduction to the principles of Computational Fluid Dynamic (CFD) analysis. It is deliberately short (at approximately 300 pages) and can be used as a text for the first part of the course of applied CFD followed by a software tutorial. The main objectives of this non-traditional format are: 1) To introduce and explain, using simple examples where possible, the principles and methods of CFD analysis and to demystify the `black box’ of a CFD software tool, and 2) To provide a basic understanding of how CFD problems are set and
Bodley, C. S.; Devers, D. A.; Park, C. A.
1975-01-01
A theoretical development and associated digital computer program system is presented. The dynamic system (spacecraft) is modeled as an assembly of rigid and/or flexible bodies not necessarily in a topological tree configuration. The computer program system may be used to investigate total system dynamic characteristics including interaction effects between rigid and/or flexible bodies, control systems, and a wide range of environmental loadings. Additionally, the program system may be used for design of attitude control systems and for evaluation of total dynamic system performance including time domain response and frequency domain stability analyses. Volume 1 presents the theoretical developments including a description of the physical system, the equations of dynamic equilibrium, discussion of kinematics and system topology, a complete treatment of momentum wheel coupling, and a discussion of gravity gradient and environmental effects. Volume 2, is a program users' guide and includes a description of the overall digital program code, individual subroutines and a description of required program input and generated program output. Volume 3 presents the results of selected demonstration problems that illustrate all program system capabilities.
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Krueger, Gerhard R F; Brandt, Michael E; Wang, Guanyu; Buja, L Maximilian
2003-01-01
Based upon a previously developed theory of dysregulative lymphoma pathogenesis, a computer model is designed in order to simulate cell changes occurring in disturbances of the T cell immune system and in lymphoproliferative diseases. The model is based upon the concept that factors identified as proliferation factors, differentiation factors and inhibition factors exert a network regulation upon development and function of the T cell system, and that selective disturbances of these factors may lead to hyperplastic, aplastic or neoplastic diseases. The resulting computer model (TCM-1) was validated by comparing it with data from human diseases such as acute HHV-6 (viral) infection, chronic persistent HHV-6 infection, progressive HIV1 infection and HTLV-1 infection, and comparing the simulation results with the actual cell data in the human patients. All these infections target the same T cell population (i.e. CD4 + T helper cells), yet cause different prototypical reactions (hyperplastic, aplastic, neoplastic). The described computer model, which was successfully used to simulate changes in the benign lymphoproliferative disease, Canale-Smith syndrome, will serve as the basis model for further supplementation to accommodate identified factorial influences such as by cytokines, chemokines and others.
Dynamic simulations of tissue welding
Energy Technology Data Exchange (ETDEWEB)
Maitland, D.J.; Eder, D.C.; London, R.A.; Glinsky, M.E. [and others
1996-02-01
The exposure of human skin to near-infrared radiation is numerically simulated using coupled laser, thermal transport and mass transport numerical models. The computer model LATIS is applied in both one-dimensional and two-dimensional geometries. Zones within the skin model are comprised of a topical solder, epidermis, dermis, and fatty tissue. Each skin zone is assigned initial optical, thermal and water density properties consistent with values listed in the literature. The optical properties of each zone (i.e. scattering, absorption and anisotropy coefficients) are modeled as a kinetic function of the temperature. Finally, the water content in each zone is computed from water diffusion where water losses are accounted for by evaporative losses at the air-solder interface. The simulation results show that the inclusion of water transport and evaporative losses in the model are necessary to match experimental observations. Dynamic temperature and damage distributions are presented for the skin simulations.
Massive Parallel Quantum Computer Simulator
De Raedt, K; De Raedt, H; Ito, N; Lippert, T; Michielsen, K; Richter, M; Trieu, B; Watanabe, H; Lippert, Th.
2006-01-01
We describe portable software to simulate universal quantum computers on massive parallel computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray X1E, a SGI Altix 3700 and clusters of PCs running Windows XP. We study the performance of the software by simulating quantum computers containing up to 36 qubits, using up to 4096 processors and up to 1 TB of memory. Our results demonstrate that the simulator exhibits nearly ideal scaling as a function of the number of processors and suggest that the simulation software described in this paper may also serve as benchmark for testing high-end parallel computers.
Simulating protein dynamics: Novel methods and applications
Vishal, V.
This Ph.D dissertation describes several methodological advances in molecular dynamics (MD) simulations. Methods like Markov State Models can be used effectively in combination with distributed computing to obtain long time scale behavior from an ensemble of short simulations. Advanced computing architectures like Graphics Processors can be used to greatly extend the scope of MD. Applications of MD techniques to problems like Alzheimer's Disease and fundamental questions in protein dynamics are described.
Strutzenberg, L. L.; Dougherty, N. S.; Liever, P. A.; West, J. S.; Smith, S. D.
2007-01-01
This paper details advances being made in the development of Reynolds-Averaged Navier-Stokes numerical simulation tools, models, and methods for the integrated Space Shuttle Vehicle at launch. The conceptual model and modeling approach described includes the development of multiple computational models to appropriately analyze the potential debris transport for critical debris sources at Lift-Off. The conceptual model described herein involves the integration of propulsion analysis for the nozzle/plume flow with the overall 3D vehicle flowfield at Lift-Off. Debris Transport Analyses are being performed using the Shuttle Lift-Off models to assess the risk to the vehicle from Lift-Off debris and appropriately prioritized mitigation of potential debris sources to continue to reduce vehicle risk. These integrated simulations are being used to evaluate plume-induced debris environments where the multi-plume interactions with the launch facility can potentially accelerate debris particles toward the vehicle.
Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam
2000-01-01
Mechanical behavior of the Si\\(111\\)/Si3N4\\(0001\\) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the \\(1¯ 1¯1\\) plane of the silicon substrate with a speed of 500 \\(+/-100\\) m/s. Time evolution of the dislocation emission and nature of defects is studied.
Energy Technology Data Exchange (ETDEWEB)
Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjoe, Ingvar; Madhukar, Anupam
2000-01-10
Mechanical behavior of the Si(111)/Si{sub 3}N{sub 4} (0001) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the (1 11) plane of the silicon substrate with a speed of 500 ({+-}100) m/s . Time evolution of the dislocation emission and nature of defects is studied. (c) 2000 The American Physical Society.
Fengjiao Liu; Zhang, John Z. H.; Ye Mei
2016-01-01
Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The re...
Energy Technology Data Exchange (ETDEWEB)
Silva, Marcelo Mariano da
2008-01-15
The search for high performance and low cost hardware and software solutions always guides the developments performed at the IEN parallel computing laboratory. In this context, this dissertation about the building of programs for visualization of computational fluid dynamics (CFD) simulations using the open source software OpenDx was written. The programs developed are useful to produce videos and images in two or three dimensions. They are interactive, easily to use and were designed to serve fluid dynamics researchers. A detailed description about how this programs were developed and the complete instructions of how to use them was done. The use of OpenDx as development tool is also introduced. There are examples that help the reader to understand how programs can be useful for many applications. (author)
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.
Institute of Scientific and Technical Information of China (English)
邵雄飞; 吴忠标
2004-01-01
The flow field of gas and liquid in a φ150mm rotating-stream-tray (RST) scrubber is simulated by using computational fluid dynamic (CFD) method. The simulation is based on the two-equation RNG κ-ε turbulence model, Eulerian multiphase model, mad a real-shape 3D model with a huge number of meshes. The simulation results include detailed information about velocity, pressure, volume fraction and so on. Some features of the flow field are obtained: liquid is atomized in a thin annular zone; a high velocity air zone prevents water drops at the bottom from flying towards the wall;the pressure varies sharply at the end of blades and so on. The results will be helpful for structure optimization and engineering design.
Computer simulation of thermal plant operations
O'Kelly, Peter
2012-01-01
This book describes thermal plant simulation, that is, dynamic simulation of plants which produce, exchange and otherwise utilize heat as their working medium. Directed at chemical, mechanical and control engineers involved with operations, control and optimization and operator training, the book gives the mathematical formulation and use of simulation models of the equipment and systems typically found in these industries. The author has adopted a fundamental approach to the subject. The initial chapters provide an overview of simulation concepts and describe a suitable computer environment.
Computer simulation in materials science
Energy Technology Data Exchange (ETDEWEB)
Arsenault, R.J.; Beeler, J.R.; Esterling, D.M.
1988-01-01
This book contains papers on the subject of modeling in materials science. Topics include thermodynamics of metallic solids and fluids, grain-boundary modeling, fracture from an atomistic point of view, and computer simulation of dislocations on an atomistic level.
Directory of Open Access Journals (Sweden)
Reza Sharifanfar
2016-10-01
Full Text Available Background and Objectives: Pomegranate juice (PJ contains large particles that stick to evaporator walls causing off flavors in the concentrate due to burning. Microfiltration is used to clarify PJ. Fouling is a limiting phenomenon that can prevent the industrialization of membrane clarification. Changes in the geometry of the membrane module such as using baffles are useful to decrease this problem. Computational fluid dynamics (CFD is a powerful numerical tool used in modeling membrane processing. Materials and Methods: The effect of baffle geometry on the efficiency of membrane clarification of pomegranate juice in a flat-sheet module was simulated using computational fluid dynamics (CFD. The geometry of the membrane unit was plotted and meshed with Gambit software, and was solved using FLUENT software. A two-dimensional double-precision method at steady state was selected to simulate the membrane process. The convective terms were discretized with a standard first-order upwind scheme in computational solution. The RNG k- model was used due to its high accuracy in eddy flows with a low Reynolds number. The effects on the process performance of the number of baffles, their angle and the distance between the baffles and the membrane surface were evaluated. Results: The results showed that the configuration with the feed-channel height of 2 cm, the baffle angle of 90o and the distance between the membrane surface and baffles of 2 mm had maximum permeate flux. Conclusions: Reducing the distance between the baffles and the membrane surface increased the permeate flux due to create an eddy flow near the membrane surface in the flat-sheet module and reduced the total and cake-layer resistances. Keywords: Baffle, Computational fluid dynamics, Juice, Membrane, Pomegranate
Computational methods for fluid dynamics
Ferziger, Joel H
2002-01-01
In its 3rd revised and extended edition the book offers an overview of the techniques used to solve problems in fluid mechanics on computers and describes in detail those most often used in practice. Included are advanced methods in computational fluid dynamics, like direct and large-eddy simulation of turbulence, multigrid methods, parallel computing, moving grids, structured, block-structured and unstructured boundary-fitted grids, free surface flows. The 3rd edition contains a new section dealing with grid quality and an extended description of discretization methods. The book shows common roots and basic principles for many different methods. The book also contains a great deal of practical advice for code developers and users, it is designed to be equally useful to beginners and experts. The issues of numerical accuracy, estimation and reduction of numerical errors are dealt with in detail, with many examples. A full-feature user-friendly demo-version of a commercial CFD software has been added, which ca...
Shiino, Yuta; Kuwazuru, Osamu; Yoshikawa, Nobuhiro
2009-07-07
A mechanism of generating passive feeding flow for the Devonian spiriferide brachiopod Paraspirifer bownockeri was theoretically elucidated through fluid dynamics simulations for flow around rigid shells. The RANS equations were used as a turbulence model, and the unsteady incompressible flow was solved using the finite volume method. Two directions of ventral and dorsal flows were investigated as typical cases where little exchange flow occurs inside the shells. The digital model of the shell was constructed using image processing of X-ray CT images of a shell replica made by molding a polycarbonate plate to a well-preserved fossil specimen of Paraspirifer. To examine the effect of flow velocity, three conditions of ambient flow velocity were adopted for both the ventral and dorsal flows. The pressure distribution along the gape showed that a relatively high pressure occurred around the sulcus in all simulated cases. This high pressure generated inflow from the sulcus and subsequent spiral internal flow, especially in fast ambient flows. This means that the sulcus generated the considerable pressure gradient around the gape passively and generated the stable intake of seawater and a spiral flow of water inside the shell for feeding. We conclude that the shell form of certain spiriferides could generate spiral flows so as to promote passive feeding, and the sulcus is interpreted as an important form for the passive intake of water.
Fluid simulation for computer graphics
Bridson, Robert
2008-01-01
Animating fluids like water, smoke, and fire using physics-based simulation is increasingly important in visual effects, in particular in movies, like The Day After Tomorrow, and in computer games. This book provides a practical introduction to fluid simulation for graphics. The focus is on animating fully three-dimensional incompressible flow, from understanding the math and the algorithms to the actual implementation.
Reservoir Thermal Recover Simulation on Parallel Computers
Li, Baoyan; Ma, Yuanle
The rapid development of parallel computers has provided a hardware background for massive refine reservoir simulation. However, the lack of parallel reservoir simulation software has blocked the application of parallel computers on reservoir simulation. Although a variety of parallel methods have been studied and applied to black oil, compositional, and chemical model numerical simulations, there has been limited parallel software available for reservoir simulation. Especially, the parallelization study of reservoir thermal recovery simulation has not been fully carried out, because of the complexity of its models and algorithms. The authors make use of the message passing interface (MPI) standard communication library, the domain decomposition method, the block Jacobi iteration algorithm, and the dynamic memory allocation technique to parallelize their serial thermal recovery simulation software NUMSIP, which is being used in petroleum industry in China. The parallel software PNUMSIP was tested on both IBM SP2 and Dawn 1000A distributed-memory parallel computers. The experiment results show that the parallelization of I/O has great effects on the efficiency of parallel software PNUMSIP; the data communication bandwidth is also an important factor, which has an influence on software efficiency. Keywords: domain decomposition method, block Jacobi iteration algorithm, reservoir thermal recovery simulation, distributed-memory parallel computer
Time reversibility, computer simulation, and chaos
Hoover, William Graham
1999-01-01
A small army of physicists, chemists, mathematicians, and engineers has joined forces to attack a classic problem, the "reversibility paradox", with modern tools. This book describes their work from the perspective of computer simulation, emphasizing the author's approach to the problem of understanding the compatibility, and even inevitability, of the irreversible second law of thermodynamics with an underlying time-reversible mechanics. Computer simulation has made it possible to probe reversibility from a variety of directions and "chaos theory" or "nonlinear dynamics" has supplied a useful
Data Systems Dynamic Simulator
Rouff, Christopher; Clark, Melana; Davenport, Bill; Message, Philip
1993-01-01
The Data System Dynamic Simulator (DSDS) is a discrete event simulation tool. It was developed for NASA for the specific purpose of evaluating candidate architectures for data systems of the Space Station era. DSDS provides three methods for meeting this requirement. First, the user has access to a library of standard pre-programmed elements. These elements represent tailorable components of NASA data systems and can be connected in any logical manner. Secondly, DSDS supports the development of additional elements. This allows the more sophisticated DSDS user the option of extending the standard element set. Thirdly, DSDS supports the use of data streams simulation. Data streams is the name given to a technique that ignores packet boundaries, but is sensitive to rate changes. Because rate changes are rare compared to packet arrivals in a typical NASA data system, data stream simulations require a fraction of the CPU run time. Additionally, the data stream technique is considerably more accurate than another commonly-used optimization technique.
Application of computer simulated persons in indoor environmental modeling
DEFF Research Database (Denmark)
Topp, C.; Nielsen, P. V.; Sørensen, Dan Nørtoft
2002-01-01
Computer simulated persons are often applied when the indoor environment is modeled by computational fluid dynamics. The computer simulated persons differ in size, shape, and level of geometrical complexity, ranging from simple box or cylinder shaped heat sources to more humanlike models. Little...
Institute of Scientific and Technical Information of China (English)
V.Nasserzadeh; J.Swithenbank
1995-01-01
With around 10 tonnes of waste being generated for every man,woman and chiled each year across the globe,safe disposal of if all has become an urgent environmental problem.In 1993,Western Europe,the United States,Canada,Japan,Australia and New Zealand produced a total of 480 million tonnes of industrial waste and 8 billion tonnes from activities such as energy production,agriculture,mining and sewage disposal,The emission to the atmosphere of both heavy metals and acid gases and perhaps more important in the longer term,the Dioxins/Furans(PCDDs/PCDFs),promises to be one of the key issuees facing not only the industry but the society as a whole over the next decade and more.Although it is increasingly likely that measures to control toxic emissions will have to be directed at a wider target than just the waste incinerators.it is equally certain that both public opinion and legislation will at least in the first instance,see the incinerators as one of the most obvious candidates for tighter regulation.These days,virtually all the new research and development techniques in combustion technology involve the application of computational fluid dynamics(CFD) to combustor design,This seems to be the best approach to solving design problems.Mathematical modelling thus is seen as an inherent part of practically all combustion research programmes.The new discipline of computational fluid dynamics can also be used to help minimise flame generated pollutants released to the atmosphere,These pollutants include:CO2,CO,SO2,NOx,HCl,Hydrocarbons.soot,particulates,eavey metals and dioxins/furans.CFD studies of their release to the atmosphere must include not only their source in the flame,but also their removal from the flue gases by scurbbing and other techniques.The governing differential equations for the process being studied must be defined and solved simultaneously if the parameters in the equations are interacing.At present,this procedure can give valualbe insight into the
Enabling Computational Technologies for Terascale Scientific Simulations
Energy Technology Data Exchange (ETDEWEB)
Ashby, S.F.
2000-08-24
We develop scalable algorithms and object-oriented code frameworks for terascale scientific simulations on massively parallel processors (MPPs). Our research in multigrid-based linear solvers and adaptive mesh refinement enables Laboratory programs to use MPPs to explore important physical phenomena. For example, our research aids stockpile stewardship by making practical detailed 3D simulations of radiation transport. The need to solve large linear systems arises in many applications, including radiation transport, structural dynamics, combustion, and flow in porous media. These systems result from discretizations of partial differential equations on computational meshes. Our first research objective is to develop multigrid preconditioned iterative methods for such problems and to demonstrate their scalability on MPPs. Scalability describes how total computational work grows with problem size; it measures how effectively additional resources can help solve increasingly larger problems. Many factors contribute to scalability: computer architecture, parallel implementation, and choice of algorithm. Scalable algorithms have been shown to decrease simulation times by several orders of magnitude.
Zheng, Zhe; Liu, Hong; Xu, Qi; Wu, Wei; Du, Liling; Chen, Hong; Zhang, Yiwen; Liu, Dongxu
2017-04-01
The changes of the upper airway after large retraction of the incisors in adult class I bimaxillary protrusion patients were assessed mainly focused on the anatomic variation and ignored the functional changes. This study aimed to investigate the changes of the upper airway in adult class I bimaxillary protrusion patients after extraction treatment using the functional images based on computational fluid dynamics (CFD). CFD was implemented after 3D reconstruction based on the CBCT of 30 patients who have completed extraction treatment. After treatment, pressure drop in the minimum area, oropharynx, and hypopharynx increased significantly. The minimum pressure and the maximum velocity mainly located in the hypopharynx in pre-treatment while they mostly occured in the oropharynx after treatment. Statistically significant correlation between pressure drop and anatomic parameters, pressure drop and treatment outcomes was found. No statistical significance changes in pressure drop and volume of nasopharynx was found. This study suggested that the risk of pharyngeal collapsing become higher after extraction treatment with maximum anchorage in bimaxillary protrusion adult patients. Those adverse changes should be taken into consideration especially for high-risk patients to avoid undesired weakening of the respiratory function in clinical treatment.
A Stochastic Dynamic Model of Computer Viruses
Directory of Open Access Journals (Sweden)
Chunming Zhang
2012-01-01
Full Text Available A stochastic computer virus spread model is proposed and its dynamic behavior is fully investigated. Specifically, we prove the existence and uniqueness of positive solutions, and the stability of the virus-free equilibrium and viral equilibrium by constructing Lyapunov functions and applying Ito's formula. Some numerical simulations are finally given to illustrate our main results.
Dynamical Systems Some Computational Problems
Guckenheimer, J; Guckenheimer, John; Worfolk, Patrick
1993-01-01
We present several topics involving the computation of dynamical systems. The emphasis is on work in progress and the presentation is informal -- there are many technical details which are not fully discussed. The topics are chosen to demonstrate the various interactions between numerical computation and mathematical theory in the area of dynamical systems. We present an algorithm for the computation of stable manifolds of equilibrium points, describe the computation of Hopf bifurcations for equilibria in parametrized families of vector fields, survey the results of studies of codimension two global bifurcations, discuss a numerical analysis of the Hodgkin and Huxley equations, and describe some of the effects of symmetry on local bifurcation.
Hock, Howard S; Schöner, Gregor; Brownlow, Stacey; Taler, Dana
2011-05-01
Four motion quartets, each ambiguous with respect to the perception of parallel-path horizontal or vertical motion, were arranged in a diamond configuration. Both global parallel-path motion (the same motion axis for all the quartets), which is typical for multiquartet stimuli, and global rotational rocking are perceived. Experiment 1 indicated that rotational rocking is established at different levels of processing. Globally, larger displacements of each quartet's elements increase the angle of rotation and, thereby, the perception of rotational rocking. Locally, larger displacements have the opposite effect, weakening motion percepts. Experiment 2 showed that global-to-local feedback affects the local perception of rotation-consistent versus rotation-inconsistent motion directions. Experiment 3 provided evidence for hysteresis effects indicative of competition between global rotational rocking and parallel-path motion. The experimental results were simulated by a two-level dynamical model incorporating global-to-local feedback, with recurrent feedforward/feedback loops creating detection instabilities that amplify activation at both global and local levels of the rotational-rocking pattern.
Liu, Fengjiao; Zhang, John Z H; Mei, Ye
2016-06-01
Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.
Liu, Fengjiao; Zhang, John Z. H.; Mei, Ye
2016-06-01
Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A
2012-12-11
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.
Colour in visualisation for computational fluid dynamics
2006-01-01
Colour is used in computational fluid dynamic (CFD) simulations in two key ways. First it is used to visualise the geometry and allow the engineers to be confident that the model constructed is a good representation of the engineering situation. Once an analysis has been completed, colour is used in post-processing the data from the simulations to illustrate the complex fluid mechanic phenomena under investigation. This paper describes these two uses of colour and provides some examples to il...
Energy Technology Data Exchange (ETDEWEB)
Celik, I.; Chattree, M.
1988-07-01
An assessment of the theoretical and numerical aspects of the computer code, PCGC-2, is made; and the results of the application of this code to the Morgantown Energy Technology Center (METC) advanced gasification facility entrained-flow reactor, ''the gasifier,'' are presented. PCGC-2 is a code suitable for simulating pulverized coal combustion or gasification under axisymmetric (two-dimensional) flow conditions. The governing equations for the gas and particulate phase have been reviewed. The numerical procedure and the related programming difficulties have been elucidated. A single-particle model similar to the one used in PCGC-2 has been developed, programmed, and applied to some simple situations in order to gain insight to the physics of coal particle heat-up, devolatilization, and char oxidation processes. PCGC-2 was applied to the METC entrained-flow gasifier to study numerically the flash pyrolysis of coal, and gasification of coal with steam or carbon dioxide. The results from the simulations are compared with measurements. The gas and particle residence times, particle temperature, and mass component history were also calculated and the results were analyzed. The results provide useful information for understanding the fundamentals of coal gasification and for assessment of experimental results performed using the reactor considered. 69 refs., 35 figs., 23 tabs.
Energy Technology Data Exchange (ETDEWEB)
Celik, I.; Chattree, M.
1988-07-01
An assessment of the theoretical and numerical aspects of the computer code, PCGC-2, is made; and the results of the application of this code to the Morgantown Energy Technology Center (METC) advanced gasification facility entrained-flow reactor, ''the gasifier,'' are presented. PCGC-2 is a code suitable for simulating pulverized coal combustion or gasification under axisymmetric (two-dimensional) flow conditions. The governing equations for the gas and particulate phase have been reviewed. The numerical procedure and the related programming difficulties have been elucidated. A single-particle model similar to the one used in PCGC-2 has been developed, programmed, and applied to some simple situations in order to gain insight to the physics of coal particle heat-up, devolatilization, and char oxidation processes. PCGC-2 was applied to the METC entrained-flow gasifier to study numerically the flash pyrolysis of coal, and gasification of coal with steam or carbon dioxide. The results from the simulations are compared with measurements. The gas and particle residence times, particle temperature, and mass component history were also calculated and the results were analyzed. The results provide useful information for understanding the fundamentals of coal gasification and for assessment of experimental results performed using the reactor considered. 69 refs., 35 figs., 23 tabs.
Numerical characteristics of quantum computer simulation
Chernyavskiy, A.; Khamitov, K.; Teplov, A.; Voevodin, V.; Voevodin, Vl.
2016-12-01
The simulation of quantum circuits is significantly important for the implementation of quantum information technologies. The main difficulty of such modeling is the exponential growth of dimensionality, thus the usage of modern high-performance parallel computations is relevant. As it is well known, arbitrary quantum computation in circuit model can be done by only single- and two-qubit gates, and we analyze the computational structure and properties of the simulation of such gates. We investigate the fact that the unique properties of quantum nature lead to the computational properties of the considered algorithms: the quantum parallelism make the simulation of quantum gates highly parallel, and on the other hand, quantum entanglement leads to the problem of computational locality during simulation. We use the methodology of the AlgoWiki project (algowiki-project.org) to analyze the algorithm. This methodology consists of theoretical (sequential and parallel complexity, macro structure, and visual informational graph) and experimental (locality and memory access, scalability and more specific dynamic characteristics) parts. Experimental part was made by using the petascale Lomonosov supercomputer (Moscow State University, Russia). We show that the simulation of quantum gates is a good base for the research and testing of the development methods for data intense parallel software, and considered methodology of the analysis can be successfully used for the improvement of the algorithms in quantum information science.
Lecarpentier, E.; Bhatt, M.; Bertin, G. I.; Deloison, B.; Salomon, L. J.; Deloron, P.; Fournier, T.; Barakat, A. I.; Tsatsaris, V.
2016-01-01
Introduction In the human placenta the maternal blood circulates in the intervillous space (IVS). The syncytiotrophoblast (STB) is in direct contact with maternal blood. The wall shear stress (WSS) exerted by the maternal blood flow on the STB has not been evaluated. Our objective was to determine the physiological WSS exerted on the surface of the STB during the third trimester of pregnancy. Material and Methods To gain insight into the shear stress levels that the STB is expected to experience in vivo, we have formulated three different computational models of varying levels of complexity that reflect different physical representations of the IVS. Computations of the flow fields in all models were performed using the CFD module of the finite element code COMSOL Multiphysics 4.4. The mean velocity of maternal blood in the IVS during the third trimester was measured in vivo with dynamic MRI (0.94±0.14 mm.s-1). To investigate if the in silico results are consistent with physiological observations, we studied the cytoadhesion of human parasitized (Plasmodium falciparum) erythrocytes to primary human STB cultures, in flow conditions with different WSS values. Results The WSS applied to the STB is highly heterogeneous in the IVS. The estimated average values are relatively low (0.5±0.2 to 2.3±1.1 dyn.cm-2). The increase of WSS from 0.15 to 5 dyn.cm-2 was associated with a significant decrease of infected erythrocyte cytoadhesion. No cytoadhesion of infected erythrocytes was observed above 5 dyn.cm-2 applied for one hour. Conclusion Our study provides for the first time a WSS estimation in the maternal placental circulation. In spite of high maternal blood flow rates, the average WSS applied at the surface of the chorionic villi is low (<5 dyn.cm-2). These results provide the basis for future physiologically-relevant in vitro studies of the biological effects of WSS on the STB. PMID:26815115
Computational Modeling of Simulation Tests.
1980-06-01
Mexico , March 1979. 14. Kinney, G. F.,.::. IeiN, .hoce 1h Ir, McMillan, p. 57, 1962. 15. Courant and Friedrichs, ,U: r. on moca an.: Jho...AD 79 275 NEW MEXICO UNIV ALBUGUERGUE ERIC H WANG CIVIL ENGINE-ETC F/6 18/3 COMPUTATIONAL MODELING OF SIMULATION TESTS.(U) JUN 80 6 LEIGH, W CHOWN, B...COMPUTATIONAL MODELING OF SIMULATION TESTS00 0G. Leigh W. Chown B. Harrison Eric H. Wang Civil Engineering Research Facility University of New Mexico
Directory of Open Access Journals (Sweden)
Qifeng Bai
Full Text Available We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD simulations and free energy calculations. To test the effectiveness of MolGridCal, we screened potential ligands for β2 adrenergic receptor (β2AR from a database containing 50,000 small molecules. MolGridCal can not only send tasks to the grid server automatically, but also can distribute tasks using the screensaver function. As for the results of virtual screening, the known agonist BI-167107 of β2AR is ranked among the top 2% of the screened candidates, indicating MolGridCal program can give reasonable results. To further study the binding mode and refine the results of MolGridCal, more accurate docking and scoring methods are used to estimate the binding affinity for the top three molecules (agonist BI-167107, neutral antagonist alprenolol and inverse agonist ICI 118,551. The results indicate agonist BI-167107 has the best binding affinity. MD simulation and free energy calculation are employed to investigate the dynamic interaction mechanism between the ligands and β2AR. The results show that the agonist BI-167107 also has the lowest binding free energy. This study can provide a new way to perform virtual screening effectively through integrating molecular docking based on grid computing, MD simulations and free energy calculations. The source codes of MolGridCal are freely available at http://molgridcal.codeplex.com.
Energy Technology Data Exchange (ETDEWEB)
Gayathri Devi, V.; Sircar, A.; Sarkar, B. [Institute of Plasma Research, Bhat, Gandhinagar, Gujarar (India)
2015-03-15
One of the most challenging tasks in the design of the fuel cycle system lies in the effective design of Tritium Extraction System (TES) which involves proper extraction and purification of tritium in the fuel cycle of the fusion reactor. Indian Lead Lithium cooled Ceramic Breeder Test Blanket Module (LLCB-TBM) would extract hydrogen isotopes through Cryogenic Molecular Sieve Bed (CMSB) adsorber system. A prototype Hydrogen Isotopes Recovery System (HIRS) is being developed to validate the concepts for tritium extraction by adsorption mass transfer mechanism. In this study, a design model has been developed and analyzed to simulate the adsorption mass transfer kinetics in a fixed bed adsorption column. The simulation leads primarily to effective design of HIRS, which is a state-of-the-art technology. The paper describes the process simulation approach and the results of Computational Fluid Dynamics (CFD) analysis. The effects of different operating conditions are studied to investigate their influence on the hydrogen isotopes adsorption capacity. The results of the present simulation study would be used to understand the best optimized transport phenomenon before realizing the TES as a system for LLCB-TBM. (authors)
Simulating Human Cognitive Using Computational Verb Theory
Institute of Scientific and Technical Information of China (English)
YANGTao
2004-01-01
Modeling and simulation of a life system is closely connected to the modeling of cognition,especially for advanced life systems. The primary difference between an advanced life system and a digital computer is that the advanced life system consists of a body with mind while a digital computer is only a mind in a formal sense. To model an advanced life system one needs to symbols into a body where a digital computer is embedded. In this paper, a computational verb theory is proposed as a new paradigm of grounding symbols into the outputs of sensors. On one hand, a computational verb can preserve the physical "meanings" of the dynamics of sensor data such that a symbolic system can be used to manipulate physical meanings instead of abstract tokens in the digital computer. On the other hand, the physical meanings of an abstract symbol/token, which is usually an output of a reasoning process in the digital computer, can be restored and fed back to the actuators. Therefore, the computational verb theory bridges the gap between symbols and physical reality from the dynamic cognition perspective.
Biomass Gasifier for Computer Simulation; Biomassa foergasare foer Computer Simulation
Energy Technology Data Exchange (ETDEWEB)
Hansson, Jens; Leveau, Andreas; Hulteberg, Christian [Nordlight AB, Limhamn (Sweden)
2011-08-15
This report is an effort to summarize the existing data on biomass gasifiers as the authors have taken part in various projects aiming at computer simulations of systems that include biomass gasification. Reliable input data is paramount for any computer simulation, but so far there is no easy-accessible biomass gasifier database available for this purpose. This study aims at benchmarking current and past gasifier systems in order to create a comprehensive database for computer simulation purposes. The result of the investigation is presented in a Microsoft Excel sheet, so that the user easily can implement the data in their specific model. In addition to provide simulation data, the technology is described briefly for every studied gasifier system. The primary pieces of information that are sought for are temperatures, pressures, stream compositions and energy consumption. At present the resulting database contains 17 gasifiers, with one or more gasifier within the different gasification technology types normally discussed in this context: 1. Fixed bed 2. Fluidised bed 3. Entrained flow. It also contains gasifiers in the range from 100 kW to 120 MW, with several gasifiers in between these two values. Finally, there are gasifiers representing both direct and indirect heating. This allows for a more qualified and better available choice of starting data sets for simulations. In addition to this, with multiple data sets available for several of the operating modes, sensitivity analysis of various inputs will improve simulations performed. However, there have been fewer answers to the survey than expected/hoped for, which could have improved the database further. However, the use of online sources and other public information has to some extent counterbalanced the low response frequency of the survey. In addition to that, the database is preferred to be a living document, continuously updated with new gasifiers and improved information on existing gasifiers.
Directory of Open Access Journals (Sweden)
Adriana Brunstein
2004-01-01
Full Text Available To evaluate the effects of non-reversibility on compositional base changes and the distribution of branch lengths along a phylogeny, we extended, by means of computer simulations, our previous sequential PCR in vitro evolution experiment. In that study a 18S rRNA gene evolved neutrally for 280 generations and a homogeneous non-stationary model of base substitution based on a non-reversible dynamics was built from the in vitro evolution data to describe the observed pattern of nucleotide substitutions. Here, the process was extended to 840 generations without selection, using the model parameters calculated from the in vitro evolution experiment. We observed that under a non-reversible model the G+C content of the sequences significantly increases when compared to simulations with a reversible model. The values of mean and variance of the branch lengths are reduced under a non-reversible dynamics although they follow a Poisson distribution. We conclude that the major implication of non-reversibility is the overall decrease of branch lengths, although no transition from a stochastic to an ordered process is observed. According to our model the result of this neutral process will be the increase in the G+C content of the descendant sequences with an overall decrease in the frequency of substitutions.
Filtration theory using computer simulations
Energy Technology Data Exchange (ETDEWEB)
Bergman, W.; Corey, I. [Lawrence Livermore National Lab., CA (United States)
1997-08-01
We have used commercially available fluid dynamics codes based on Navier-Stokes theory and the Langevin particle equation of motion to compute the particle capture efficiency and pressure drop through selected two- and three-dimensional fiber arrays. The approach we used was to first compute the air velocity vector field throughout a defined region containing the fiber matrix. The particle capture in the fiber matrix is then computed by superimposing the Langevin particle equation of motion over the flow velocity field. Using the Langevin equation combines the particle Brownian motion, inertia and interception mechanisms in a single equation. In contrast, most previous investigations treat the different capture mechanisms separately. We have computed the particle capture efficiency and the pressure drop through one, 2-D and two, 3-D fiber matrix elements. 5 refs., 11 figs.
The DYNAMO Simulation Language--An Alternate Approach to Computer Science Education.
Bronson, Richard
1986-01-01
Suggests the use of computer simulation of continuous systems as a problem solving approach to computer languages. Outlines the procedures that the system dynamics approach employs in computer simulations. Explains the advantages of the special purpose language, DYNAMO. (ML)
Computer simulation of hard-core models for liquid crystals
Frenkel, D.
1987-01-01
A review is presented of computer simulations of liquid crystal systems. It will be shown that the shape of hard-core particles is of crucial importance for the stability of the phases. Both static and dynamic properties of the systems are obtained by means of computer simulation.
Energy Technology Data Exchange (ETDEWEB)
Hoffmann, Alexander; Merk, Bruno [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany); Hirsch, Tobias; Pitz-Paal, Robert [DLR Deutsches Zentrum fuer Luft- und Raumfahrt e.V., Stuttgart (Germany). Inst. fuer Solarforschung
2014-06-15
In the present feasibility study the system code ATHLET, which originates from nuclear engineering, is applied to a parabolic trough test facility. A model of the DISS (DIrect Solar Steam) test facility at Plataforma Solar de Almeria in Spain is assembled and the results of the simulations are compared to measured data and the simulation results of the Modelica library 'DissDyn'. A profound comparison between ATHLET Mod 3.0 Cycle A and the 'DissDyn' library reveals the capabilities of these codes. The calculated mass and energy balance in the ATHLET simulations are in good agreement with the results of the measurements and confirm the applicability for thermodynamic simulations of DSG processes in principle. Supplementary, the capabilities of the 6-equation model with transient momentum balances in ATHLET are used to study the slip between liquid and gas phases and to investigate pressure wave oscillations after a sudden valve closure. (orig.)
Plasma physics via computer simulation
Birdsall, CK
2004-01-01
PART 1: PRIMER Why attempting to do plasma physics via computer simulation using particles makes good sense Overall view of a one dimensional electrostatic program A one dimensional electrostatic program ES1 Introduction to the numerical methods used Projects for ES1 A 1d electromagnetic program EM1 Projects for EM1 PART 2: THEORY Effects of the spatial grid Effects of the finitw time ste Energy-conserving simulation models Multipole models Kinetic theory for fluctuations and noise; collisions Kinetic properties: theory, experience and heuristic estimates PART 3: PRACTIC
Akinkunmi, Frederick O; Jahn, David A; Giovambattista, Nicolas
2015-05-21
Glycerol-water solutions are relevant in technological and scientific applications, such as in the preservation of biomolecules and tissues at low temperatures. We perform molecular dynamics simulations of glycerol-water mixtures with glycerol molar fractions of χg = 0-100% at P = 0.1 MPa and T = 210-460 K. We focus on the effects of temperature and concentration on the thermodynamic (density ρ, thermal expansion coefficient αP, isobaric specific heat cP, compressibility κT) and dynamical (glycerol and water diffusion coefficients, Dg and Dw) properties of the mixtures. In particular, we test the sensitivity of computer simulation results to the glycerol force field and water model (TIP3P and TIP4P/2005) employed. All mixture models underestimate ρ at high T and tend to overestimate ρ at low T; only the mixture model based on TIP4P/2005 water exhibits a density maximum at low χg, as expected. All models overestimate αP, cP, and κT; they are able to reproduce qualitatively the T dependence of αP and κT but fail in the case of cP. In all cases, Dg and Dw follow the Vogel-Tamman-Fulcher equation and decouple at low T, with Dw/Dg increasing upon cooling. Overall, the mixture based on TIP4P/2005 water provides better thermodynamic and dynamical properties than the mixtures based on TIP3P water, even at χg = 20%.
Spiking network simulation code for petascale computers
Kunkel, Susanne; Schmidt, Maximilian; Eppler, Jochen M.; Plesser, Hans E.; Masumoto, Gen; Igarashi, Jun; Ishii, Shin; Fukai, Tomoki; Morrison, Abigail; Diesmann, Markus; Helias, Moritz
2014-01-01
Brain-scale networks exhibit a breathtaking heterogeneity in the dynamical properties and parameters of their constituents. At cellular resolution, the entities of theory are neurons and synapses and over the past decade researchers have learned to manage the heterogeneity of neurons and synapses with efficient data structures. Already early parallel simulation codes stored synapses in a distributed fashion such that a synapse solely consumes memory on the compute node harboring the target neuron. As petaflop computers with some 100,000 nodes become increasingly available for neuroscience, new challenges arise for neuronal network simulation software: Each neuron contacts on the order of 10,000 other neurons and thus has targets only on a fraction of all compute nodes; furthermore, for any given source neuron, at most a single synapse is typically created on any compute node. From the viewpoint of an individual compute node, the heterogeneity in the synaptic target lists thus collapses along two dimensions: the dimension of the types of synapses and the dimension of the number of synapses of a given type. Here we present a data structure taking advantage of this double collapse using metaprogramming techniques. After introducing the relevant scaling scenario for brain-scale simulations, we quantitatively discuss the performance on two supercomputers. We show that the novel architecture scales to the largest petascale supercomputers available today. PMID:25346682
Spiking network simulation code for petascale computers
Directory of Open Access Journals (Sweden)
Susanne eKunkel
2014-10-01
Full Text Available Brain-scale networks exhibit a breathtaking heterogeneity in the dynamical properties and parameters of their constituents. At cellular resolution, the entities of theory are neurons and synapses and over the past decade researchers have learned to manage the heterogeneity of neurons and synapses with efficient data structures. Already early parallel simulation codes stored synapses in a distributed fashion such that a synapse solely consumes memory on the compute node harboring the target neuron. As petaflop computers with some 100,000 nodes become increasingly available for neuroscience, new challenges arise for neuronal network simulation software: Each neuron contacts on the order of 10,000 other neurons and thus has targets only on a fraction of all compute nodes; furthermore, for any given source neuron, at most a single synapse is typically created on any compute node. From the viewpoint of an individual compute node, the heterogeneity in the synaptic target lists thus collapses along two dimensions: the dimension of the types of synapses and the dimension of the number of synapses of a given type. Here we present a data structure taking advantage of this double collapse using metaprogramming techniques. After introducing the relevant scaling scenario for brain-scale simulations, we quantitatively discuss the performance on two supercomputers. We show that the novel architecture scales to the largest petascale supercomputers available today.
Computer Modelling of Dynamic Processes
Directory of Open Access Journals (Sweden)
B. Rybakin
2000-10-01
Full Text Available Results of numerical modeling of dynamic problems are summed in the article up. These problems are characteristic for various areas of human activity, in particular for problem solving in ecology. The following problems are considered in the present work: computer modeling of dynamic effects on elastic-plastic bodies, calculation and determination of performances of gas streams in gas cleaning equipment, modeling of biogas formation processes.
Computer simulation of aeolian bedforms
Institute of Scientific and Technical Information of China (English)
苗天德; 慕青松; 武生智
2001-01-01
A discrete model is set up using the cellular automaton method and applied to simulate the formation and evolution of aeolian bedforms. The calculated bedforms resemble the actual shape of natural sand ripples and dunes.This reveals that the sand movement is a typical nonlinear dynamical process, and that the nesting configuration of sand ripples, dunes and draas are a self-organized system with a fractal characteristic, and evotves simultaneously at various scales in the sand-airflow.
Uncertainty and error in computational simulations
Energy Technology Data Exchange (ETDEWEB)
Oberkampf, W.L.; Diegert, K.V.; Alvin, K.F.; Rutherford, B.M.
1997-10-01
The present paper addresses the question: ``What are the general classes of uncertainty and error sources in complex, computational simulations?`` This is the first step of a two step process to develop a general methodology for quantitatively estimating the global modeling and simulation uncertainty in computational modeling and simulation. The second step is to develop a general mathematical procedure for representing, combining and propagating all of the individual sources through the simulation. The authors develop a comprehensive view of the general phases of modeling and simulation. The phases proposed are: conceptual modeling of the physical system, mathematical modeling of the system, discretization of the mathematical model, computer programming of the discrete model, numerical solution of the model, and interpretation of the results. This new view is built upon combining phases recognized in the disciplines of operations research and numerical solution methods for partial differential equations. The characteristics and activities of each of these phases is discussed in general, but examples are given for the fields of computational fluid dynamics and heat transfer. They argue that a clear distinction should be made between uncertainty and error that can arise in each of these phases. The present definitions for uncertainty and error are inadequate and. therefore, they propose comprehensive definitions for these terms. Specific classes of uncertainty and error sources are then defined that can occur in each phase of modeling and simulation. The numerical sources of error considered apply regardless of whether the discretization procedure is based on finite elements, finite volumes, or finite differences. To better explain the broad types of sources of uncertainty and error, and the utility of their categorization, they discuss a coupled-physics example simulation.
Modelling of dusty plasma properties by computer simulation methods
Energy Technology Data Exchange (ETDEWEB)
Baimbetov, F B [IETP, Al Farabi Kazakh National University, 96a, Tole bi St, Almaty 050012 (Kazakhstan); Ramazanov, T S [IETP, Al Farabi Kazakh National University, 96a, Tole bi St, Almaty 050012 (Kazakhstan); Dzhumagulova, K N [IETP, Al Farabi Kazakh National University, 96a, Tole bi St, Almaty 050012 (Kazakhstan); Kadyrsizov, E R [Institute for High Energy Densities of RAS, Izhorskaya 13/19, Moscow 125412 (Russian Federation); Petrov, O F [IETP, Al Farabi Kazakh National University, 96a, Tole bi St, Almaty 050012 (Kazakhstan); Gavrikov, A V [IETP, Al Farabi Kazakh National University, 96a, Tole bi St, Almaty 050012 (Kazakhstan)
2006-04-28
Computer simulation of dusty plasma properties is performed. The radial distribution functions, the diffusion coefficient are calculated on the basis of the Langevin dynamics. A comparison with the experimental data is made.
Inversion based on computational simulations
Energy Technology Data Exchange (ETDEWEB)
Hanson, K.M.; Cunningham, G.S.; Saquib, S.S.
1998-09-01
A standard approach to solving inversion problems that involve many parameters uses gradient-based optimization to find the parameters that best match the data. The authors discuss enabling techniques that facilitate application of this approach to large-scale computational simulations, which are the only way to investigate many complex physical phenomena. Such simulations may not seem to lend themselves to calculation of the gradient with respect to numerous parameters. However, adjoint differentiation allows one to efficiently compute the gradient of an objective function with respect to all the variables of a simulation. When combined with advanced gradient-based optimization algorithms, adjoint differentiation permits one to solve very large problems of optimization or parameter estimation. These techniques will be illustrated through the simulation of the time-dependent diffusion of infrared light through tissue, which has been used to perform optical tomography. The techniques discussed have a wide range of applicability to modeling including the optimization of models to achieve a desired design goal.
Study of Nanowires Using Molecular Dynamics Simulations
Monk, Joshua D
2007-01-01
In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...
FPGA-accelerated simulation of computer systems
Angepat, Hari; Chung, Eric S; Hoe, James C; Chung, Eric S
2014-01-01
To date, the most common form of simulators of computer systems are software-based running on standard computers. One promising approach to improve simulation performance is to apply hardware, specifically reconfigurable hardware in the form of field programmable gate arrays (FPGAs). This manuscript describes various approaches of using FPGAs to accelerate software-implemented simulation of computer systems and selected simulators that incorporate those techniques. More precisely, we describe a simulation architecture taxonomy that incorporates a simulation architecture specifically designed f
Computational Fluid Dynamics in Combustion
Directory of Open Access Journals (Sweden)
P. J. Paul
2010-10-01
Full Text Available Computational fluid dynamics has reached a stage where flow field in practical situation can be predicted to aid the design and to probe into the fundamental flow physics to understand and resolve the issues in fundamental fluid mechanics. The study examines the computation of reacting flows. After exploring the conservation equations for species and energy, the methods of closing the reaction rate terms in turbulent flow have been examined briefly. Two cases of computation, where combustion-flow interaction plays important role, have been discussed to illustrate the computational aspects and the physical insight that can be gained by the reacting flow computation.Defence Science Journal, 2010, 60(6, pp.577-582, DOI:http://dx.doi.org/10.14429/dsj.60.600
Applications of Computer Simulations and Statistical Mechanics in Surface Electrochemistry
Rikvold, P A; Juwono, T; Robb, D T; Novotny, M A; 10.1007/978-0-387-49586-6_4
2009-01-01
We present a brief survey of methods that utilize computer simulations and quantum and statistical mechanics in the analysis of electrochemical systems. The methods, Molecular Dynamics and Monte Carlo simulations and quantum-mechanical density-functional theory, are illustrated with examples from simulations of lithium-battery charging and electrochemical adsorption of bromine on single-crystal silver electrodes.
Computational Fluid Dynamics in Ventilation
DEFF Research Database (Denmark)
Nielsen, Peter V.; Allard, Francis; Awbi, Hazim B.;
2008-01-01
Computational Fluid Dynamics in Ventilation Design is a new title in the is a new title in the REHVA guidebook series. The guidebook is written for people who need to use and discuss results based on CFD predictions, and it gives insight into the subject for those who are not used to work with CFD...
Brolin, Gustav; Sjögreen Gleisner, Katarina; Ljungberg, Michael
2013-05-01
In dynamic renal scintigraphy, the main interest is the radiopharmaceutical redistribution as a function of time. Quality control (QC) of renal procedures often relies on phantom experiments to compare image-based results with the measurement setup. A phantom with a realistic anatomy and time-varying activity distribution is therefore desirable. This work describes a pharmacokinetic (PK) compartment model for 99mTc-MAG3, used for defining a dynamic whole-body activity distribution within a digital phantom (XCAT) for accurate Monte Carlo (MC)-based images for QC. Each phantom structure is assigned a time-activity curve provided by the PK model, employing parameter values consistent with MAG3 pharmacokinetics. This approach ensures that the total amount of tracer in the phantom is preserved between time points, and it allows for modifications of the pharmacokinetics in a controlled fashion. By adjusting parameter values in the PK model, different clinically realistic scenarios can be mimicked, regarding, e.g., the relative renal uptake and renal transit time. Using the MC code SIMIND, a complete set of renography images including effects of photon attenuation, scattering, limited spatial resolution and noise, are simulated. The obtained image data can be used to evaluate quantitative techniques and computer software in clinical renography.
Understanding membrane fouling mechanisms through computational simulations
Xiang, Yuan
This dissertation focuses on a computational simulation study on the organic fouling mechanisms of reverse osmosis and nanofiltration (RO/NF) membranes, which have been widely used in industry for water purification. The research shows that through establishing a realistic computational model based on available experimental data, we are able to develop a deep understanding of membrane fouling mechanism. This knowledge is critical for providing a strategic plan for membrane experimental community and RO/NF industry for further improvements in membrane technology for water treatment. This dissertation focuses on three major research components (1) Development of the realistic molecular models, which could well represent the membrane surface properties; (2) Investigation of the interactions between the membrane surface and foulants by steered molecular dynamics simulations, in order to determine the major factors that contribute to surface fouling; and (3) Studies of the interactions between the surface-modified membranes (polyethylene glycol) to provide strategies for antifouling.
Time reversibility, computer simulation, algorithms, chaos
Hoover, William Graham
2012-01-01
A small army of physicists, chemists, mathematicians, and engineers has joined forces to attack a classic problem, the "reversibility paradox", with modern tools. This book describes their work from the perspective of computer simulation, emphasizing the author's approach to the problem of understanding the compatibility, and even inevitability, of the irreversible second law of thermodynamics with an underlying time-reversible mechanics. Computer simulation has made it possible to probe reversibility from a variety of directions and "chaos theory" or "nonlinear dynamics" has supplied a useful vocabulary and a set of concepts, which allow a fuller explanation of irreversibility than that available to Boltzmann or to Green, Kubo and Onsager. Clear illustration of concepts is emphasized throughout, and reinforced with a glossary of technical terms from the specialized fields which have been combined here to focus on a common theme. The book begins with a discussion, contrasting the idealized reversibility of ba...
Computer simulation of molecular sorption in zeolites
Calmiano, M D
2001-01-01
The work presented in this thesis encompasses the computer simulation of molecular sorption. In Chapter 1 we outline the aims and objectives of this work. Chapter 2 follows in which an introduction to sorption in zeolites is presented, with discussion of structure and properties of the main zeolites studied. Chapter 2 concludes with a description of the principles and theories of adsorption. In Chapter 3 we describe the methodology behind the work carried out in this thesis. In Chapter 4 we present our first computational study, that of the sorption of krypton in silicalite. We describe work carried out to investigate low energy sorption sites of krypton in silicalite where we observe krypton to preferentially sorb into straight and sinusoidal channels over channel intersections. We simulate single step type I adsorption isotherms and use molecular dynamics to study the diffusion of krypton and obtain division coefficients and the activation energy. We compare our results to previous experimental and computat...
Radar Landmass Simulation Computer Programming (Interim Report).
RADAR SCANNING, TERRAIN), (*NAVAL TRAINING, RADAR OPERATORS), (*FLIGHT SIMULATORS, TERRAIN AVOIDANCE), (* COMPUTER PROGRAMMING , INSTRUCTION MANUALS), PLAN POSITION INDICATORS, REAL TIME, DISPLAY SYSTEMS, RADAR IMAGES, SIMULATION
Halyo, Nesim; Choi, Sang H.; Chrisman, Dan A., Jr.; Samms, Richard W.
1987-01-01
Dynamic models and computer simulations were developed for the radiometric sensors utilized in the Earth Radiation Budget Experiment (ERBE). The models were developed to understand performance, improve measurement accuracy by updating model parameters and provide the constants needed for the count conversion algorithms. Model simulations were compared with the sensor's actual responses demonstrated in the ground and inflight calibrations. The models consider thermal and radiative exchange effects, surface specularity, spectral dependence of a filter, radiative interactions among an enclosure's nodes, partial specular and diffuse enclosure surface characteristics and steady-state and transient sensor responses. Relatively few sensor nodes were chosen for the models since there is an accuracy tradeoff between increasing the number of nodes and approximating parameters such as the sensor's size, material properties, geometry, and enclosure surface characteristics. Given that the temperature gradients within a node and between nodes are small enough, approximating with only a few nodes does not jeopardize the accuracy required to perform the parameter estimates and error analyses.
Mohd Adib, Mohd Azrul Hisham; Ii, Satoshi; Watanabe, Yoshiyuki; Wada, Shigeo
2017-02-04
The integration of phase-contrast magnetic resonance images (PC-MRI) and computational fluid dynamics (CFD) is a way to obtain detailed information of patient-specific hemodynamics. This study proposes a novel strategy for imposing a pressure condition on the outlet boundary (called the outlet pressure) in CFD to minimize velocity differences between the PC-MRI measurement and the CFD simulation, and to investigate the effects of outlet pressure on the numerical solution. The investigation involved ten patient-specific aneurysms reconstructed from a digital subtraction angiography image, specifically on aneurysms located at the bifurcation region. To evaluate the effects of imposing the outlet pressure, three different approaches were used, namely: a pressure-fixed (P-fixed) approach; a flow rate control (Q-control) approach; and a velocity-field-optimized (V-optimized) approach. Numerical investigations show that the highest reduction in velocity difference always occurs in the V-optimized approach, where the mean of velocity difference (normalized by inlet velocity) is 19.3%. Additionally, the highest velocity differences appear near to the wall and vessel bifurcation for 60% of the patients, resulting in differences in wall shear stress. These findings provide a new methodology for PC-MRI integrated CFD simulation and are useful for understanding the evaluation of velocity difference between the PC-MRI and CFD.
A T Borojeni, Azadeh; Frank-Ito, Dennis O; Kimbell, Julia S; Rhee, John S; Garcia, Guilherme J M
2017-05-01
Virtual surgery planning based on computational fluid dynamics (CFD) simulations has the potential to improve surgical outcomes for nasal airway obstruction patients, but the benefits of virtual surgery planning must outweigh the risks of radiation exposure. Cone beam computed tomography (CT) scans represent an attractive imaging modality for virtual surgery planning due to lower costs and lower radiation exposures compared with conventional CT scans. However, to minimize the radiation exposure, the cone beam CT sinusitis protocol sometimes images only the nasal cavity, excluding the nasopharynx. The goal of this study was to develop an idealized nasopharynx geometry for accurate representation of outlet boundary conditions when the nasopharynx geometry is unavailable. Anatomically accurate models of the nasopharynx created from 30 CT scans were intersected with planes rotated at different angles to obtain an average geometry. Cross sections of the idealized nasopharynx were approximated as ellipses with cross-sectional areas and aspect ratios equal to the average in the actual patient-specific models. CFD simulations were performed to investigate whether nasal airflow patterns were affected when the CT-based nasopharynx was replaced by the idealized nasopharynx in 10 nasal airway obstruction patients. Despite the simple form of the idealized geometry, all biophysical variables (nasal resistance, airflow rate, and heat fluxes) were very similar in the idealized vs patient-specific models. The results confirmed the expectation that the nasopharynx geometry has a minimal effect in the nasal airflow patterns during inspiration. The idealized nasopharynx geometry will be useful in future CFD studies of nasal airflow based on medical images that exclude the nasopharynx. Copyright © 2016 John Wiley & Sons, Ltd.
Accelerating Climate Simulations Through Hybrid Computing
Zhou, Shujia; Sinno, Scott; Cruz, Carlos; Purcell, Mark
2009-01-01
Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.
Colour in visualisation for computational fluid dynamics
Kinnear, David; Atherton, Mark; Collins, Michael; Dokhan, Jason; Karayiannis, Tassos
2006-06-01
Colour is used in computational fluid dynamic (CFD) simulations in two key ways. First it is used to visualise the geometry and allow the engineer to be confident that the model constructed is a good representation of the engineering situation. Once an analysis has been completed, colour is used in post-processing the data from the simulations to illustrate the complex fluid mechanic phenomena under investigation. This paper describes these two uses of colour and provides some examples to illustrate the key visualisation approaches used in CFD.
Rajamanikandan, Sundaraj; Jeyakanthan, Jeyaraman; Srinivasan, Pappu
2017-01-01
Quorum sensing (QS) plays an important role in the biofilm formation, production of virulence factors and stress responses in Vibrio harveyi. Therefore, interrupting QS is a possible approach to modulate bacterial behavior. In the present study, three docking protocols, such as Rigid Receptor Docking (RRD), Induced Fit Docking (IFD), and Quantum Polarized Ligand Docking (QPLD) were used to elucidate the binding mode of boronic acid derivatives into the binding pocket of LuxP protein in V. harveyi. Among the three docking protocols, IFD accurately predicted the correct binding mode of the studied inhibitors. Molecular dynamics (MD) simulations of the protein-ligand complexes indicates that the inter-molecular hydrogen bonds formed between the protein and ligand complex remains stable during the simulation time. Pharmacophore and shape-based virtual screening were performed to find selective and potent compounds from ChemBridge database. Five hit compounds were selected and subjected to IFD and MD simulations to validate the binding mode. In addition, enrichment calculation was performed to discriminate and separate active compounds from the inactive compounds. Based on the computational studies, the potent Bicyclo [2.2.1] hept-5-ene-2,3-dicarboxylic acid-2,6-dimethylpyridine 1-oxide (ChemBridge_5144368) was selected for in vitro assays. The compound exhibited dose dependent inhibition in bioluminescence and also inhibits biofilm formation in V. harveyi to the level of 64.25 %. The result from the study suggests that ChemBridge_5144368 could serve as an anti-quorum sensing molecule for V. harveyi.
Directory of Open Access Journals (Sweden)
Guangya Jin
2017-01-01
Full Text Available Aqueous crude oil often contains large amounts of produced water and heavy sediment, which seriously threats the safety of crude oil storage and transportation. Therefore, the proper design of crude oil tank drainage device is prerequisite for efficient purification of aqueous crude oil. In this work, the composition and physicochemical properties of crude oil samples were tested under the actual conditions encountered. Based on these data, an appropriate crude oil tank drainage device was developed using the principle of floating ball and multiphase flow. In addition, the flow field characteristics in the device were simulated and the contours and streamtraces of velocity magnitude at different nine moments were obtained. Meanwhile, the improvement of flow field characteristics after the addition of grids in crude oil tank drainage device was validated. These findings provide insights into the development of effective selection methods and serve as important references for oil-water separation process.
Computer simulation to arc spraying
Institute of Scientific and Technical Information of China (English)
梁志芳; 李午申; 王迎娜
2004-01-01
The arc spraying process is divided into two stages: the first stage is atomization-spraying stream (ASS) and the second one is spraying deposition (SD). Then study status is described of both stages' physical model and corresponding controlling-equation. Based on the analysis of study status, the conclusion as follows is got. The heat and mass transfer models with two or three dimensions in ASS stage should be established to far deeply analyses the dynamical and thermal behavior of the overheat droplet. The statistics law of overheated droplets should be further studied by connecting simulation with experiments. More proper validation experiments should be designed for flattening simulation to modify the models in SD stage.
Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow
Archereau, Aurelien Y M; Willmott, Geoff R
2016-01-01
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.
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...
Molecular dynamics simulation of diffusivity
Institute of Scientific and Technical Information of China (English)
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Computer simulations in the science classroom
Richards, John; Barowy, William; Levin, Dov
1992-03-01
In this paper we describe software for science instruction that is based upon a constructivist epistemology of learning. From a constructivist perspective, the process of learning is viewed as an active construction of knowledge, rather than a passive reception of information. The computer has the potential to provide an environment in which students can explore their understanding and better construct scientific knowledge. The Explorer is an interactive environment that integrates animated computer models with analytic capabilities for learning and teaching science. The system include graphs, a spreadsheet, scripting, and interactive tools. During formative evaluation of Explorer in the classroom, we have focused on learning the function and effectiveness of computer models in teaching science. Models have helped students relate theory to experiment when used in conjunction with hands-on activities and when the simulation addressed students' naive understanding of the phenomena. Two classroom examples illustrate our findings. The first is based on the dynamics of colliding objects. The second describes a class modeling the function of simple electric circuits. The simulations bridge between phenomena and theory by providing an abstract representation on which students may make measurements. Simulations based on scientific theory help to provide a set of interrelated experiences that challenge students' informal understanding of the science.
Dynamic Procedure for Filtered Gyrokinetic Simulations
Morel, Pierre; Albrecht-Marc, Michel; Carati, Daniele; Merz, Florian; Görler, Tobias; Jenko, Frank
2011-01-01
Large Eddy Simulations (LES) of gyrokinetic plasma turbulence are investigated as interesting candidates to decrease the computational cost. A dynamic procedure is implemented in the GENE code, allowing for dynamic optimization of the free parameters of the LES models (setting the amplitudes of dissipative terms). Employing such LES methods, one recovers the free energy and heat flux spectra obtained from highly resolved Direct Numerical Simulations (DNS). Systematic comparisons are performed for different values of the temperature gradient and magnetic shear, parameters which are of prime importance in Ion Temperature Gradient (ITG) driven turbulence. Moreover, the degree of anisotropy of the problem, that can vary with parameters, can be adapted dynamically by the method that shows Gyrokinetic Large Eddy Simulation (GyroLES) to be a serious candidate to reduce numerical cost of gyrokinetic solvers.
Computer simulations applied in materials
Energy Technology Data Exchange (ETDEWEB)
NONE
2003-07-01
This workshop takes stock of the simulation methods applied to nuclear materials and discusses the conditions in which these methods can predict physical results when no experimental data are available. The main topic concerns the radiation effects in oxides and includes also the behaviour of fission products in ceramics, the diffusion and segregation phenomena and the thermodynamical properties under irradiation. This document brings together a report of the previous 2002 workshop and the transparencies of 12 presentations among the 15 given at the workshop: accommodation of uranium and plutonium in pyrochlores; radiation effects in La{sub 2}Zr{sub 2}O{sub 7} pyrochlores; first principle calculations of defects formation energies in the Y{sub 2}(Ti,Sn,Zr){sub 2}O{sub 7} pyrochlore system; an approximate approach to predicting radiation tolerant materials; molecular dynamics study of the structural effects of displacement cascades in UO{sub 2}; composition defect maps for A{sup 3+}B{sup 3+}O{sub 3} perovskites; NMR characterization of radiation damaged materials: using simulation to interpret the data; local structure in damaged zircon: a first principle study; simulation studies on SiC; insertion and diffusion of He in 3C-SiC; a review of helium in silica; self-trapped holes in amorphous silicon dioxide: their short-range structure revealed from electron spin resonance and optical measurements and opportunities for inferring intermediate range structure by theoretical modelling. (J.S.)
Computer simulations applied in materials
Energy Technology Data Exchange (ETDEWEB)
NONE
2003-07-01
This workshop takes stock of the simulation methods applied to nuclear materials and discusses the conditions in which these methods can predict physical results when no experimental data are available. The main topic concerns the radiation effects in oxides and includes also the behaviour of fission products in ceramics, the diffusion and segregation phenomena and the thermodynamical properties under irradiation. This document brings together a report of the previous 2002 workshop and the transparencies of 12 presentations among the 15 given at the workshop: accommodation of uranium and plutonium in pyrochlores; radiation effects in La{sub 2}Zr{sub 2}O{sub 7} pyrochlores; first principle calculations of defects formation energies in the Y{sub 2}(Ti,Sn,Zr){sub 2}O{sub 7} pyrochlore system; an approximate approach to predicting radiation tolerant materials; molecular dynamics study of the structural effects of displacement cascades in UO{sub 2}; composition defect maps for A{sup 3+}B{sup 3+}O{sub 3} perovskites; NMR characterization of radiation damaged materials: using simulation to interpret the data; local structure in damaged zircon: a first principle study; simulation studies on SiC; insertion and diffusion of He in 3C-SiC; a review of helium in silica; self-trapped holes in amorphous silicon dioxide: their short-range structure revealed from electron spin resonance and optical measurements and opportunities for inferring intermediate range structure by theoretical modelling. (J.S.)
Principles of computational fluid dynamics
Wesseling, Pieter
2001-01-01
The book is aimed at graduate students, researchers, engineers and physicists involved in flow computations. An up-to-date account is given of the present state-of-the-art of numerical methods employed in computational fluid dynamics. The underlying numerical principles are treated with a fair amount of detail, using elementary mathematical analysis. Attention is given to difficulties arising from geometric complexity of the flow domain and of nonuniform structured boundary-fitted grids. Uniform accuracy and efficiency for singular perturbation problems is studied, pointing the way to accurate computation of flows at high Reynolds number. Much attention is given to stability analysis, and useful stability conditions are provided, some of them new, for many numerical schemes used in practice. Unified methods for compressible and incompressible flows are discussed. Numerical analysis of the shallow-water equations is included. The theory of hyperbolic conservation laws is treated. Godunov's order barrier and ho...
Directory of Open Access Journals (Sweden)
Barzegar Ramin
2013-01-01
Full Text Available In the present paper, the combustion process and emission formation in the Lister 8.1 I.D.I Diesel engine have been investigated using a Computational Fluid Dynamics (CFD code. The utilized model includes detailed spray atomization, mixture formation and distribution model which enable modeling the combustion process in spray/wall and spray/swirl interactions along with flow configurations. The analysis considers both part load and full load states. The global properties are presented separately resolved for the swirl chamber (pre-chamber and the main chamber. The results of model verify the fact that the equal amount of the fuel is burned in the main and pre-chamber at full load state while at part load the majority of the fuel is burned in the main chamber. Also, it is shown that the adherence of fuel spray on the pre-chamber walls is due to formation of a stagnation zone which prevents quick spray evaporation and plays an important role in the increase of soot mass fractions at this zone at full load conditions. The simulation results, such as the mean in-cylinder pressure, heat release rate and exhaust emissions are compared with the experimental data and show good agreement. This work also demonstrates the usefulness of multidimensional modeling for complex chamber geometries, such as in I.D.I Diesel engines, to gain more insight into the flow field, combustion process and emission formation.
Kindgen, Sarah; Wachtel, Herbert; Abrahamsson, Bertil; Langguth, Peter
2015-09-01
Disintegration of oral solid dosage forms is a prerequisite for drug dissolution and absorption and is to a large extent dependent on the pressures and hydrodynamic conditions in the solution that the dosage form is exposed to. In this work, the hydrodynamics in the PhEur/USP disintegration tester were investigated using computational fluid dynamics (CFD). Particle image velocimetry was used to validate the CFD predictions. The CFD simulations were performed with different Newtonian and non-Newtonian fluids, representing fasted and fed states. The results indicate that the current design and operating conditions of the disintegration test device, given by the pharmacopoeias, are not reproducing the in vivo situation. This holds true for the hydrodynamics in the disintegration tester that generates Reynolds numbers dissimilar to the reported in vivo situation. Also, when using homogenized US FDA meal, representing the fed state, too high viscosities and relative pressures are generated. The forces acting on the dosage form are too small for all fluids compared to the in vivo situation. The lack of peristaltic contractions, which generate hydrodynamics and shear stress in vivo, might be the major drawback of the compendial device resulting in the observed differences between predicted and in vivo measured hydrodynamics.
Energy Technology Data Exchange (ETDEWEB)
Papukchiev, Angel, E-mail: angel.papukchiev@grs.de [Gesellschaft fuer Anlagen- und Reaktorsicherheit (GRS) mbH, Garching n. Munich (Germany); Roelofs, Ferry; Shams, Afaque [Nuclear Research and Consultancy Group, Petten (Netherlands); Lecrivain, Gregory [Institute of Fluid Dynamics, Helmholtz-Zentrum Dresden-Rossendorf, Dresden (Germany); Ambrosini, Walter [University of Pisa, Pisa (Italy)
2015-08-15
Highlights: • Thermal–hydraulic crosscutting issues related to Generation IV reactor concepts have been investigated within the European Project THINS. • New nuclear systems are characterized by various non-unity Prandtl number coolants. • Improvements in the turbulence modeling for innovative coolants have been achieved. • Extensive development and validation work has been done. - Abstract: Today computational fluid dynamics (CFD) is widely used in industrial companies, research institutes and technical safety organizations to supplement the design and analysis of diverse technical components and large systems. Such numerical programs are applied to better understand complex fluid flow and heat transfer phenomena. In the last decades there is an increasing interest in the nuclear community to utilize such advanced programs for the evaluation of different nuclear reactor safety issues, where traditional analysis tools show deficiencies. Within the FP7 European project THINS (Thermal Hydraulics of Innovative Nuclear Systems), CFD and coupled 1D-3D thermal–hydraulic simulations are being carried out. These are dedicated to the analysis of the thermal–hydraulics of gas, liquid metal and supercritical water cooled reactors. Such concepts utilize innovative fluids, which have different properties from the ones used in the current nuclear reactors. In order to improve the thermal–hydraulic predictions of their behavior, CFD development, application and validation activities are performed within THINS. This overview paper highlights some of the CFD related work within the European project.
Directory of Open Access Journals (Sweden)
Regine Schmidt
2013-01-01
Full Text Available Contrast-enhanced first-pass magnetic resonance imaging (MRI in combination with a tracer kinetic model, for example, MMID4, can be used to determine myocardial blood flow (MBF and myocardial perfusion reserve (MPR. Typically, the arterial input function (AIF required for this methodology is estimated from the left ventricle (LV. Dispersion of the contrast agent bolus might occur between the LV and the myocardial tissue. Negligence of bolus dispersion could cause an error in MBF determination. The aim of this study was to investigate the influence of bolus dispersion in a simplified coronary bifurcation geometry including one healthy and one stenotic branch on the quantification of MBF and MPR. Computational fluid dynamics (CFD simulations were combined with MMID4. Different inlet boundary conditions describing pulsatile and constant flows for rest and hyperemia and differing outflow conditions have been investigated. In the bifurcation region, the increase of the dispersion was smaller than inside the straight vessels. A systematic underestimation of MBF values up to −16.1% for pulsatile flow and an overestimation of MPR up to 7.5% were found. It was shown that, under the conditions considered in this study, bolus dispersion can significantly influence the results of quantitative myocardial MR-perfusion measurements.
Mixcoha, Edgar; Campos-Terán, José; Piñeiro, Ángel
2014-06-26
The structural simplicity of native cyclodextrins (CDs) contrasts with their complex behavior in the bulk of aqueous solutions, mainly when they are combined with other cosolutes. Many scientific and industrial applications based on these molecules are supported only by empirical information. The lack of fundamental knowledge, which would allow one to rationally optimize many of these applications, is notable mainly at the solution/air interface. Basic information on phenomena such as the spontaneous adsorption of native CDs or on the structure of CD aggregates in the bulk solution is really scarce. In order to fill these gaps, a detailed computational study on the adsorption and aggregation of α- and β-CDs as a function of temperature is presented here. Our simulations reproduce, at atomic resolution, the experimentally observed much higher ability of β-CD to aggregate compared to that of α-CD at 298 K, as well as their dependence on temperature. The adsorption of both individual CDs and small CD aggregates (up to 20 molecules) to the solution/air interface is found to be negligible. 0.8 μs long trajectories of single CD molecules in aqueous solution reveal that the main differences in the behavior of both CDs are their flexibility, higher for β-CD, and the occupancy of individual intramolecular hydrogen bonds that is significantly longer for the same cyclodextrin. The aggregation pattern of α- and β-CDs is followed at the hundreds of ns time scale, allowing both the spontaneous self-assembly of cyclodextrins and their redistribution along the aggregates to be observed. This is the first attempt to study the adsorption and aggregation of native cyclodextrins by atomistic molecular dynamics simulations.
Simulation of computational fluid dynamics in ozone contactor%臭氧接触池的计算流体力学模拟
Institute of Scientific and Technical Information of China (English)
王静; 邓保庆; 陆丽; 李勋栋
2012-01-01
The hydraulic characteristic of ozone contactor has a great impact on the disinfection effect of microorganism. Computational fluid dynamics ( CFD) technique was used to simulate the flow field of a single - column ozone contactor. The Eulerian multiphase model and the standard k - e turbulent model were used in the simulation. The results show that ozone distribution is relatively uniform in the single -column contactor. In general, there does not exist the phenomenon of "dead zone" , which helps to guarantee high disinfection efficiency. However, gas bubble was found to accumulate underneath the outlet trough. The results offer a sample for optimizing the ozonation system.%臭氧接触池的水力特性直接影响着微生物消毒效果.利用计算流体力学(CFD)技术,采用欧拉多相流模型和标准k-ε湍流模型对单管臭氧接触池内的流场进行数值模拟.结果表明:单管式臭氧接触池内臭氧分布比较均匀,基本上没有“死区”现象的产生,可以保证较高的消毒效率,但是气体气泡大量聚集在接触池出口槽下方.模拟结果对单管式臭氧接触池的优化有一定的借鉴作用.
Dynamics modeling and simulation of flexible airships
Li, Yuwen
The resurgence of airships has created a need for dynamics models and simulation capabilities of these lighter-than-air vehicles. The focus of this thesis is a theoretical framework that integrates the flight dynamics, structural dynamics, aerostatics and aerodynamics of flexible airships. The study begins with a dynamics model based on a rigid-body assumption. A comprehensive computation of aerodynamic effects is presented, where the aerodynamic forces and moments are categorized into various terms based on different physical effects. A series of prediction approaches for different aerodynamic effects are unified and applied to airships. The numerical results of aerodynamic derivatives and the simulated responses to control surface deflection inputs are verified by comparing to existing wind-tunnel and flight test data. With the validated aerodynamics and rigid-body modeling, the equations of motion of an elastic airship are derived by the Lagrangian formulation. The airship is modeled as a free-free Euler-Bernoulli beam and the bending deformations are represented by shape functions chosen as the free-free normal modes. In order to capture the coupling between the aerodynamic forces and the structural elasticity, local velocity on the deformed vehicle is used in the computation of aerodynamic forces. Finally, with the inertial, gravity, aerostatic and control forces incorporated, the dynamics model of a flexible airship is represented by a single set of nonlinear ordinary differential equations. The proposed model is implemented as a dynamics simulation program to analyze the dynamics characteristics of the Skyship-500 airship. Simulation results are presented to demonstrate the influence of structural deformation on the aerodynamic forces and the dynamics behavior of the airship. The nonlinear equations of motion are linearized numerically for the purpose of frequency domain analysis and for aeroelastic stability analysis. The results from the latter for the
Computer Simulation of Radial Immunodiffusion
Trautman, Rodes
1972-01-01
Theories of diffusion with chemical reaction are reviewed as to their contributions toward developing an algorithm needed for computer simulation of immunodiffusion. The Spiers-Augustin moving sink and the Engelberg stationary sink theories show how the antibody-antigen reaction can be incorporated into boundary conditions of the free diffusion differential equations. For this, a stoichiometric precipitate was assumed and the location of precipitin lines could be predicted. The Hill simultaneous linear adsorption theory provides a mathematical device for including another special type of antibody-antigen reaction in antigen excess regions of the gel. It permits an explanation for the lowered antigen diffusion coefficient, observed in the Oudin arrangement of single linear diffusion, but does not enable prediction of the location of precipitin lines. The most promising mathematical approach for a general solution is implied in the Augustin alternating cycle theory. This assumes the immunodiffusion process can be evaluated by alternating computation cycles: free diffusion without chemical reaction and chemical reaction without diffusion. The algorithm for the free diffusion update cycle, extended to both linear and radial geometries, is given in detail since it was based on gross flow rather than more conventional expressions in terms of net flow. Limitations on the numerical integration process using this algorithm are illustrated for free diffusion from a cylindrical well. PMID:4629869
Computer Code for Nanostructure Simulation
Filikhin, Igor; Vlahovic, Branislav
2009-01-01
Due to their small size, nanostructures can have stress and thermal gradients that are larger than any macroscopic analogue. These gradients can lead to specific regions that are susceptible to failure via processes such as plastic deformation by dislocation emission, chemical debonding, and interfacial alloying. A program has been developed that rigorously simulates and predicts optoelectronic properties of nanostructures of virtually any geometrical complexity and material composition. It can be used in simulations of energy level structure, wave functions, density of states of spatially configured phonon-coupled electrons, excitons in quantum dots, quantum rings, quantum ring complexes, and more. The code can be used to calculate stress distributions and thermal transport properties for a variety of nanostructures and interfaces, transport and scattering at nanoscale interfaces and surfaces under various stress states, and alloy compositional gradients. The code allows users to perform modeling of charge transport processes through quantum-dot (QD) arrays as functions of inter-dot distance, array order versus disorder, QD orientation, shape, size, and chemical composition for applications in photovoltaics and physical properties of QD-based biochemical sensors. The code can be used to study the hot exciton formation/relation dynamics in arrays of QDs of different shapes and sizes at different temperatures. It also can be used to understand the relation among the deposition parameters and inherent stresses, strain deformation, heat flow, and failure of nanostructures.
Optically simulated universal quantum computation
Francisco, D.; Ledesma, S.
2008-04-01
Recently, classical optics based systems to emulate quantum information processing have been proposed. The analogy is based on the possibility of encoding a quantum state of a system with a 2N-dimensional Hilbert space as an image in the input of an optical system. The probability amplitude of each state of a certain basis is associated with the complex amplitude of the electromagnetic field in a given slice of the laser wavefront. Temporal evolution is represented as the change of the complex amplitude of the field when the wavefront pass through a certain optical arrangement. Different modules that represent universal gates for quantum computation have been implemented. For instance, unitary operations acting on the qbits space (or U(2) gates) are represented by means of two phase plates, two spherical lenses and a phase grating in a typical image processing set up. In this work, we present CNOT gates which are emulated by means of a cube prism that splits a pair of adjacent rays incoming from the input image. As an example of application, we present an optical module that can be used to simulate the quantum teleportation process. We also show experimental results that illustrate the validity of the analogy. Although the experimental results obtained are promising and show the capability of the system for simulate the real quantum process, we must take into account that any classical simulation of quantum phenomena, has as fundamental limitation the impossibility of representing non local entanglement. In this classical context, quantum teleportation has only an illustrative interpretation.
QCE : A Simulator for Quantum Computer Hardware
Michielsen, Kristel; Raedt, Hans De
2003-01-01
The Quantum Computer Emulator (QCE) described in this paper consists of a simulator of a generic, general purpose quantum computer and a graphical user interface. The latter is used to control the simulator, to define the hardware of the quantum computer and to debug and execute quantum algorithms.
Multibody dynamic simulation of knee contact mechanics.
Bei, Yanhong; Fregly, Benjamin J
2004-11-01
Multibody dynamic musculoskeletal models capable of predicting muscle forces and joint contact pressures simultaneously would be valuable for studying clinical issues related to knee joint degeneration and restoration. Current three-dimensional multibody knee models are either quasi-static with deformable contact or dynamic with rigid contact. This study proposes a computationally efficient methodology for combining multibody dynamic simulation methods with a deformable contact knee model. The methodology requires preparation of the articular surface geometry, development of efficient methods to calculate distances between contact surfaces, implementation of an efficient contact solver that accounts for the unique characteristics of human joints, and specification of an application programming interface for integration with any multibody dynamic simulation environment. The current implementation accommodates natural or artificial tibiofemoral joint models, small or large strain contact models, and linear or nonlinear material models. Applications are presented for static analysis (via dynamic simulation) of a natural knee model created from MRI and CT data and dynamic simulation of an artificial knee model produced from manufacturer's CAD data. Small and large strain natural knee static analyses required 1 min of CPU time and predicted similar contact conditions except for peak pressure, which was higher for the large strain model. Linear and nonlinear artificial knee dynamic simulations required 10 min of CPU time and predicted similar contact force and torque but different contact pressures, which were lower for the nonlinear model due to increased contact area. This methodology provides an important step toward the realization of dynamic musculoskeletal models that can predict in vivo knee joint motion and loading simultaneously.
Computer simulations of the mouse spermatogenic cycle
Directory of Open Access Journals (Sweden)
Debjit Ray
2014-12-01
Full Text Available The spermatogenic cycle describes the periodic development of germ cells in the testicular tissue. The temporal–spatial dynamics of the cycle highlight the unique, complex, and interdependent interaction between germ and somatic cells, and are the key to continual sperm production. Although understanding the spermatogenic cycle has important clinical relevance for male fertility and contraception, there are a number of experimental obstacles. For example, the lengthy process cannot be visualized through dynamic imaging, and the precise action of germ cells that leads to the emergence of testicular morphology remains uncharacterized. Here, we report an agent-based model that simulates the mouse spermatogenic cycle on a cross-section of the seminiferous tubule over a time scale of hours to years, while considering feedback regulation, mitotic and meiotic division, differentiation, apoptosis, and movement. The computer model is able to elaborate the germ cell dynamics in a time-lapse movie format, allowing us to trace individual cells as they change state and location. More importantly, the model provides mechanistic understanding of the fundamentals of male fertility, namely how testicular morphology and sperm production are achieved. By manipulating cellular behaviors either individually or collectively in silico, the model predicts causal events for the altered arrangement of germ cells upon genetic or environmental perturbations. This in silico platform can serve as an interactive tool to perform long-term simulation and to identify optimal approaches for infertility treatment and contraceptive development.
Soliton dynamics in computational anatomy.
Holm, Darryl D; Ratnanather, J Tilak; Trouvé, Alain; Younes, Laurent
2004-01-01
Computational anatomy (CA) has introduced the idea of anatomical structures being transformed by geodesic deformations on groups of diffeomorphisms. Among these geometric structures, landmarks and image outlines in CA are shown to be singular solutions of a partial differential equation that is called the geodesic EPDiff equation. A recently discovered momentum map for singular solutions of EPDiff yields their canonical Hamiltonian formulation, which in turn provides a complete parameterization of the landmarks by their canonical positions and momenta. The momentum map provides an isomorphism between landmarks (and outlines) for images and singular soliton solutions of the EPDiff equation. This isomorphism suggests a new dynamical paradigm for CA, as well as new data representation.
Computational Fluid Dynamics Demonstration of Rigid Bodies in Motion
Camarena, Ernesto; Vu, Bruce T.
2011-01-01
The Design Analysis Branch (NE-Ml) at the Kennedy Space Center has not had the ability to accurately couple Rigid Body Dynamics (RBD) and Computational Fluid Dynamics (CFD). OVERFLOW-D is a flow solver that has been developed by NASA to have the capability to analyze and simulate dynamic motions with up to six Degrees of Freedom (6-DOF). Two simulations were prepared over the course of the internship to demonstrate 6DOF motion of rigid bodies under aerodynamic loading. The geometries in the simulations were based on a conceptual Space Launch System (SLS). The first simulation that was prepared and computed was the motion of a Solid Rocket Booster (SRB) as it separates from its core stage. To reduce computational time during the development of the simulation, only half of the physical domain with respect to the symmetry plane was simulated. Then a full solution was prepared and computed. The second simulation was a model of the SLS as it departs from a launch pad under a 20 knot crosswind. This simulation was reduced to Two Dimensions (2D) to reduce both preparation and computation time. By allowing 2-DOF for translations and 1-DOF for rotation, the simulation predicted unrealistic rotation. The simulation was then constrained to only allow translations.
An introduction to computer simulation methods applications to physical systems
Gould, Harvey; Christian, Wolfgang
2007-01-01
Now in its third edition, this book teaches physical concepts using computer simulations. The text incorporates object-oriented programming techniques and encourages readers to develop good programming habits in the context of doing physics. Designed for readers at all levels , An Introduction to Computer Simulation Methods uses Java, currently the most popular programming language. Introduction, Tools for Doing Simulations, Simulating Particle Motion, Oscillatory Systems, Few-Body Problems: The Motion of the Planets, The Chaotic Motion of Dynamical Systems, Random Processes, The Dynamics of Many Particle Systems, Normal Modes and Waves, Electrodynamics, Numerical and Monte Carlo Methods, Percolation, Fractals and Kinetic Growth Models, Complex Systems, Monte Carlo Simulations of Thermal Systems, Quantum Systems, Visualization and Rigid Body Dynamics, Seeing in Special and General Relativity, Epilogue: The Unity of Physics For all readers interested in developing programming habits in the context of doing phy...
Understanding Islamist political violence through computational social simulation
Energy Technology Data Exchange (ETDEWEB)
Watkins, Jennifer H [Los Alamos National Laboratory; Mackerrow, Edward P [Los Alamos National Laboratory; Patelli, Paolo G [Los Alamos National Laboratory; Eberhardt, Ariane [Los Alamos National Laboratory; Stradling, Seth G [Los Alamos National Laboratory
2008-01-01
Understanding the process that enables political violence is of great value in reducing the future demand for and support of violent opposition groups. Methods are needed that allow alternative scenarios and counterfactuals to be scientifically researched. Computational social simulation shows promise in developing 'computer experiments' that would be unfeasible or unethical in the real world. Additionally, the process of modeling and simulation reveals and challenges assumptions that may not be noted in theories, exposes areas where data is not available, and provides a rigorous, repeatable, and transparent framework for analyzing the complex dynamics of political violence. This paper demonstrates the computational modeling process using two simulation techniques: system dynamics and agent-based modeling. The benefits and drawbacks of both techniques are discussed. In developing these social simulations, we discovered that the social science concepts and theories needed to accurately simulate the associated psychological and social phenomena were lacking.
Computational fluid dynamics in cardiovascular disease.
Lee, Byoung-Kwon
2011-08-01
Computational fluid dynamics (CFD) is a mechanical engineering field for analyzing fluid flow, heat transfer, and associated phenomena, using computer-based simulation. CFD is a widely adopted methodology for solving complex problems in many modern engineering fields. The merit of CFD is developing new and improved devices and system designs, and optimization is conducted on existing equipment through computational simulations, resulting in enhanced efficiency and lower operating costs. However, in the biomedical field, CFD is still emerging. The main reason why CFD in the biomedical field has lagged behind is the tremendous complexity of human body fluid behavior. Recently, CFD biomedical research is more accessible, because high performance hardware and software are easily available with advances in computer science. All CFD processes contain three main components to provide useful information, such as pre-processing, solving mathematical equations, and post-processing. Initial accurate geometric modeling and boundary conditions are essential to achieve adequate results. Medical imaging, such as ultrasound imaging, computed tomography, and magnetic resonance imaging can be used for modeling, and Doppler ultrasound, pressure wire, and non-invasive pressure measurements are used for flow velocity and pressure as a boundary condition. Many simulations and clinical results have been used to study congenital heart disease, heart failure, ventricle function, aortic disease, and carotid and intra-cranial cerebrovascular diseases. With decreasing hardware costs and rapid computing times, researchers and medical scientists may increasingly use this reliable CFD tool to deliver accurate results. A realistic, multidisciplinary approach is essential to accomplish these tasks. Indefinite collaborations between mechanical engineers and clinical and medical scientists are essential. CFD may be an important methodology to understand the pathophysiology of the development and
Evolutionary computation for dynamic optimization problems
Yao, Xin
2013-01-01
This book provides a compilation on the state-of-the-art and recent advances of evolutionary computation for dynamic optimization problems. The motivation for this book arises from the fact that many real-world optimization problems and engineering systems are subject to dynamic environments, where changes occur over time. Key issues for addressing dynamic optimization problems in evolutionary computation, including fundamentals, algorithm design, theoretical analysis, and real-world applications, are presented. "Evolutionary Computation for Dynamic Optimization Problems" is a valuable reference to scientists, researchers, professionals and students in the field of engineering and science, particularly in the areas of computational intelligence, nature- and bio-inspired computing, and evolutionary computation.
Computational Fluid Dynamics of rising droplets
Energy Technology Data Exchange (ETDEWEB)
Wagner, Matthew [Lake Superior State University; Francois, Marianne M. [Los Alamos National Laboratory
2012-09-05
The main goal of this study is to perform simulations of droplet dynamics using Truchas, a LANL-developed computational fluid dynamics (CFD) software, and compare them to a computational study of Hysing et al.[IJNMF, 2009, 60:1259]. Understanding droplet dynamics is of fundamental importance in liquid-liquid extraction, a process used in the nuclear fuel cycle to separate various components. Simulations of a single droplet rising by buoyancy are conducted in two-dimensions. Multiple parametric studies are carried out to ensure the problem set-up is optimized. An Interface Smoothing Length (ISL) study and mesh resolution study are performed to verify convergence of the calculations. ISL is a parameter for the interface curvature calculation. Further, wall effects are investigated and checked against existing correlations. The ISL study found that the optimal ISL value is 2.5{Delta}x, with {Delta}x being the mesh cell spacing. The mesh resolution study found that the optimal mesh resolution is d/h=40, for d=drop diameter and h={Delta}x. In order for wall effects on terminal velocity to be insignificant, a conservative wall width of 9d or a nonconservative wall width of 7d can be used. The percentage difference between Hysing et al.[IJNMF, 2009, 60:1259] and Truchas for the velocity profiles vary from 7.9% to 9.9%. The computed droplet velocity and interface profiles are found in agreement with the study. The CFD calculations are performed on multiple cores, using LANL's Institutional High Performance Computing.
Quantum Simulation for Open-System Dynamics
Wang, Dong-Sheng; de Oliveira, Marcos Cesar; Berry, Dominic; Sanders, Barry
2013-03-01
Simulations are essential for predicting and explaining properties of physical and mathematical systems yet so far have been restricted to classical and closed quantum systems. Although forays have been made into open-system quantum simulation, the strict algorithmic aspect has not been explored yet is necessary to account fully for resource consumption to deliver bounded-error answers to computational questions. An open-system quantum simulator would encompass classical and closed-system simulation and also solve outstanding problems concerning, e.g. dynamical phase transitions in non-equilibrium systems, establishing long-range order via dissipation, verifying the simulatability of open-system dynamics on a quantum Turing machine. We construct an efficient autonomous algorithm for designing an efficient quantum circuit to simulate many-body open-system dynamics described by a local Hamiltonian plus decoherence due to separate baths for each particle. The execution time and number of gates for the quantum simulator both scale polynomially with the system size. DSW funded by USARO. MCO funded by AITF and Brazilian agencies CNPq and FAPESP through Instituto Nacional de Ciencia e Tecnologia-Informacao Quantica (INCT-IQ). DWB funded by ARC Future Fellowship (FT100100761). BCS funded by AITF, CIFAR, NSERC and USARO.
Energy Technology Data Exchange (ETDEWEB)
1979-09-01
A listing of a CASY computer run is presented. It was initiated from a demand terminal and, therefore, contains the identification ST0952. This run also contains an INDEX listing of the subroutine UPDATE. The run includes a simulated scram transient at 30 seconds.
Energy Technology Data Exchange (ETDEWEB)
Eraslan, A.H.; Van Winkle, W.; Sharp, R.D.; Christensen, S.W.; Goodyear, C.P.; Rush, R.M.; Fulkerson, W.
1975-09-01
This report presents a daily transient (tidal-averaged), longitudinally one-dimensional (cross-section-averaged) computer simulation model for the assessment of the entrainment and impingement impacts of power plant operations on young-of-the-year populations of the striped bass, Morone saxatilis, in the Hudson River.
Flow simulations using particles - Bridging Computer Graphics and CFD
Koumoutsakos, Petros; Cottet, Georges-Henri; Rossinelli, Diego
2008-01-01
International audience; The simulation of fluid flows using particles is becoming increasingly popular in Computer Graphics (CG). The grid-free character of particles, the flexibility in handling complex flow configurations and the possibility to obtain visually realistic results with a small number of computational elements are some of the main reasons for the success of these methods. In the Computational Fluid Dynamics (CFD) community, the realization that by periodically regularizing the ...
Nonlinear dynamics as an engine of computation.
Kia, Behnam; Lindner, John F; Ditto, William L
2017-03-06
Control of chaos teaches that control theory can tame the complex, random-like behaviour of chaotic systems. This alliance between control methods and physics-cybernetical physics-opens the door to many applications, including dynamics-based computing. In this article, we introduce nonlinear dynamics and its rich, sometimes chaotic behaviour as an engine of computation. We review our work that has demonstrated how to compute using nonlinear dynamics. Furthermore, we investigate the interrelationship between invariant measures of a dynamical system and its computing power to strengthen the bridge between physics and computation.This article is part of the themed issue 'Horizons of cybernetical physics'.
Nonlinear dynamics as an engine of computation
Kia, Behnam; Lindner, John F.; Ditto, William L.
2017-03-01
Control of chaos teaches that control theory can tame the complex, random-like behaviour of chaotic systems. This alliance between control methods and physics-cybernetical physics-opens the door to many applications, including dynamics-based computing. In this article, we introduce nonlinear dynamics and its rich, sometimes chaotic behaviour as an engine of computation. We review our work that has demonstrated how to compute using nonlinear dynamics. Furthermore, we investigate the interrelationship between invariant measures of a dynamical system and its computing power to strengthen the bridge between physics and computation. This article is part of the themed issue 'Horizons of cybernetical physics'.
Computational simulation of liquid fuel rocket injectors
Landrum, D. Brian
1994-01-01
A major component of any liquid propellant rocket is the propellant injection system. Issues of interest include the degree of liquid vaporization and its impact on the combustion process, the pressure and temperature fields in the combustion chamber, and the cooling of the injector face and chamber walls. The Finite Difference Navier-Stokes (FDNS) code is a primary computational tool used in the MSFC Computational Fluid Dynamics Branch. The branch has dedicated a significant amount of resources to development of this code for prediction of both liquid and solid fuel rocket performance. The FDNS code is currently being upgraded to include the capability to model liquid/gas multi-phase flows for fuel injection simulation. An important aspect of this effort is benchmarking the code capabilities to predict existing experimental injection data. The objective of this MSFC/ASEE Summer Faculty Fellowship term was to evaluate the capabilities of the modified FDNS code to predict flow fields with liquid injection. Comparisons were made between code predictions and existing experimental data. A significant portion of the effort included a search for appropriate validation data. Also, code simulation deficiencies were identified.
The Guide to Computer Simulations and Games
Becker, K
2011-01-01
The first computer simulation book for anyone designing or building a game Answering the growing demand for a book catered for those who design, develop, or use simulations and games this book teaches you exactly what you need to know in order to understand the simulations you build or use all without having to earn another degree. Organized into three parts, this informative book first defines computer simulations and describes how they are different from live-action and paper-based simulations. The second section builds upon the previous, with coverage of the technical details of simulations
Biomes computed from simulated climatologies
National Research Council Canada - National Science Library
Claussen, M; Esch, M
1992-01-01
The biome model of Prentice is used to predict global patterns of potential natural plant formations, or biomes, from climatologies simulated by ECHAM, a model used for climate simulations at the Max...
Computer Simulation of Developmental Processes and ...
Rationale: Recent progress in systems toxicology and synthetic biology have paved the way to new thinking about in vitro/in silico modeling of developmental processes and toxicities, both for embryological and reproductive impacts. Novel in vitro platforms such as 3D organotypic culture models, engineered microscale tissues and complex microphysiological systems (MPS), together with computational models and computer simulation of tissue dynamics, lend themselves to a integrated testing strategies for predictive toxicology. As these emergent methodologies continue to evolve, they must be integrally tied to maternal/fetal physiology and toxicity of the developing individual across early lifestage transitions, from fertilization to birth, through puberty and beyond. Scope: This symposium will focus on how the novel technology platforms can help now and in the future, with in vitro/in silico modeling of complex biological systems for developmental and reproductive toxicity issues, and translating systems models into integrative testing strategies. The symposium is based on three main organizing principles: (1) that novel in vitro platforms with human cells configured in nascent tissue architectures with a native microphysiological environments yield mechanistic understanding of developmental and reproductive impacts of drug/chemical exposures; (2) that novel in silico platforms with high-throughput screening (HTS) data, biologically-inspired computational models of
Computer Simulation of the UMER Gridded Gun
Haber, Irving; Friedman, Alex; Grote, D P; Kishek, Rami A; Reiser, Martin; Vay, Jean-Luc; Zou, Yun
2005-01-01
The electron source in the University of Maryland Electron Ring (UMER) injector employs a grid 0.15 mm from the cathode to control the current waveform. Under nominal operating conditions, the grid voltage during the current pulse is sufficiently positive relative to the cathode potential to form a virtual cathode downstream of the grid. Three-dimensional computer simulations have been performed that use the mesh refinement capability of the WARP particle-in-cell code to examine a small region near the beam center in order to illustrate some of the complexity that can result from such a gridded structure. These simulations have been found to reproduce the hollowed velocity space that is observed experimentally. The simulations also predict a complicated time-dependent response to the waveform applied to the grid during the current turn-on. This complex temporal behavior appears to result directly from the dynamics of the virtual cathode formation and may therefore be representative of the expected behavior in...
Framework for utilizing computational devices within simulation
Directory of Open Access Journals (Sweden)
Miroslav Mintál
2013-12-01
Full Text Available Nowadays there exist several frameworks to utilize a computation power of graphics cards and other computational devices such as FPGA, ARM and multi-core processors. The best known are either low-level and need a lot of controlling code or are bounded only to special graphic cards. Furthermore there exist more specialized frameworks, mainly aimed to the mathematic field. Described framework is adjusted to use in a multi-agent simulations. Here it provides an option to accelerate computations when preparing simulation and mainly to accelerate a computation of simulation itself.
Computational Fluid Dynamics in Hypersonic Aerothermodynamics
Directory of Open Access Journals (Sweden)
Krishnendu Sinha
2010-10-01
Full Text Available Hypersonic flows are characterised by high Mach number and high total enthalpy. An elevated temperature often results in thermo-chemical reactions in the gas, which p lay a major role in aerothermodynamic characterisation of high-speed aerospace vehicles. Hypersonic flows in propulsion components are usually turbulent, resulting in additional effects. Computational simulation of such flows, therefore, need to account for a range of physical phenomena. Further, the numerical challenges involved in resolving strong gradients and discontinuities add to the complexity of computational fluid dynamics (CFD simulation. In this article, physical modelling and numerical methodology-related issues involved in hypersonic flow simulation are highlighted. State-of-the-art CFD challenges are discussed in the context of two prominent applications-the flow in a scramjet inlet and the flow field around a re-entry capsule.Defence Science Journal, 2010, 60(6, pp.663-671, DOI:http://dx.doi.org/10.14429/dsj.60.604
Dynamics of Information as Natural Computation
Directory of Open Access Journals (Sweden)
Gordana Dodig Crnkovic
2011-08-01
Full Text Available Processes considered rendering information dynamics have been studied, among others in: questions and answers, observations, communication, learning, belief revision, logical inference, game-theoretic interactions and computation. This article will put the computational approaches into a broader context of natural computation, where information dynamics is not only found in human communication and computational machinery but also in the entire nature. Information is understood as representing the world (reality as an informational web for a cognizing agent, while information dynamics (information processing, computation realizes physical laws through which all the changes of informational structures unfold. Computation as it appears in the natural world is more general than the human process of calculation modeled by the Turing machine. Natural computing is epitomized through the interactions of concurrent, in general asynchronous computational processes which are adequately represented by what Abramsky names “the second generation models of computation” [1] which we argue to be the most general representation of information dynamics.
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.
Molecular dynamics simulation of pyridine
Trumpakaj, Zygmunt; Linde, Bogumił
2015-04-01
Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.
Understanding Emergency Care Delivery through Computer Simulation Modeling.
Laker, Lauren F; Torabi, Elham; France, Daniel J; Froehle, Craig M; Goldlust, Eric J; Hoot, Nathan R; Kasaie, Parastu; Lyons, Michael S; Barg-Walkow, Laura H; Ward, Michael J; Wears, Robert L
2017-08-10
In 2017, Academic Emergency Medicine convened a consensus conference entitled, "Catalyzing System Change through Health Care Simulation: Systems, Competency, and Outcomes." This manuscript, a product of the breakout session on "understanding complex interactions through systems modeling," explores the role that computer simulation modeling can and should play in research and development of emergency care delivery systems. This manuscript discusses areas central to the use of computer simulation modeling in emergency care research. The four central approaches to computer simulation modeling are described (Monte Carlo Simulation, System Dynamics modeling, Discrete-Event Simulation, and Agent Based Simulation), along with problems amenable to their use and relevant examples to emergency care. Also discussed is an introduction to available software modeling platforms and how to explore their use for research, along with a research agenda for computer simulation modeling. Through this manuscript, our goal is to enhance adoption of computer simulation, a set of methods which hold great promise in addressing emergency care organization and design challenges. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Molecular dynamics simulation of benzene
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
FEL Simulation Using Distributed Computing
Energy Technology Data Exchange (ETDEWEB)
Einstein, Joshua [Fermilab; Bernabeu Altayo, Gerard [Fermilab; Biedron, Sandra [Ljubljana U.; Freund, Henry [Colorado State U., Fort Collins; Milton, Stephen [Colorado State U., Fort Collins; van der Slot, Peter [Colorado State U., Fort Collins
2016-06-01
While simulation tools are available and have been used regularly for simulating light sources, the increasing availability and lower cost of GPU-based processing opens up new opportunities. This poster highlights a method of how accelerating and parallelizing code processing through the use of COTS software interfaces.
Model dynamics for quantum computing
Tabakin, Frank
2017-08-01
A model master equation suitable for quantum computing dynamics is presented. In an ideal quantum computer (QC), a system of qubits evolves in time unitarily and, by virtue of their entanglement, interfere quantum mechanically to solve otherwise intractable problems. In the real situation, a QC is subject to decoherence and attenuation effects due to interaction with an environment and with possible short-term random disturbances and gate deficiencies. The stability of a QC under such attacks is a key issue for the development of realistic devices. We assume that the influence of the environment can be incorporated by a master equation that includes unitary evolution with gates, supplemented by a Lindblad term. Lindblad operators of various types are explored; namely, steady, pulsed, gate friction, and measurement operators. In the master equation, we use the Lindblad term to describe short time intrusions by random Lindblad pulses. The phenomenological master equation is then extended to include a nonlinear Beretta term that describes the evolution of a closed system with increasing entropy. An external Bath environment is stipulated by a fixed temperature in two different ways. Here we explore the case of a simple one-qubit system in preparation for generalization to multi-qubit, qutrit and hybrid qubit-qutrit systems. This model master equation can be used to test the stability of memory and the efficacy of quantum gates. The properties of such hybrid master equations are explored, with emphasis on the role of thermal equilibrium and entropy constraints. Several significant properties of time-dependent qubit evolution are revealed by this simple study.
Dynamic simulation of regulatory networks using SQUAD
Directory of Open Access Journals (Sweden)
Xenarios Ioannis
2007-11-01
Full Text Available Abstract Background The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. Results We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. Conclusion The simulation of regulatory networks aims at predicting the behavior of a whole system when subject
Nanodrop contact angles from molecular dynamics simulations
Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim
2016-11-01
The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.
Mendoza, John Cadiz
1995-01-01
The computational fluid dynamics code, PARC3D, is tested to see if its use of non-physical artificial dissipation affects the accuracy of its results. This is accomplished by simulating a shock-laminar boundary layer interaction and several hypersonic flight conditions of the Pegasus(TM) launch vehicle using full artificial dissipation, low artificial dissipation, and the Engquist filter. Before the filter is applied to the PARC3D code, it is validated in one-dimensional and two-dimensional form in a MacCormack scheme against the Riemann and convergent duct problem. For this explicit scheme, the filter shows great improvements in accuracy and computational time as opposed to the nonfiltered solutions. However, for the implicit PARC3D code it is found that the best estimate of the Pegasus experimental heat fluxes and surface pressures is the simulation utilizing low artificial dissipation and no filter. The filter does improve accuracy over the artificially dissipative case but at a computational expense greater than that achieved by the low artificial dissipation case which has no computational time penalty and shows better results. For the shock-boundary layer simulation, the filter does well in terms of accuracy for a strong impingement shock but not as well for weaker shock strengths. Furthermore, for the latter problem the filter reduces the required computational time to convergence by 18.7 percent.
Energy Technology Data Exchange (ETDEWEB)
Shinn, J; Gouveia, F J
2001-08-22
Progress in development of CFD models has shown their great potential for prediction of air flow, heat dissipation, and dispersion of air pollutants in the urban environment. Work at Lawrence Livermore National Laboratory has progressed using the finite element code FEM3 which has been ''massively parallelized'' to produce flow fields and pollutant dispersion in a grid encompassing many city blocks and with high resolution. While it may be argued that urban CFD models are not yet economical for emergency response applications, there are many applications in assessments and air quality management where CFD models are unrivaled in the level of detail that they provide. We have conducted field experiments to define the flow field and air tracer dispersion around buildings as a means of critiquing and evaluating the CFD models. The first experiment, the ''B170 study'', was a study of flow field, turbulence, and tracer dispersion in separation zones around a complex, single building. The second was the URBAN 2000 experiment in downtown Salt Lake City where flow fields and tracers were studied in nested resolution from the single building scale up to larger scales of 25 city blocks, and out to 6 km. For the future an URBAN 2003 experiment is being planned. We review the salient features of these experiments. A ''breakthrough'' technology in urban diffusion modeling is the use of modified computational fluid dynamics models (CFD) that use the meteorological conventions of large eddy simulation to represent the flow field. These CFD models have been initialized from the output of mesoscale atmospheric models with 4 km grid resolution, apparently with no problems although questions remain about aliasing and sources of bias. While more work remains, it is clear that should progress continue a remarkable tool should be available for such applications as: (1) Vulnerability studies for chemical, biological, and nuclear
An Automated High Aspect Ratio Mesher for Computational Fluid Dynamics Project
National Aeronautics and Space Administration — Computational fluid dynamics (CFD) simulations are routinely used while designing, analyzing, and optimizing air- and spacecraft. An important component of CFD...
Computer simulation in physics and engineering
Steinhauser, Martin Oliver
2013-01-01
This work is a needed reference for widely used techniques and methods of computer simulation in physics and other disciplines, such as materials science. The work conveys both: the theoretical foundations of computer simulation as well as applications and "tricks of the trade", that often are scattered across various papers. Thus it will meet a need and fill a gap for every scientist who needs computer simulations for his/her task at hand. In addition to being a reference, case studies and exercises for use as course reading are included.
Directory of Open Access Journals (Sweden)
Luciano T. Costa
2010-01-01
Full Text Available Computational methods for the calculation of dynamical properties of fluids might consider the system as a continuum or as an assembly of molecules. Molecular dynamics (MD simulation includes molecular resolution, whereas computational fluid dynamics (CFD considers the fluid as a continuum. This work provides a review of hybrid methods MD/CFD recently proposed in the literature. Theoretical foundations, basic approaches of computational methods, and dynamical properties typically calculated by MD and CFD are first presented in order to appreciate the similarities and differences between these two methods. Then, methods for coupling MD and CFD, and applications of hybrid simulations MD/CFD, are presented.
Simulating the Immune Response on a Distributed Parallel Computer
Castiglione, F.; Bernaschi, M.; Succi, S.
The application of ideas and methods of statistical mechanics to problems of biological relevance is one of the most promising frontiers of theoretical and computational mathematical physics.1,2 Among others, the computer simulation of the immune system dynamics stands out as one of the prominent candidates for this type of investigations. In the recent years immunological research has been drawing increasing benefits from the resort to advanced mathematical modeling on modern computers.3,4 Among others, Cellular Automata (CA), i.e., fully discrete dynamical systems evolving according to boolean laws, appear to be extremely well suited to computer simulation of biological systems.5 A prominent example of immunological CA is represented by the Celada-Seiden automaton, that has proven capable of providing several new insights into the dynamics of the immune system response. To date, the Celada-Seiden automaton was not in a position to exploit the impressive advances of computer technology, and notably parallel processing, simply because no parallel version of this automaton had been developed yet. In this paper we fill this gap and describe a parallel version of the Celada-Seiden cellular automaton aimed at simulating the dynamic response of the immune system. Details on the parallel implementation as well as performance data on the IBM SP2 parallel platform are presented and commented on.
Omeltchenko, Andrey; Bachlechner, Martina E.; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam; Messina, Paul
2000-01-01
Parallel molecular dynamics simulations are performed to determine atomic-level stresses in Si\\(111\\)/Si3N4\\(0001\\) and Si\\(111\\)/a-Si3N4 nanopixels. Compared to the crystalline case, the stresses in amorphous Si3N4 are highly inhomogeneous in the plane of the interface. In silicon below the interface, for a 25 nm square mesa stress domains with triangular symmetry are observed, whereas for a rectangular, 54 nm×33 nm, mesa tensile stress domains \\(~300 Å\\) are separated by Y-shaped compressive domain wall. Maximum stresses in the domains and domain walls are -2 GPa and +2 GPa, respectively.
Omeltchenko; Bachlechner; Nakano; Kalia; Vashishta; Ebbsjo; Madhukar; Messina
2000-01-10
Parallel molecular dynamics simulations are performed to determine atomic-level stresses in Si(111)/Si(3)N4(0001) and Si(111)/a-Si3N4 nanopixels. Compared to the crystalline case, the stresses in amorphous Si3N4 are highly inhomogeneous in the plane of the interface. In silicon below the interface, for a 25 nm square mesa stress domains with triangular symmetry are observed, whereas for a rectangular, 54 nmx33 nm, mesa tensile stress domains ( approximately 300 A) are separated by Y-shaped compressive domain wall. Maximum stresses in the domains and domain walls are -2 GPa and +2 GPa, respectively.
Advances in Computational Social Science and Social Simulation
2014-01-01
Aquesta conferència és la celebració conjunta de la "10th Artificial Economics Conference AE", la "10th Conference of the European Social Simulation Association ESSA" i la "1st Simulating the Past to Understand Human History SPUHH". Conferència organitzada pel Laboratory for Socio-Historical Dynamics Simulation (LSDS-UAB) de la Universitat Autònoma de Barcelona. Readers will find results of recent research on computational social science and social simulation economics, management, so...
Implicit Finite-Size Effects in Computer Simulations
Denton, A. R.; EGELSTAFF, P. A.
1997-01-01
The influence of periodic boundary conditions (implicit finite-size effects) on the anisotropy of pair correlations in computer simulations is studied for a dense classical fluid of pair-wise interacting krypton atoms near the triple point. Molecular dynamics simulation data for the pair distribution function of N-particle systems, as a function of radial distance, polar angle, and azimuthal angle are compared directly with corresponding theoretical predictions [L. R. Pratt and S. W. Haan, J....
Augmented Reality Simulations on Handheld Computers
Squire, Kurt; Klopfer, Eric
2007-01-01
Advancements in handheld computing, particularly its portability, social interactivity, context sensitivity, connectivity, and individuality, open new opportunities for immersive learning environments. This article articulates the pedagogical potential of augmented reality simulations in environmental engineering education by immersing students in…
Computer Simulation in Information and Communication Engineering
Anton Topurov
2005-01-01
CSICE'05 Sofia, Bulgaria 20th - 22nd October, 2005 On behalf of the International Scientific Committee, we would like to invite you all to Sofia, the capital city of Bulgaria, to the International Conference in Computer Simulation in Information and Communication Engineering CSICE'05. The Conference is aimed at facilitating the exchange of experience in the field of computer simulation gained not only in traditional fields (Communications, Electronics, Physics...) but also in the areas of biomedical engineering, environment, industrial design, etc. The objective of the Conference is to bring together lectures, researchers and practitioners from different countries, working in the fields of computer simulation in information engineering, in order to exchange information and bring new contribution to this important field of engineering design and education. The Conference will bring you the latest ideas and development of the tools for computer simulation directly from their inventors. Contribution describ...
Molecular Dynamics Simulations of Network Glasses
Drabold, David A.
The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References
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.
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...
Energy Technology Data Exchange (ETDEWEB)
HOLM,ELIZABETH A.; BATTAILE,CORBETT C.; BUCHHEIT,THOMAS E.; FANG,HUEI ELIOT; RINTOUL,MARK DANIEL; VEDULA,VENKATA R.; GLASS,S. JILL; KNOROVSKY,GERALD A.; NEILSEN,MICHAEL K.; WELLMAN,GERALD W.; SULSKY,DEBORAH; SHEN,YU-LIN; SCHREYER,H. BUCK
2000-04-01
Computational materials simulations have traditionally focused on individual phenomena: grain growth, crack propagation, plastic flow, etc. However, real materials behavior results from a complex interplay between phenomena. In this project, the authors explored methods for coupling mesoscale simulations of microstructural evolution and micromechanical response. In one case, massively parallel (MP) simulations for grain evolution and microcracking in alumina stronglink materials were dynamically coupled. In the other, codes for domain coarsening and plastic deformation in CuSi braze alloys were iteratively linked. this program provided the first comparison of two promising ways to integrate mesoscale computer codes. Coupled microstructural/micromechanical codes were applied to experimentally observed microstructures for the first time. In addition to the coupled codes, this project developed a suite of new computational capabilities (PARGRAIN, GLAD, OOF, MPM, polycrystal plasticity, front tracking). The problem of plasticity length scale in continuum calculations was recognized and a solution strategy was developed. The simulations were experimentally validated on stockpile materials.
Grand canonical Molecular Dynamics Simulations
Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K
2011-01-01
For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.
Study Development of the Cardiac Computer Simulations
Institute of Scientific and Technical Information of China (English)
VOLKERHellemanns; ZHANGHong; SEKOUSingare; ZHANGZhen-xi; KONGXiang-yun
2004-01-01
The technique of computer simulations is a very efficient method in investigating mechanisms of many diseases. This paper reviews how the simulations of the human heart started as a simple mathematical models in the past and developed to the point where genetic information is needed to do suitable work like finding out new medicaments against heart diseases. Also the Influence of the development of computer performance in the future as well as the data presentation is described.
Security Dynamics of Cloud Computing
Khaled M. Khan
2009-01-01
This paper explores various dimensions of cloud computing security. It argues that security concerns of cloud computing need to be addressed from the perspective of individual stakeholder. Security focuses of cloud computing are essentially different in terms of its characteristics and business model. Conventional way of viewing as well as addressing security such as ‘bolting-in’ on the top of cloud computing may not work well. The paper attempts to portray the security spectrum necessary for...
Quantum chemistry simulation on quantum computers: theories and experiments.
Lu, Dawei; Xu, Boruo; Xu, Nanyang; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng
2012-07-14
It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.
Parallel Monte Carlo Simulation of Aerosol Dynamics
Directory of Open Access Journals (Sweden)
Kun Zhou
2014-02-01
Full Text Available A highly efficient Monte Carlo (MC algorithm is developed for the numerical simulation of aerosol dynamics, that is, nucleation, surface growth, and coagulation. Nucleation and surface growth are handled with deterministic means, while coagulation is simulated with a stochastic method (Marcus-Lushnikov stochastic process. Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI. The parallel computing efficiency is investigated through numerical examples. Near 60% parallel efficiency is achieved for the maximum testing case with 3.7 million MC particles running on 93 parallel computing nodes. The algorithm is verified through simulating various testing cases and comparing the simulation results with available analytical and/or other numerical solutions. Generally, it is found that only small number (hundreds or thousands of MC particles is necessary to accurately predict the aerosol particle number density, volume fraction, and so forth, that is, low order moments of the Particle Size Distribution (PSD function. Accurately predicting the high order moments of the PSD needs to dramatically increase the number of MC particles.
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.
Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations
De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut
2011-01-01
With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices c
INCORPORATING DYNAMIC 3D SIMULATION INTO PRA
Energy Technology Data Exchange (ETDEWEB)
Steven R Prescott; Curtis Smith
2011-07-01
Through continued advancement in computational resources, development that was previously done by trial and error production is now performed through computer simulation. These virtual physical representations have the potential to provide accurate and valid modeling results and are being used in many different technical fields. Risk assessment now has the opportunity to use 3D simulation to improve analysis results and insights, especially for external event analysis. By using simulations, the modeler only has to determine the likelihood of an event without having to also predict the results of that event. The 3D simulation automatically determines not only the outcome of the event, but when those failures occur. How can we effectively incorporate 3D simulation into traditional PRA? Most PRA plant modeling is made up of components with different failure modes, probabilities, and rates. Typically, these components are grouped into various systems and then are modeled together (in different combinations) as a “system” with logic structures to form fault trees. Applicable fault trees are combined through scenarios, typically represented by event tree models. Though this method gives us failure results for a given model, it has limitations when it comes to time-based dependencies or dependencies that are coupled to physical processes which may themselves be space- or time-dependent. Since, failures from a 3D simulation are naturally time related, they should be used in that manner. In our simulation approach, traditional static models are converted into an equivalent state diagram representation with start states, probabilistic driven movements between states and terminal states. As the state model is run repeatedly, it converges to the same results as the PRA model in cases where time-related factors are not important. In cases where timing considerations are important (e.g., when events are dependent upon each other), then the simulation approach will typically
Direct modeling for computational fluid dynamics
Xu, Kun
2015-06-01
All fluid dynamic equations are valid under their modeling scales, such as the particle mean free path and mean collision time scale of the Boltzmann equation and the hydrodynamic scale of the Navier-Stokes (NS) equations. The current computational fluid dynamics (CFD) focuses on the numerical solution of partial differential equations (PDEs), and its aim is to get the accurate solution of these governing equations. Under such a CFD practice, it is hard to develop a unified scheme that covers flow physics from kinetic to hydrodynamic scales continuously because there is no such governing equation which could make a smooth transition from the Boltzmann to the NS modeling. The study of fluid dynamics needs to go beyond the traditional numerical partial differential equations. The emerging engineering applications, such as air-vehicle design for near-space flight and flow and heat transfer in micro-devices, do require further expansion of the concept of gas dynamics to a larger domain of physical reality, rather than the traditional distinguishable governing equations. At the current stage, the non-equilibrium flow physics has not yet been well explored or clearly understood due to the lack of appropriate tools. Unfortunately, under the current numerical PDE approach, it is hard to develop such a meaningful tool due to the absence of valid PDEs. In order to construct multiscale and multiphysics simulation methods similar to the modeling process of constructing the Boltzmann or the NS governing equations, the development of a numerical algorithm should be based on the first principle of physical modeling. In this paper, instead of following the traditional numerical PDE path, we introduce direct modeling as a principle for CFD algorithm development. Since all computations are conducted in a discretized space with limited cell resolution, the flow physics to be modeled has to be done in the mesh size and time step scales. Here, the CFD is more or less a direct
Computation simulation of the nonlinear response of suspension bridges
Energy Technology Data Exchange (ETDEWEB)
McCallen, D.B.; Astaneh-Asl, A.
1997-10-01
Accurate computational simulation of the dynamic response of long- span bridges presents one of the greatest challenges facing the earthquake engineering community The size of these structures, in terms of physical dimensions and number of main load bearing members, makes computational simulation of transient response an arduous task. Discretization of a large bridge with general purpose finite element software often results in a computational model of such size that excessive computational effort is required for three dimensional nonlinear analyses. The aim of the current study was the development of efficient, computationally based methodologies for the nonlinear analysis of cable supported bridge systems which would allow accurate characterization of a bridge with a relatively small number of degrees of freedom. This work has lead to the development of a special purpose software program for the nonlinear analysis of cable supported bridges and the methodologies and software are described and illustrated in this paper.
A dynamic skull model for simulation of cerebral cortex folding.
Chen, Hanbo; Guo, Lei; Nie, Jingxin; Zhang, Tuo; Hu, Xintao; Liu, Tianming
2010-01-01
The mechanisms of human cerebral cortex folding and their interactions during brain development are largely unknown, partly due to the difficulties in biological experiments and data acquisition for the developing fetus brain. Computational modeling and simulation provide a novel approach to the understanding of cortex folding processes in normal or aberrant neurodevelopment. Based on our recently developed computational model of the cerebral cortex folding using neuronal growth model and mechanical skull constraint, this paper presents a computational dynamic model of the brain skull that regulates the cortical folding simulation. Our simulation results show that the dynamic skull model is more biologically realistic and significantly improves our cortical folding simulation results. This work provides further computational support to the hypothesis that skull is an important regulator of cortical folding.
Quantum Computation and Quantum Spin Dynamics
Raedt, Hans De; Michielsen, Kristel; Hams, Anthony; Miyashita, Seiji; Saito, Keiji
2001-01-01
We analyze the stability of quantum computations on physically realizable quantum computers by simulating quantum spin models representing quantum computer hardware. Examples of logically identical implementations of the controlled-NOT operation are used to demonstrate that the results of a quantum
Quantum Computation and Quantum Spin Dynamics
Raedt, Hans De; Michielsen, Kristel; Hams, Anthony; Miyashita, Seiji; Saito, Keiji
2001-01-01
We analyze the stability of quantum computations on physically realizable quantum computers by simulating quantum spin models representing quantum computer hardware. Examples of logically identical implementations of the controlled-NOT operation are used to demonstrate that the results of a quantum
Salesperson Ethics: An Interactive Computer Simulation
Castleberry, Stephen
2014-01-01
A new interactive computer simulation designed to teach sales ethics is described. Simulation learner objectives include gaining a better understanding of legal issues in selling; realizing that ethical dilemmas do arise in selling; realizing the need to be honest when selling; seeing that there are conflicting demands from a salesperson's…
Salesperson Ethics: An Interactive Computer Simulation
Castleberry, Stephen
2014-01-01
A new interactive computer simulation designed to teach sales ethics is described. Simulation learner objectives include gaining a better understanding of legal issues in selling; realizing that ethical dilemmas do arise in selling; realizing the need to be honest when selling; seeing that there are conflicting demands from a salesperson's…
Computer simulation and vehicle front optimisation.
Sluis, J. van der
1993-01-01
The influence of the stiffness and shape of a car-front on injuries of bicyclists caused by side collisions was studied by computer simulation. Simulation was a suitable method in this case because of two reasons: variation of shape and stiffness is more difficult to perform in case of an experiment
[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.
Institute of Scientific and Technical Information of China (English)
邵雄飞; 吴忠标
2004-01-01
The flow field of gas and liquid in a φ150 mm rotating-stream-tray (RST) scrubber is simulated by using computational fluid dynamic (CFD) method. The simulation is based on the two-equation RNG k-εturbulence model, Eulerian multiphase model, and a real-shape 3D model with a huge number of meshes. The simulation results include detailed information about velocity,pressure, volume fraction and so on. Some features of the flow field are obtained: liquid is atomized in a thin annular zone; a high velocity air zone prevents water drops at the bottom from flying towards the wall; the pressure varies sharply at the end of blades and so on. The results will be helpful for structure optimization and engineering design.
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 ...
Computer simulation of gear tooth manufacturing processes
Mavriplis, Dimitri; Huston, Ronald L.
1990-01-01
The use of computer graphics to simulate gear tooth manufacturing procedures is discussed. An analytical basis for the simulation is established for spur gears. The simulation itself, however, is developed not only for spur gears, but for straight bevel gears as well. The applications of the developed procedure extend from the development of finite element models of heretofore intractable geometrical forms, to exploring the fabrication of nonstandard tooth forms.
Molecular Dynamics Simulations for Predicting Surface Wetting
Directory of Open Access Journals (Sweden)
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
Atomistic computer simulations a practical guide
Brazdova, Veronika
2013-01-01
Many books explain the theory of atomistic computer simulations; this book teaches you how to run them This introductory ""how to"" title enables readers to understand, plan, run, and analyze their own independent atomistic simulations, and decide which method to use and which questions to ask in their research project. It is written in a clear and precise language, focusing on a thorough understanding of the concepts behind the equations and how these are used in the simulations. As a result, readers will learn how to design the computational model and which parameters o
Bibliography for Verification and Validation in Computational Simulations
Energy Technology Data Exchange (ETDEWEB)
Oberkampf, W.L.
1998-10-01
A bibliography has been compiled dealing with the verification and validation of computational simulations. The references listed in this bibliography are concentrated in the field of computational fluid dynamics (CFD). However, references from the following fields are also included: operations research, heat transfer, solid dynamics, software quality assurance, software accreditation, military systems, and nuclear reactor safety. This bibliography, containing 221 references, is not meant to be comprehensive. It was compiled during the last ten years in response to the author's interest and research in the methodology for verification and validation. The emphasis in the bibliography is in the following areas: philosophy of science underpinnings, development of terminology and methodology, high accuracy solutions for CFD verification, experimental datasets for CFD validation, and the statistical quantification of model validation. This bibliography should provide a starting point for individual researchers in many fields of computational simulation in science and engineering.
Polymer Composites Corrosive Degradation: A Computational Simulation
Chamis, Christos C.; Minnetyan, Levon
2007-01-01
A computational simulation of polymer composites corrosive durability is presented. The corrosive environment is assumed to manage the polymer composite degradation on a ply-by-ply basis. The degradation is correlated with a measured pH factor and is represented by voids, temperature and moisture which vary parabolically for voids and linearly for temperature and moisture through the laminate thickness. The simulation is performed by a computational composite mechanics computer code which includes micro, macro, combined stress failure and laminate theories. This accounts for starting the simulation from constitutive material properties and up to the laminate scale which exposes the laminate to the corrosive environment. Results obtained for one laminate indicate that the ply-by-ply degradation degrades the laminate to the last one or the last several plies. Results also demonstrate that the simulation is applicable to other polymer composite systems as well.
Computer-Aided Simulation of Mastoidectomy
Institute of Scientific and Technical Information of China (English)
CHEN He-xin; MA Zhi-chao; Wang Zhang-feng; GUO Jie-bo; WEN Wei-ping; XU Geng
2008-01-01
Objective To establish a three-dimensional model of the temporal bone using CT scan images for study of temporal bone structures and simulation of mastoidectomy procedures. Methods CT scan images from 6 individuals (12 temporal bones) were used to reconstruct the Fallopian canal, internal auditory canal, cochlea, semicircular canals, sigmoid sinus, posterior fossa floor and jugular bulb on a computer platform. Their anatomical relations within the temporal bone were restored in the computed model. The same model was used to simulate mastoidectomy procedures. Results The reconstructed computer model provided accurate and clear three-dimensional images of temporal bone structures. Simulation of mastoidectomy using these images provided procedural experiences closely mimicking the real surgical procedure. Conclusion Computeraided three dimensional reconstruction of temporal bone structures using CT scan images is a useful tool in surgical simulation and can aid surgical procedure planning.
Humanoid robot simulator: a realistic dynamics approach
Lima, José; Gonçalves, José; Costa, Paulo; Moreira, António
2008-01-01
This paper describes a humanoid robot simulator with realistic dynamics. As simulation is a powerful tool for speeding up the control software development, the suggested accurate simulator allows to accomplish this goal. The simulator, based on the Open Dynamics Engine and GLScene graphics library, provides instant visual feedback and allows the user to test any control strategy without damaging the real robot in the early stages of the development. The proposed simulator also captures some c...
Computational Fluid and Particle Dynamics in the Human Respiratory System
Tu, Jiyuan; Ahmadi, Goodarz
2013-01-01
Traditional research methodologies in the human respiratory system have always been challenging due to their invasive nature. Recent advances in medical imaging and computational fluid dynamics (CFD) have accelerated this research. This book compiles and details recent advances in the modelling of the respiratory system for researchers, engineers, scientists, and health practitioners. It breaks down the complexities of this field and provides both students and scientists with an introduction and starting point to the physiology of the respiratory system, fluid dynamics and advanced CFD modeling tools. In addition to a brief introduction to the physics of the respiratory system and an overview of computational methods, the book contains best-practice guidelines for establishing high-quality computational models and simulations. Inspiration for new simulations can be gained through innovative case studies as well as hands-on practice using pre-made computational code. Last but not least, students and researcher...
Huang, Jianke; Ying, Jiangguo; Fan, Fei; Yang, Qijian; Wang, Jun; Li, Yuanguang
2016-12-01
Aiming to culture algae with high efficiency, a novel vertical multi-column airlift photobioreactor (VMAPBR) has been developed. It was constructed with a series of vertically arranged parallel columns with easy scalability. The hydrodynamic, irradiation and shear stress characteristics of the photobioreactor were studied by computational fluid dynamics (CFD). Accordingly, the optimal aeration manner and aeration rate were determined. When the novel airlift PBR was alternately aerated with aeration rate of 0.2vvm, the biomass concentration of Chlorella pyrenoidosa under outdoor condition reached 1.30gL(-1) within the prototype PBR and was further increased to 1.56gL(-1) within the optimized PBR. The result of cultivation experiment had good agreement with that of CFD prediction.
Energy Technology Data Exchange (ETDEWEB)
Omeltchenko, Andrey; Bachlechner, Martina E.; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjoe, Ingvar; Madhukar, Anupam; Messina, Paul
2000-01-10
Parallel molecular dynamics simulations are performed to determine atomic-level stresses in Si(111)/Si {sub 3}N{sub 4}(0001) and Si(111)/a-Si {sub 3}N{sub 4} nanopixels. Compared to the crystalline case, the stresses in amorphous Si{sub 3}N {sub 4} are highly inhomogeneous in the plane of the interface. In silicon below the interface, for a 25 nm square mesa stress domains with triangular symmetry are observed, whereas for a rectangular, 54 nmx33 nm , mesa tensile stress domains ({approx}300 Angstrom) are separated by Y-shaped compressive domain wall. Maximum stresses in the domains and domain walls are -2 GPa and +2 GPa , respectively. (c) 2000 The American Physical Society.
Monoamine transporters: Insights from molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Julie eGrouleff
2015-10-01
Full Text Available The human monoamine transporters facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia and Parkinson’s disease. Inhibition of the monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the monoamine transporters, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.
Monoamine transporters: insights from molecular dynamics simulations
Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit
2015-01-01
The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185
Microchannel Emulsification: From Computational Fluid Dynamics to Predictive Analytical Model
Dijke, van K.C.; Schroën, C.G.P.H.; Boom, R.M.
2008-01-01
Emulsion droplet formation was investigated in terrace-based microchannel systems that generate droplets through spontaneous Laplace pressure driven snap-off. The droplet formation mechanism was investigated through high-speed imaging and computational fluid dynamics (CFD) simulation, and we found g
Computational fluid dynamics applications to improve crop production systems
Computational fluid dynamics (CFD), numerical analysis and simulation tools of fluid flow processes have emerged from the development stage and become nowadays a robust design tool. It is widely used to study various transport phenomena which involve fluid flow, heat and mass transfer, providing det...
Computer simulation of FCC riser reactors.
Energy Technology Data Exchange (ETDEWEB)
Chang, S. L.; Golchert, B.; Lottes, S. A.; Petrick, M.; Zhou, C. Q.
1999-04-20
A three-dimensional computational fluid dynamics (CFD) code, ICRKFLO, was developed to simulate the multiphase reacting flow system in a fluid catalytic cracking (FCC) riser reactor. The code solve flow properties based on fundamental conservation laws of mass, momentum, and energy for gas, liquid, and solid phases. Useful phenomenological models were developed to represent the controlling FCC processes, including droplet dispersion and evaporation, particle-solid interactions, and interfacial heat transfer between gas, droplets, and particles. Techniques were also developed to facilitate numerical calculations. These techniques include a hybrid flow-kinetic treatment to include detailed kinetic calculations, a time-integral approach to overcome numerical stiffness problems of chemical reactions, and a sectional coupling and blocked-cell technique for handling complex geometry. The copyrighted ICRKFLO software has been validated with experimental data from pilot- and commercial-scale FCC units. The code can be used to evaluate the impacts of design and operating conditions on the production of gasoline and other oil products.
Factors promoting engaged exploration with computer simulations
Directory of Open Access Journals (Sweden)
Noah S. Podolefsky
2010-10-01
Full Text Available This paper extends prior research on student use of computer simulations (sims to engage with and explore science topics, in this case wave interference. We describe engaged exploration; a process that involves students actively interacting with educational materials, sense making, and exploring primarily via their own questioning. We analyze interviews with college students using PhET sims in order to demonstrate engaged exploration, and to identify factors that can promote this type of inquiry. With minimal explicit guidance, students explore the topic of wave interference in ways that bear similarity to how scientists explore phenomena. PhET sims are flexible tools which allow students to choose their own learning path, but also provide constraints such that students’ choices are generally productive. This type of inquiry is supported by sim features such as concrete connections to the real world, representations that are not available in the real world, analogies to help students make meaning of and connect across multiple representations and phenomena, and a high level of interactivity with real-time, dynamic feedback from the sim. These features of PhET sims enable students to pose questions and answer them in ways that may not be supported by more traditional educational materials.
Energy Technology Data Exchange (ETDEWEB)
Boo, Myung-Hwan [Korea Hydro and Nuclear Power Company, Daejeon (Korea, Republic of); Oh, Chang-Kyun; Kim, Hyun-Su [KEPCO Engineering and Construction Company, Gimcheon (Korea, Republic of); Choi, Choeng-Ryul [ELSOLTEC, Inc., Yongin (Korea, Republic of)
2017-05-15
Owing to the fact that thermal fatigue is a well-known damage mechanism in nuclear power plants, accurate stress and fatigue evaluation are highly important. Operating experience shows that the design condition is conservative compared to the actual one. Therefore, various fatigue monitoring methods have been extensively utilized to consider the actual operating data. However, defining the local temperature in the piping is difficult because temperature-measuring instruments are limited. The purpose of this paper is to define accurate local temperature in the piping and evaluate thermal stress using Green’s function (GF) by performing a series of computational fluid dynamics analyses considering the complex fluid conditions. Also, the thermal stress is determined by adopting GF and comparing it with that of the design condition. The fluid dynamics analysis result indicates that the fluid temperature slowly varies compared to the designed one even when the flow rate changes abruptly. In addition, the resulting thermal stress can significantly decrease when reflecting the actual temperature.
Energy Technology Data Exchange (ETDEWEB)
Midulla, Marco; Pruvo, Jean-Pierre [University Hospital of Lille, Cardiovascular Radiology, Lille (France); Moreno, Ramiro; Rousseau, Herve [Rangueil University Hospital, Radiology, Toulouse (France); University of Toulouse 3 Paul Sabatier, INSERM/UMR 1048 Cardiovascular and Metabolic Diseases, Toulouse (France); Baali, Adil; Negre-Salvayre, Anne [University of Toulouse 3 Paul Sabatier, INSERM/UMR 1048 Cardiovascular and Metabolic Diseases, Toulouse (France); Chau, Ming [ASA, Advanced Solutions Accelerator, University of Toulouse 3 Paul Sabatier, Montpellier (France); Nicoud, Franck [University Montpellier II - CNRS UMR 5149 I3M, CC 051, Montpellier (France); Haulon, Stephan [University Hospital of Lille, Vascular Surgery, Lille (France)
2012-10-15
In the last decade, there was been increasing interest in finding imaging techniques able to provide a functional vascular imaging of the thoracic aorta. The purpose of this paper is to present an imaging method combining magnetic resonance imaging (MRI) and computational fluid dynamics (CFD) to obtain a patient-specific haemodynamic analysis of patients treated by thoracic endovascular aortic repair (TEVAR). MRI was used to obtain boundary conditions. MR angiography (MRA) was followed by cardiac-gated cine sequences which covered the whole thoracic aorta. Phase contrast imaging provided the inlet and outlet profiles. A CFD mesh generator was used to model the arterial morphology, and wall movements were imposed according to the cine imaging. CFD runs were processed using the finite volume (FV) method assuming blood as a homogeneous Newtonian fluid. Twenty patients (14 men; mean age 62.2 years) with different aortic lesions were evaluated. Four-dimensional mapping of velocity and wall shear stress were obtained, depicting different patterns of flow (laminar, turbulent, stenosis-like) and local alterations of parietal stress in-stent and along the native aorta. A computational method using a combined approach with MRI appears feasible and seems promising to provide detailed functional analysis of thoracic aorta after stent-graft implantation. (orig.)
Bioreactor Studies and Computational Fluid Dynamics
Singh, H.; Hutmacher, D. W.
The hydrodynamic environment “created” by bioreactors for the culture of a tissue engineered construct (TEC) is known to influence cell migration, proliferation and extra cellular matrix production. However, tissue engineers have looked at bioreactors as black boxes within which TECs are cultured mainly by trial and error, as the complex relationship between the hydrodynamic environment and tissue properties remains elusive, yet is critical to the production of clinically useful tissues. It is well known in the chemical and biotechnology field that a more detailed description of fluid mechanics and nutrient transport within process equipment can be achieved via the use of computational fluid dynamics (CFD) technology. Hence, the coupling of experimental methods and computational simulations forms a synergistic relationship that can potentially yield greater and yet, more cohesive data sets for bioreactor studies. This review aims at discussing the rationale of using CFD in bioreactor studies related to tissue engineering, as fluid flow processes and phenomena have direct implications on cellular response such as migration and/or proliferation. We conclude that CFD should be seen by tissue engineers as an invaluable tool allowing us to analyze and visualize the impact of fluidic forces and stresses on cells and TECs.
Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit
Xu, Ji; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai
2010-01-01
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further spee...
Computational Methods for Dynamic Stability and Control Derivatives
Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.
2004-01-01
Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.
Computational fluid dynamics modeling in yarn engineering
CSIR Research Space (South Africa)
Patanaik, A
2011-07-01
Full Text Available This chapter deals with the application of computational fluid dynamics (CFD) modeling in reducing yarn hairiness during the ring spinning process and thereby “engineering” yarn with desired properties. Hairiness significantly affects the appearance...
A Computational Fluid Dynamics Algorithm on a Massively Parallel Computer
Jespersen, Dennis C.; Levit, Creon
1989-01-01
The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. We investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicit time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. We find that the Connection Machine ran achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as today's most powerful conventional supercomputers.
Computer Simulation Instruction: Carrying out Chemical Experiments
Directory of Open Access Journals (Sweden)
Ibtesam Al-Mashaqbeh
2014-05-01
Full Text Available The purpose of this study was to investigate the effect of computer simulation Instruction (CSI on students' achievements: Carrying out chemical experiments to acquire chemical concepts for eleventh grade students. The subject of the study consisted two sections of a one girl's high school in Jordan. One section was randomly assigned to experimental group in which computer simulation Instruction (CSI was used, and the other section was randomly assigned to control group in which students were instructed by using the traditional teaching instruction. The findings indicated that there is progress on the part of the experimental group which used the computer simulation Instruction (CSI and this was reflected positively in the students’ achievement in carrying out chemical experiments to acquire chemical concepts.
Automatic temperature computation for realistic IR simulation
Le Goff, Alain; Kersaudy, Philippe; Latger, Jean; Cathala, Thierry; Stolte, Nilo; Barillot, Philippe
2000-07-01
Polygon temperature computation in 3D virtual scenes is fundamental for IR image simulation. This article describes in detail the temperature calculation software and its current extensions, briefly presented in [1]. This software, called MURET, is used by the simulation workshop CHORALE of the French DGA. MURET is a one-dimensional thermal software, which accurately takes into account the material thermal attributes of three-dimensional scene and the variation of the environment characteristics (atmosphere) as a function of the time. Concerning the environment, absorbed incident fluxes are computed wavelength by wavelength, for each half an hour, druing 24 hours before the time of the simulation. For each polygon, incident fluxes are compsed of: direct solar fluxes, sky illumination (including diffuse solar fluxes). Concerning the materials, classical thermal attributes are associated to several layers, such as conductivity, absorption, spectral emissivity, density, specific heat, thickness and convection coefficients are taken into account. In the future, MURET will be able to simulate permeable natural materials (water influence) and vegetation natural materials (woods). This model of thermal attributes induces a very accurate polygon temperature computation for the complex 3D databases often found in CHORALE simulations. The kernel of MUET consists of an efficient ray tracer allowing to compute the history (over 24 hours) of the shadowed parts of the 3D scene and a library, responsible for the thermal computations. The great originality concerns the way the heating fluxes are computed. Using ray tracing, the flux received in each 3D point of the scene accurately takes into account the masking (hidden surfaces) between objects. By the way, this library supplies other thermal modules such as a thermal shows computation tool.
Structural Composites Corrosive Management by Computational Simulation
Chamis, Christos C.; Minnetyan, Levon
2006-01-01
A simulation of corrosive management on polymer composites durability is presented. The corrosive environment is assumed to manage the polymer composite degradation on a ply-by-ply basis. The degradation is correlated with a measured Ph factor and is represented by voids, temperature, and moisture which vary parabolically for voids and linearly for temperature and moisture through the laminate thickness. The simulation is performed by a computational composite mechanics computer code which includes micro, macro, combined stress failure, and laminate theories. This accounts for starting the simulation from constitutive material properties and up to the laminate scale which exposes the laminate to the corrosive environment. Results obtained for one laminate indicate that the ply-by-ply managed degradation degrades the laminate to the last one or the last several plies. Results also demonstrate that the simulation is applicable to other polymer composite systems as well.
Electric Propulsion Plume Simulations Using Parallel Computer
Directory of Open Access Journals (Sweden)
Joseph Wang
2007-01-01
Full Text Available A parallel, three-dimensional electrostatic PIC code is developed for large-scale electric propulsion simulations using parallel supercomputers. This code uses a newly developed immersed-finite-element particle-in-cell (IFE-PIC algorithm designed to handle complex boundary conditions accurately while maintaining the computational speed of the standard PIC code. Domain decomposition is used in both field solve and particle push to divide the computation among processors. Two simulations studies are presented to demonstrate the capability of the code. The first is a full particle simulation of near-thruster plume using real ion to electron mass ratio. The second is a high-resolution simulation of multiple ion thruster plume interactions for a realistic spacecraft using a domain enclosing the entire solar array panel. Performance benchmarks show that the IFE-PIC achieves a high parallel efficiency of ≥ 90%
Shen, Wenfeng; Wei, Daming; Xu, Weimin; Zhu, Xin; Yuan, Shizhong
2010-10-01
Biological computations like electrocardiological modelling and simulation usually require high-performance computing environments. This paper introduces an implementation of parallel computation for computer simulation of electrocardiograms (ECGs) in a personal computer environment with an Intel CPU of Core (TM) 2 Quad Q6600 and a GPU of Geforce 8800GT, with software support by OpenMP and CUDA. It was tested in three parallelization device setups: (a) a four-core CPU without a general-purpose GPU, (b) a general-purpose GPU plus 1 core of CPU, and (c) a four-core CPU plus a general-purpose GPU. To effectively take advantage of a multi-core CPU and a general-purpose GPU, an algorithm based on load-prediction dynamic scheduling was developed and applied to setting (c). In the simulation with 1600 time steps, the speedup of the parallel computation as compared to the serial computation was 3.9 in setting (a), 16.8 in setting (b), and 20.0 in setting (c). This study demonstrates that a current PC with a multi-core CPU and a general-purpose GPU provides a good environment for parallel computations in biological modelling and simulation studies. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.
Computer model simulation of null-flux magnetic suspension and guidance
Energy Technology Data Exchange (ETDEWEB)
He, Jianliang; Rote, D.M.
1992-06-01
This paper discusses the magnetic force computations in a null-flux suspension system using dynamic circuit theory. A computer simulation model that can be used to compute magnetic forces and predict the system performance is developed on the basis of dynamic circuit theory. Numerical examples are presented to demonstrate the application of the model. The performance of the null-flux suspension system is simulated and discussed. 8 refs.
Computer model simulation of null-flux magnetic suspension and guidance
Energy Technology Data Exchange (ETDEWEB)
He, Jianliang; Rote, D.M.
1992-01-01
This paper discusses the magnetic force computations in a null-flux suspension system using dynamic circuit theory. A computer simulation model that can be used to compute magnetic forces and predict the system performance is developed on the basis of dynamic circuit theory. Numerical examples are presented to demonstrate the application of the model. The performance of the null-flux suspension system is simulated and discussed. 8 refs.
Yang, Zongbo; Cheng, Jun; Ye, Qing; Liu, Jianzhong; Zhou, Junhu; Cen, Kefa
2016-11-01
In this study, computational fluid dynamics (CFD) was used to systemically analyze the movement of algae in a vortex flow field produced by up-down chute baffles. The average cell light/dark (L/D) cycle period, vertical fluid velocity, fraction of time the algae was resides in light zone and the L/D cycle period were investigated under different paddlewheel speeds and microalgal concentrations. Results showed that the L/D cycle period decreased but the vertical fluid velocity increased when the up-down chute baffles were used. The L/D cycle period decreased by 24% (from 5.1s to 3.9s), and vertical fluid velocity increased by 75% when up-down chute baffles were used with paddlewheel speed of 30r/min. The probability of L/D cycle period of 3s increased by 52% from 0.29 to 0.44 with the up-down chute baffles. This led to approximately 22% increase in biomass yield without changing the paddlewheel speed.
Directory of Open Access Journals (Sweden)
Yuxin Zhang
2012-02-01
Full Text Available Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π–π, CH–π and CH–CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.
Engineering Applications of Computational Fluid Dynamics: Volume 2
Directory of Open Access Journals (Sweden)
Maher A.R. Sadiq Al-Baghdadi
2013-01-01
Full Text Available Chapter 1: CFD Modeling of Methane Reforming in Compact Reformers. Meng Ni Chapter 2: FEM Based Solution of Thermo Fluid Dynamic Phenomena in Solid Oxide Fuel Cells (SOFCS. F. Arpino, A. Carotenuto, N. Massarotti, A. Mauro Chapter 3: Computational Fluid Dynamics in the Development of a 3D Simulator for Testing Pollution Monitoring Robotic Fishes. John Oyekan, Bowen Lu, Huosheng Hu Chapter 4: CFD Applications in Electronic Packaging. C.Y. Khor, Chun-Sean Lau, M.Z. Abdullah Chapter 5: CFD Simulation of Savonius Wind Turbine Operation. Jo?o Vicente Akwa, Adriane Prisco Petry Chapter 6: Intermittency Modelling of Transitional Boundary Layer Flows on Steam and Gas Turbine Blades. Erik Dick, Slawomir Kubacki, Koen Lodefier, Witold Elsner Chapter 7: Numerical Analysis of the Flow through Fitting in Air Conditioning Systems. N.C. Uz?rraga-Rodriguez, A. Gallegos-Mu?oz, J.M. Belman-Flores, J.C. Rubio-Arana Chapter 8: Design and Optimization of Food Processing Equipments using Computational Fluid Dynamics Modeling. N. Chhanwal and C. Anandharamakrishnan Chapter 9: Fuel and Intake Systems Optimization of a Converted LPG Engine: Steady and Unsteady in-Cylinder Flow CFD Investigations and Experiments Validation. M. A. Jemni, G. Kantchev, Z. Driss, M. S. Abid Chapter 10: Computational Fluid Dynamics Application for Thermal Management in Underground Mines. Agus P. Sasmito, Jundika C. Kurnia, Guan Mengzhao, Erik Birgersson, Arun S. Mujumdar Chapter 11: Computational Fluid Dynamics and its Applications. R.Parthiban, C.Muthuraj, A.Rajakumar
Role of computational efficiency in process simulation
Directory of Open Access Journals (Sweden)
Kurt Strand
1989-07-01
Full Text Available It is demonstrated how efficient numerical algorithms may be combined to yield a powerful environment for analysing and simulating dynamic systems. The importance of using efficient numerical algorithms is emphasized and demonstrated through examples from the petrochemical industry.
Acoustic Simulation with Dynamic Mechanisms in Virtual Reality
Institute of Scientific and Technical Information of China (English)
张琼; 石教英
1998-01-01
Although most investigators have realized the importance of acoustic simulation in sophisticated VR systems,large computational load involved in this process often contradicts the requirements of real-time interaction,which in return bring on applying the expensive hardware or VR-specific workstations to this area.In order to reduce the computational cost and try to realize the real-time acoustic simulation in software with (or even without)some low-cost hardware,this paper proposes some dynamic mechanisms which can be used as possible strategies embedded into acoustic simulation in VR.Preliminary implementation of those mechanisms has proved to be fairly effective.
Macromod: Computer Simulation For Introductory Economics
Ross, Thomas
1977-01-01
The Macroeconomic model (Macromod) is a computer assisted instruction simulation model designed for introductory economics courses. An evaluation of its utilization at a community college indicates that it yielded a 10 percent to 13 percent greater economic comprehension than lecture classes and that it met with high student approval. (DC)
Computer Simulation Study of Bipolaron Formation
Raedt, H. De; Lagendijk, A.
1986-01-01
Monte Carlo computer simulation techniques are used to study the formation of bipolarons on a lattice. The transition between the three possible states, extended, two-polaron, and bipolaron is studied. The phase diagram as a function of the strengths of the electron-phonon coupling and repulsive int
Computer simulations of phospholipid - membrane thermodynamic fluctuations
DEFF Research Database (Denmark)
Pedersen, U.R.; Peters, Günther H.j.; Schröder, T.B.
2008-01-01
This paper reports all-atom computer simulations of five phospholipid membranes, DMPC, DPPC, DMPG, DMPS, and DMPSH, with a focus on the thermal equilibrium fluctuations of volume, energy, area, thickness, and order parameter. For the slow fluctuations at constant temperature and pressure (defined...
GENMAP--A Microbial Genetics Computer Simulation.
Day, M. J.; And Others
1985-01-01
An interactive computer program in microbial genetics is described. The simulation allows students to work at their own pace and develop understanding of microbial techniques as they choose donor bacterial strains, specify selective media, and interact with demonstration experiments. Sample questions and outputs are included. (DH)
CONSTRUCTION COST INTEGRATED CONTROL BASED ON COMPUTER SIMULATION
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Construction cost control is a complex system engineering. Thetraditional controlling method cannot dynamically control in advance the construction cost because of its hysteresis. This paper proposes a computer simulation based construction cost integrated control method, which combines the cost with PERT systematically, so that the construction cost can be predicted and optimized systematically and effectively. The new method overcomes the hysteresis of the traditional systems, and is a distinct improvement over them in effect and practicality.
Dynamics and computation in functional shifts
Namikawa, Jun; Hashimoto, Takashi
2004-07-01
We introduce a new type of shift dynamics as an extended model of symbolic dynamics, and investigate the characteristics of shift spaces from the viewpoints of both dynamics and computation. This shift dynamics is called a functional shift, which is defined by a set of bi-infinite sequences of some functions on a set of symbols. To analyse the complexity of functional shifts, we measure them in terms of topological entropy, and locate their languages in the Chomsky hierarchy. Through this study, we argue that considering functional shifts from the viewpoints of both dynamics and computation gives us opposite results about the complexity of systems. We also describe a new class of shift spaces whose languages are not recursively enumerable.
Unsteady computational fluid dynamics in aeronautics
Tucker, P G
2014-01-01
The field of Large Eddy Simulation (LES) and hybrids is a vibrant research area. This book runs through all the potential unsteady modelling fidelity ranges, from low-order to LES. The latter is probably the highest fidelity for practical aerospace systems modelling. Cutting edge new frontiers are defined. One example of a pressing environmental concern is noise. For the accurate prediction of this, unsteady modelling is needed. Hence computational aeroacoustics is explored. It is also emerging that there is a critical need for coupled simulations. Hence, this area is also considered and the tensions of utilizing such simulations with the already expensive LES. This work has relevance to the general field of CFD and LES and to a wide variety of non-aerospace aerodynamic systems (e.g. cars, submarines, ships, electronics, buildings). Topics treated include unsteady flow techniques; LES and hybrids; general numerical methods; computational aeroacoustics; computational aeroelasticity; coupled simulations and...
Dynamic Routing Protocol for Computer Networks with Clustering Topology
Institute of Scientific and Technical Information of China (English)
无
1999-01-01
This paper presents a hierarchical dynamic routing protocol (HDRP) based on the discrete dynamic programming principle. The proposed protocol can adapt to the dynamic and large computer networks (DLCN) with clustering topology. The procedures for realizing routing update and decision are presented in this paper. The proof of correctness and complexity analysis of the protocol are also made. The performance measures of the HDRP including throughput and average message delay are evaluated by using of simulation. The study shows that the HDRP provides a new available approach to the routing decision for DLCN or high speed networks with clustering topology.
Astrophysical Fluid Dynamics via Direct Statistical Simulation
Tobias, S M; Marston, J B
2010-01-01
In this paper we introduce the concept of Direct Statistical Simulation (DSS) for astrophysical flows. This technique may be appropriate for problems in astrophysical fluids where the instantaneous dynamics of the flows are of secondary importance to their statistical properties. We give examples of such problems including mixing and transport in planets, stars and disks. The method is described for a general set of evolution equations, before we consider the specific case of a spectral method optimised for problems on a spherical surface. The method is illustrated for the simplest non-trivial example of hydrodynamics and MHD on a rotating spherical surface. We then discuss possible extensions of the method both in terms of computational methods and the range of astrophysical problems that are of interest.
Computational algorithms for simulations in atmospheric optics.
Konyaev, P A; Lukin, V P
2016-04-20
A computer simulation technique for atmospheric and adaptive optics based on parallel programing is discussed. A parallel propagation algorithm is designed and a modified spectral-phase method for computer generation of 2D time-variant random fields is developed. Temporal power spectra of Laguerre-Gaussian beam fluctuations are considered as an example to illustrate the applications discussed. Implementation of the proposed algorithms using Intel MKL and IPP libraries and NVIDIA CUDA technology is shown to be very fast and accurate. The hardware system for the computer simulation is an off-the-shelf desktop with an Intel Core i7-4790K CPU operating at a turbo-speed frequency up to 5 GHz and an NVIDIA GeForce GTX-960 graphics accelerator with 1024 1.5 GHz processors.
Mathematical Model of ComputerHeat Treatment and Its Simulation
Institute of Scientific and Technical Information of China (English)
PanJiansheng; ZhangWeimin; TianDong; GuJianfeng; HuMingjuan
2004-01-01
Computer simulation on heat treatment is the foundation of intelligent heat treatment. The simulations of temperature field,phase transformation, stress/strain complicate quenching operation were realized by using the model of three dimensional non-linear finite element method and the treatment methods of abruptly changing interface conditions. The simulation results basically fit those measured in experiments. The intelligent sealed multipurpose furnace production line has been developed based on the combination of computer simulation on gaseous carburizing and computer control technology. More than 3000 batches of workpieces have been processed on this production line, and all are up to standard. The application of computer simulation technology can significantly improve the loading ability and reliability of nitriding and carburizing workpieces, reduce heat treatment distortion, and shorten carburizing duration. It is recommended that the reliable product design without redundancy should be performed with the combination of the CAD of mechanical products, the CAE of materials selection and heat treatment, and the dynamic evaluation technology of product reliability.
Cokonis, T. J.
The papers presented in this volume provide examples of the impact of computers on present engineering practice and indicate some future trends in computer-aided design, manufacturing, and simulation. Topics discussed include computer-aided design of turbine cycle configuration, managing and development of engineering computer systems, computer-aided manufacturing with robots in the automotive industry, and computer-aided design/analysis techniques of composite materials in the cure phase. Papers are also presented on computer simulation of vehicular propulsion systems, the performance of a hydraulic system simulator in a CAD environment, and computer simulation of hovercraft heave dynamics and control.
Neural circuits as computational dynamical systems.
Sussillo, David
2014-04-01
Many recent studies of neurons recorded from cortex reveal complex temporal dynamics. How such dynamics embody the computations that ultimately lead to behavior remains a mystery. Approaching this issue requires developing plausible hypotheses couched in terms of neural dynamics. A tool ideally suited to aid in this question is the recurrent neural network (RNN). RNNs straddle the fields of nonlinear dynamical systems and machine learning and have recently seen great advances in both theory and application. I summarize recent theoretical and technological advances and highlight an example of how RNNs helped to explain perplexing high-dimensional neurophysiological data in the prefrontal cortex.
Computational Simulation of Complex Structure Fancy Yarns
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
A study is reported for mathematical model and simulation of complex structure fancy yarns. The investigated complex structure fancy yarns have a multithread structure composed of three components -core, effect, and binder yams. In current research the precondition was accepted that the cross-sections of the both two yarns of the effect intermediate product in the complex structure fancy yarn remain the circles shaped, and this shape does not change during manufacturing of the fancy yarn. Mathematical model of complex structure fancy yarn is established based on parameter equation of space helix line and computer simulation is further carried out using the computational mathematical tool Matlab 6.5. Theoretical structure of fancy yarn is compared with an experimental sample. The simulation system would help for further the set ofinformation in designing of new assortment of the complex structure fancy yarns and prediction of visual effects of fancy yarns in end-use fabrics.
Cosmological Simulations on a Grid of Computers
Depardon, Benjamin; Desprez, Frédéric; Blaizot, Jérémy; Courtois, Hélène M
2010-01-01
The work presented in this paper aims at restricting the input parameter values of the semi-analytical model used in GALICS and MOMAF, so as to derive which parameters influence the most the results, e.g., star formation, feedback and halo recycling efficiencies, etc. Our approach is to proceed empirically: we run lots of simulations and derive the correct ranges of values. The computation time needed is so large, that we need to run on a grid of computers. Hence, we model GALICS and MOMAF execution time and output files size, and run the simulation using a grid middleware: DIET. All the complexity of accessing resources, scheduling simulations and managing data is harnessed by DIET and hidden behind a web portal accessible to the users.
Three-Dimensional Computational Fluid Dynamics
Energy Technology Data Exchange (ETDEWEB)
Haworth, D.C.; O' Rourke, P.J.; Ranganathan, R.
1998-09-01
Computational fluid dynamics (CFD) is one discipline falling under the broad heading of computer-aided engineering (CAE). CAE, together with computer-aided design (CAD) and computer-aided manufacturing (CAM), comprise a mathematical-based approach to engineering product and process design, analysis and fabrication. In this overview of CFD for the design engineer, our purposes are three-fold: (1) to define the scope of CFD and motivate its utility for engineering, (2) to provide a basic technical foundation for CFD, and (3) to convey how CFD is incorporated into engineering product and process design.
Single neuron dynamics and computation.
Brunel, Nicolas; Hakim, Vincent; Richardson, Magnus J E
2014-04-01
At the single neuron level, information processing involves the transformation of input spike trains into an appropriate output spike train. Building upon the classical view of a neuron as a threshold device, models have been developed in recent years that take into account the diverse electrophysiological make-up of neurons and accurately describe their input-output relations. Here, we review these recent advances and survey the computational roles that they have uncovered for various electrophysiological properties, for dendritic arbor anatomy as well as for short-term synaptic plasticity.
Energy Technology Data Exchange (ETDEWEB)
Frauenfelder, T.; Alkadhi, H.; Marincek, B.; Schertler, T. [Universitaetsspital Zuerich, Institut fuer Diagnostische Radiologie, Zuerich (Switzerland); Boutsianis, E. [ETH Zuerich, Labor fuer Computerwissenschaften und Engineering, Zuerich (Switzerland)
2007-11-15
The goal of numeric analysis of aortic blood flow is to evaluate the mechanisms leading to an aortic aneurysm with regard to the risk of a rupture and to describe the effect of interventional therapy. Numeric analysis is based on virtual models of vascular structures and the physical characteristics of the vessel wall, of blood as fluidum, and the blood flow. Using this information, numeric analysis solves the appropriate equations. The results can be displayed quantitatively and qualitatively. The results of numeric flow simulation show that in abdominal aortic aneurysms the wall pressure, which is of vital importance for the risk of rupture, depends on several factors, one being the location of the intraluminal thrombus. In models of aneurysms after stent grafting, numeric analysis can be used to evaluate factors leading to stent migration. Although numeric analysis of aortic blood flow still has several limitations, recent studies have shown that this method has the potential for improved estimation of the rupture risk of aortic aneurysms in the near future. (orig.) [German] Das Ziel der numerischen Simulation des Blutflusses in der Aorta ist, die Mechanik der Entstehung von Aortenaneurysmen im Hinblick auf das Rupturrisiko zu untersuchen und die Wirkungen interventioneller Massnahmen zu beschreiben. Die Grundlage der numerischen Simulation sind virtuelle Modelle von Gefaessen und die physikalischen Eigenschaften der Gefaessbestandteile, des Blutes und der Stroemung. Basierend auf diesen Angaben werden mit Hilfe numerischer Methoden die stroemungsmechanischen Probleme des Blutflusses naeherungsweise geloest. Die Ergebnisse koennen dann quantitativ und qualitativ dargestellt werden. Die Ergebnisse der numerischen Flusssimulation zeigen, dass in abdominellen Aortenaneurysmen die Hoehe des Wanddrucks, der von entscheidender Bedeutung fuer das Rupturrisiko ist, von verschiedenen Faktoren, wie z. B. der Lage des Wandthrombus, abhaengt. In Modellen mit Stentgrafts
1991-01-01
Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper develops a straightforward but effective algorithm for molecular dynamics simulations using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a netw...
Computational social dynamic modeling of group recruitment.
Energy Technology Data Exchange (ETDEWEB)
Berry, Nina M.; Lee, Marinna; Pickett, Marc; Turnley, Jessica Glicken (Sandia National Laboratories, Albuquerque, NM); Smrcka, Julianne D. (Sandia National Laboratories, Albuquerque, NM); Ko, Teresa H.; Moy, Timothy David (Sandia National Laboratories, Albuquerque, NM); Wu, Benjamin C.
2004-01-01
The Seldon software toolkit combines concepts from agent-based modeling and social science to create a computationally social dynamic model for group recruitment. The underlying recruitment model is based on a unique three-level hybrid agent-based architecture that contains simple agents (level one), abstract agents (level two), and cognitive agents (level three). This uniqueness of this architecture begins with abstract agents that permit the model to include social concepts (gang) or institutional concepts (school) into a typical software simulation environment. The future addition of cognitive agents to the recruitment model will provide a unique entity that does not exist in any agent-based modeling toolkits to date. We use social networks to provide an integrated mesh within and between the different levels. This Java based toolkit is used to analyze different social concepts based on initialization input from the user. The input alters a set of parameters used to influence the values associated with the simple agents, abstract agents, and the interactions (simple agent-simple agent or simple agent-abstract agent) between these entities. The results of phase-1 Seldon toolkit provide insight into how certain social concepts apply to different scenario development for inner city gang recruitment.
Lou, Wentao; Zhu, Miaoyong
2014-10-01
A computation fluid dynamics-simultaneous reaction model (CFD-SRM) coupled model has been proposed to describe the desulfurization behavior in a gas-stirred ladle. For the desulfurization thermodynamics, different models were investigated to determine sulfide capacity and oxygen activity. For the desulfurization kinetic, the effect of bubbly plume flow, as well as oxygen absorption and oxidation reactions in slag eyes are considered. The thermodynamic and kinetic modification coefficients are proposed to fit the measured data, respectively. Finally, the effects of slag basicity and gas flow rate on the desulfurization efficiency are investigated. The results show that as the interfacial reactions (Al2O3)-(FeO)-(SiO2)-(MnO)-[S]-[O] simultaneous kinetic equilibrium is adopted to determine the oxygen activity, and the Young's model with the modification coefficient R th of 1.5 is adopted to determine slag sulfide capacity, the predicted sulfur distribution ratio LS agrees well with the measured data. With an increase of the gas blowing time, the predicted desulfurization rate gradually decreased, and when the modification parameter R k is 0.8, the predicted sulfur content changing with time in ladle agrees well with the measured data. If the oxygen absorption and oxidation reactions in slag eyes are not considered in this model, then the sulfur removal rate in the ladle would be overestimated, and this trend would become more obvious with an increase of the gas flow rate and decrease of the slag layer height. With the slag basicity increasing, the total desulfurization ratio increases; however, the total desulfurization ratio changes weakly as the slag basicity exceeds 7. With the increase of the gas flow rate, the desulfurization ratio first increases and then decreases. When the gas flow rate is 200 NL/min, the desulfurization ratio reaches a maximum value in an 80-ton gas-stirred ladle.
Computational fluid dynamics modelling in cardiovascular medicine.
Morris, Paul D; Narracott, Andrew; von Tengg-Kobligk, Hendrik; Silva Soto, Daniel Alejandro; Hsiao, Sarah; Lungu, Angela; Evans, Paul; Bressloff, Neil W; Lawford, Patricia V; Hose, D Rodney; Gunn, Julian P
2016-01-01
This paper reviews the methods, benefits and challenges associated with the adoption and translation of computational fluid dynamics (CFD) modelling within cardiovascular medicine. CFD, a specialist area of mathematics and a branch of fluid mechanics, is used routinely in a diverse range of safety-critical engineering systems, which increasingly is being applied to the cardiovascular system. By facilitating rapid, economical, low-risk prototyping, CFD modelling has already revolutionised research and development of devices such as stents, valve prostheses, and ventricular assist devices. Combined with cardiovascular imaging, CFD simulation enables detailed characterisation of complex physiological pressure and flow fields and the computation of metrics which cannot be directly measured, for example, wall shear stress. CFD models are now being translated into clinical tools for physicians to use across the spectrum of coronary, valvular, congenital, myocardial and peripheral vascular diseases. CFD modelling is apposite for minimally-invasive patient assessment. Patient-specific (incorporating data unique to the individual) and multi-scale (combining models of different length- and time-scales) modelling enables individualised risk prediction and virtual treatment planning. This represents a significant departure from traditional dependence upon registry-based, population-averaged data. Model integration is progressively moving towards 'digital patient' or 'virtual physiological human' representations. When combined with population-scale numerical models, these models have the potential to reduce the cost, time and risk associated with clinical trials. The adoption of CFD modelling signals a new era in cardiovascular medicine. While potentially highly beneficial, a number of academic and commercial groups are addressing the associated methodological, regulatory, education- and service-related challenges.
In silico FRET from simulated dye dynamics
Hoefling, Martin; Grubmüller, Helmut
2013-03-01
Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via the Förster formula, E=1/(1+(). The energy transfer however also depends on the mutual orientation of the two dyes used as distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on approximations, which reduce the accuracy of these distance measurements. A common approximation is an isotropic and uncorrelated dye orientation distribution. To assess the impact of such approximations, we present the algorithms and implementation of a computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated using a Monte Carlo algorithm. The application of the developed toolkit on a poly-proline system demonstrated good agreement between smFRET simulations and experimental results and therefore confirms our computational method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity. The presented computational toolkit is written in Python, available as open-source, applicable to arbitrary systems and can easily be extended and adapted to further problems. Catalogue identifier: AENV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3, the bundled SIMD friendly Mersenne twister implementation [1] is provided under the SFMT-License. No. of lines in distributed program, including test data, etc.: 317880 No. of bytes in distributed program, including test data, etc.: 54774217 Distribution format: tar.gz Programming language
Computer simulation of tritium systems for fusion technology
Energy Technology Data Exchange (ETDEWEB)
Gabowitsch, E.; Spannagel, G. (Kernforschungszentrum Karlsruhe GmbH Institut fur Datenverarbeitung in der Technik Postfach 3640, D-7500 Karlsruhe 1 (DE))
1989-09-01
The KATRIM computer code is presented. It calculates key values of tritium systems, especially those related to complete fuel cycles. First, a deterministic model is discussed. Then, a stochastic model is presented based on dynamic systems with different dynamic states, each with its own system of equations. Such an approach allows the modeling of reactors with different degrees of availability and/or different operational strategies. Results of simulations for different availabilities, variable frequencies of interruptions in reactor operation, and changing tritium burnup in the plasma are presented.
Modeling and simulation the computer science of illusion
Raczynski, Stanislaw
2006-01-01
Simulation is the art of using tools - physical or conceptual models, or computer hardware and software, to attempt to create the illusion of reality. The discipline has in recent years expanded to include the modelling of systems that rely on human factors and therefore possess a large proportion of uncertainty, such as social, economic or commercial systems. These new applications make the discipline of modelling and simulation a field of dynamic growth and new research. Stanislaw Raczynski outlines the considerable and promising research that is being conducted to counter the problems of
Computational Challenges in Nuclear Weapons Simulation
Energy Technology Data Exchange (ETDEWEB)
McMillain, C F; Adams, T F; McCoy, M G; Christensen, R B; Pudliner, B S; Zika, M R; Brantley, P S; Vetter, J S; May, J M
2003-08-29
After a decade of experience, the Stockpile Stewardship Program continues to ensure the safety, security and reliability of the nation's nuclear weapons. The Advanced Simulation and Computing (ASCI) program was established to provide leading edge, high-end simulation capabilities needed to meet the program's assessment and certification requirements. The great challenge of this program lies in developing the tools and resources necessary for the complex, highly coupled, multi-physics calculations required to simulate nuclear weapons. This paper describes the hardware and software environment we have applied to fulfill our nuclear weapons responsibilities. It also presents the characteristics of our algorithms and codes, especially as they relate to supercomputing resource capabilities and requirements. It then addresses impediments to the development and application of nuclear weapon simulation software and hardware and concludes with a summary of observations and recommendations on an approach for working with industry and government agencies to address these impediments.
Molecular dynamics simulations of barrier crossings in the condensed phase
den Otter, Wouter K.
1998-01-01
The isomerisation rates of a calix[4]arene in vacuo and in two solvents have been computed by means of molecular dynamics simulations (MD). In MD the equations of classical mechanics are used to calculate the motion of the reacting molecule and the surrounding solvent molecules. Thus, the intricate
Energy Technology Data Exchange (ETDEWEB)
Jin, Shuangshuang; Chen, Yousu; Diao, Ruisheng; Huang, Zhenyu (Henry); Perkins, William; Palmer, Bruce
2016-12-01
This paper describes the GridPACK™ software framework for developing power grid simulations that can run on high performance computing platforms, with several example applications (dynamic simulation, static contingency analysis, and dynamic contingency analysis) that have been developed using GridPACK.
Vashishta, Priya; Bachlechner, Martina; Nakano, Aiichiro; Campbell, Timothy J.; Kalia, Rajiv K.; Kodiyalam, Sanjay; Ogata, Shuji; Shimojo, Fuyuki; Walsh, Phillip
2001-10-01
We have developed scalable space-time multiresolution algorithms to enable molecular dynamics simulations involving up to a billion atoms on massively parallel computers. Large-scale molecular dynamics simulations have been used to study stress domains and interfacial fracture in semiconductor/dielectric nanopixels, nanoindentation, and oxidation of metallic nanoparticles.
Interactive Computer Assisted Instruction in Teaching of Process Analysis and Simulation.
Nuttall, Herbert E., Jr.; Himmelblau, David M.
To improve the instructional process, time shared computer-assisted instructional methods were developed to teach upper division undergraduate chemical engineering students the concepts of process simulation and analysis. The interactive computer simulation aimed at enabling the student to learn the difficult concepts of process dynamics by…
Dynamic Associations in Nonlinear Computing Arrays
Huberman, B. A.; Hogg, T.
1985-10-01
We experimentally show that nonlinear parallel arrays can be made to compute with attractors. This leads to fast adaptive behavior in which dynamical associations can be made between different inputs which initially produce sharply distinct outputs. We first define a set of simple local procedures which allow a general computing structure to change its state in time so as to produce classical Pavlovian conditioning. We then examine the dynamics of coalescence and dissociation of attractors with a number of quantitative experiments. We also show how such arrays exhibit generalization and differentiation of inputs in their behavior.
An introduction to Computational Fluid Dynamics
DEFF Research Database (Denmark)
Sørensen, Lars Schiøtt
1999-01-01
CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building.......CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building....
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
WANG; Hui(
2001-01-01
［1］Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.［2］Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.［3］Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.［4］Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.［5］Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.［6］Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.［7］Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.［8］Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.［9］Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.［10］Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.［11］Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.［12］Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.［13］Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.
Computer simulation of randomly cross-linked polymer networks
Williams, T P
2002-01-01
In this work, Monte Carlo and Stochastic Dynamics computer simulations of mesoscale model randomly cross-linked networks were undertaken. Task parallel implementations of the lattice Monte Carlo Bond Fluctuation model and Kremer-Grest Stochastic Dynamics bead-spring continuum model were designed and used for this purpose. Lattice and continuum precursor melt systems were prepared and then cross-linked to varying degrees. The resultant networks were used to study structural changes during deformation and relaxation dynamics. The effects of a random network topology featuring a polydisperse distribution of strand lengths and an abundance of pendant chain ends, were qualitatively compared to recent published work. A preliminary investigation into the effects of temperature on the structural and dynamical properties was also undertaken. Structural changes during isotropic swelling and uniaxial deformation, revealed a pronounced non-affine deformation dependant on the degree of cross-linking. Fractal heterogeneiti...
Inverse problems in stochastic computational dynamics
Capiez-Lernout, Evangéline; Soize, Christian
2008-01-01
International audience; This paper deals with robust updating of dynamical systems using stochastic computational models for which model and parameter uncertainties are taken into account by the nonparametric probabilistic approach. Such a problem is formulated as an inverse problem consisting in identifying the parameters of the mean computational model and the parameters of the probabilistic model of uncertainties. This inverse problem leads us to solve an optimization problem for which the...
Computer Simulation for Emergency Incident Management
Energy Technology Data Exchange (ETDEWEB)
Brown, D L
2004-12-03
This report describes the findings and recommendations resulting from the Department of Homeland Security (DHS) Incident Management Simulation Workshop held by the DHS Advanced Scientific Computing Program in May 2004. This workshop brought senior representatives of the emergency response and incident-management communities together with modeling and simulation technologists from Department of Energy laboratories. The workshop provided an opportunity for incident responders to describe the nature and substance of the primary personnel roles in an incident response, to identify current and anticipated roles of modeling and simulation in support of incident response, and to begin a dialog between the incident response and simulation technology communities that will guide and inform planned modeling and simulation development for incident response. This report provides a summary of the discussions at the workshop as well as a summary of simulation capabilities that are relevant to incident-management training, and recommendations for the use of simulation in both incident management and in incident management training, based on the discussions at the workshop. In addition, the report discusses areas where further research and development will be required to support future needs in this area.
Computer Simulation of Convective Plasma Cells
Carboni, Rodrigo
2015-01-01
Computer simulations of plasmas are relevant nowadays, because it helps us understand physical processes taking place in the sun and other stellar objects. We developed a program called PCell which is intended for displaying the evolution of the magnetic field in a 2D convective plasma cell with perfect conducting walls for different stationary plasma velocity fields. Applications of this program are presented. This software works interactively with the mouse and the users can create their own movies in MPEG format. The programs were written in Fortran and C. There are two versions of the program (GNUPLOT and OpenGL). GNUPLOT and OpenGL are used to display the simulation.
On sequential dynamical systems and simulation
Energy Technology Data Exchange (ETDEWEB)
Barrett, C.L.; Mortveit, H.S.; Reidys, C.M.
1999-06-01
The generic structure of computer simulations motivates a new class of discrete dynamical systems that captures this structure in a mathematically precise way. This class of systems consists of (1) a loopfree graph {Upsilon} with vertex set {l_brace}1,2,{hor_ellipsis},n{r_brace} where each vertex has a binary state, (2) a vertex labeled set of functions (F{sub i,{Upsilon}}:F{sub 2}{sup n} {r_arrow} F{sub 2}{sup n}){sub i} and (3) a permutation {pi} {element_of} S{sub n}. The function F{sub i,{Upsilon}} updates the state of vertex i as a function of the states of vertex i and its {Upsilon}-neighbors and leaves the states of all other vertices fixed. The permutation {pi} represents the update ordering, i.e., the order in which the functions F{sub i,{Upsilon}} are applied. By composing the functions F{sub i,{Upsilon}} in the order given by {pi} one obtains the dynamical system (equation given in paper) which the authors refer to as a sequential dynamical system, or SDS for short. The authors will present bounds for the number of functionally different systems and for the number of nonisomorphic digraphs {Gamma}[F{sub {Upsilon}},{pi}] that can be obtained by varying the update order and applications of these to specific graphs and graph classes. This will be done using both combinatorial/algebraic techniques and probabilistic techniques. Finally the authors give results on dynamical system properties for some special systems.
Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments
Energy Technology Data Exchange (ETDEWEB)
Jin, Shuangshuang; Chen, Yousu; Wu, Di; Diao, Ruisheng; Huang, Zhenyu
2015-12-09
Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.
Cosmic reionization on computers. I. Design and calibration of simulations
Energy Technology Data Exchange (ETDEWEB)
Gnedin, Nickolay Y., E-mail: gnedin@fnal.gov [Particle Astrophysics Center, Fermi National Accelerator Laboratory, Batavia, IL 60510 (United States)
2014-09-20
Cosmic Reionization On Computers is a long-term program of numerical simulations of cosmic reionization. Its goal is to model fully self-consistently (albeit not necessarily from the first principles) all relevant physics, from radiative transfer to gas dynamics and star formation, in simulation volumes of up to 100 comoving Mpc, and with spatial resolution approaching 100 pc in physical units. In this method paper, we describe our numerical method, the design of simulations, and the calibration of numerical parameters. Using several sets (ensembles) of simulations in 20 h {sup –1} Mpc and 40 h {sup –1} Mpc boxes with spatial resolution reaching 125 pc at z = 6, we are able to match the observed galaxy UV luminosity functions at all redshifts between 6 and 10, as well as obtain reasonable agreement with the observational measurements of the Gunn-Peterson optical depth at z < 6.
Simulations of Energetic Particles Interacting with Dynamical Magnetic Turbulence
Hussein, M.; Shalchi, A.
2016-02-01
We explore the transport of energetic particles in interplanetary space by using test-particle simulations. In previous work such simulations have been performed by using either magnetostatic turbulence or undamped propagating plasma waves. In the current paper we simulate for the first time particle transport in dynamical turbulence. To do so we employ two models, namely the damping model of dynamical turbulence and the random sweeping model. We compute parallel and perpendicular diffusion coefficients and compare our numerical findings with solar wind observations. We show that good agreement can be found between simulations and the Palmer consensus range for both dynamical turbulence models if the ratio of turbulent magnetic field and mean field is δB/B0 = 0.5.
Computer Simulations of Lipid Bilayers and Proteins
DEFF Research Database (Denmark)
Sonne, Jacob
2006-01-01
, Pressure profile calculations in lipid bilayers: A lipid bilayer is merely $\\sim$5~nm thick, but the lateral pressure (parallel to the bilayer plane) varies several hundred bar on this short distance (normal to the bilayer). These variations in the lateral pressure are commonly referred to as the pressure...... of neglecting pressure contributions from long range electrostatic interactions. The first issue is addressed by comparing two methods for calculating pressure profiles, and judged by the similar results obtained by these two methods the pressure profile appears to be well-defined for fluid phase lipid bilayers......The importance of computer simulations in lipid bilayer research has become more prominent for the last couple of decades and as computers get even faster, simulations will play an increasingly important part of understanding the processes that take place in and across cell membranes. This thesis...
Computer Modelling and Simulation for Inventory Control
Directory of Open Access Journals (Sweden)
G.K. Adegoke
2012-07-01
Full Text Available This study concerns the role of computer simulation as a device for conducting scientific experiments on inventory control. The stores function utilizes a bulk of physical assets and engages a bulk of financial resources in a manufacturing outfit therefore there is a need for an efficient inventory control. The reason being that inventory control reduces cost of production and thereby facilitates the effective and efficient accomplishment of production objectives of an organization. Some mathematical and statistical models were used to compute the Economic Order Quantity (EOQ. Test data were gotten from a manufacturing company and same were simulated. The results generated were used to predict a real life situation and have been presented and discussed. The language of implementation for the three models is Turbo Pascal due to its capability, generality and flexibility as a scientific programming language.
SPINET: A Parallel Computing Approach to Spine Simulations
Directory of Open Access Journals (Sweden)
Peter G. Kropf
1996-01-01
Full Text Available Research in scientitic programming enables us to realize more and more complex applications, and on the other hand, application-driven demands on computing methods and power are continuously growing. Therefore, interdisciplinary approaches become more widely used. The interdisciplinary SPINET project presented in this article applies modern scientific computing tools to biomechanical simulations: parallel computing and symbolic and modern functional programming. The target application is the human spine. Simulations of the spine help us to investigate and better understand the mechanisms of back pain and spinal injury. Two approaches have been used: the first uses the finite element method for high-performance simulations of static biomechanical models, and the second generates a simulation developmenttool for experimenting with different dynamic models. A finite element program for static analysis has been parallelized for the MUSIC machine. To solve the sparse system of linear equations, a conjugate gradient solver (iterative method and a frontal solver (direct method have been implemented. The preprocessor required for the frontal solver is written in the modern functional programming language SML, the solver itself in C, thus exploiting the characteristic advantages of both functional and imperative programming. The speedup analysis of both solvers show very satisfactory results for this irregular problem. A mixed symbolic-numeric environment for rigid body system simulations is presented. It automatically generates C code from a problem specification expressed by the Lagrange formalism using Maple.
DEFF Research Database (Denmark)
Papaleo, Elena
2015-01-01
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the pos......In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....
Dynamics simulations for engineering macromolecular interactions
Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey
2013-06-01
The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could
Computer Simulation of Convective Plasma Cells
Carboni, Rodrigo; Frutos-Alfaro, Francisco
2015-01-01
Computer simulations of plasmas are relevant nowadays, because it helps us understand physical processes taking place in the sun and other stellar objects. We developed a program called PCell which is intended for displaying the evolution of the magnetic field in a 2D convective plasma cell with perfect conducting walls for different stationary plasma velocity fields. Applications of this program are presented. This software works interactively with the mouse and the users can create their ow...
Computer simulations of the random barrier model
DEFF Research Database (Denmark)
Schrøder, Thomas; Dyre, Jeppe
2002-01-01
A brief review of experimental facts regarding ac electronic and ionic conduction in disordered solids is given followed by a discussion of what is perhaps the simplest realistic model, the random barrier model (symmetric hopping model). Results from large scale computer simulations are presented......, focusing on universality of the ac response in the extreme disorder limit. Finally, some important unsolved problems relating to hopping models for ac conduction are listed....
Computer simulation of the micropulse imaging lidar
Dai, Yongjiang; Zhao, Hongwei; Zhao, Yu; Wang, Xiaoou
2000-10-01
In this paper a design method of the Micro Pulse Lidar (MPL) is introduced, that is a computer simulation of the MPL. Some of the MPL parameters concerned air scattered and the effects on the performance of the lidar are discussed. The design software for the lidar with diode pumped solid laser is programmed by MATLAB. This software is consisted of six modules, that is transmitter, atmosphere, target, receiver, processor and display system. The method can be extended some kinds of lidar.
Computer simulation of complexity in plasmas
Energy Technology Data Exchange (ETDEWEB)
Hayashi, Takaya; Sato, Tetsuya [National Inst. for Fusion Science, Toki, Gifu (Japan)
1998-08-01
By making a comprehensive comparative study of many self-organizing phenomena occurring in magnetohydrodynamics and kinetic plasmas, we came up with a hypothetical grand view of self-organization. This assertion is confirmed by a recent computer simulation for a broader science field, specifically, the structure formation of short polymer chains, where the nature of the interaction is completely different from that of plasmas. It is found that the formation of the global orientation order proceeds stepwise. (author)
Computer Simulation of Multidimensional Archaeological Artefacts
Directory of Open Access Journals (Sweden)
Vera Moitinho de Almeida
2012-11-01
Our project focuses on the Neolithic lakeside site of La Draga (Banyoles, Catalonia. In this presentation we will begin by providing a clear overview of the major guidelines used to capture and process 3D digital data of several wooden artefacts. Then, we shall present the use of semi-automated relevant feature extractions. Finally, we intend to share preliminary computer simulation issues.
Sensitivity Analysis of Fire Dynamics Simulation
DEFF Research Database (Denmark)
Brohus, Henrik; Nielsen, Peter V.; Petersen, Arnkell J.
2007-01-01
equations require solution of the issues of combustion and gas radiation to mention a few. This paper performs a sensitivity analysis of a fire dynamics simulation on a benchmark case where measurement results are available for comparison. The analysis is performed using the method of Elementary Effects......In case of fire dynamics simulation requirements to reliable results are most often very high due to the severe consequences of erroneous results. At the same time it is a well known fact that fire dynamics simulation constitutes rather complex physical phenomena which apart from flow and energy...
Coarse-grained protein molecular dynamics simulations
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
QCWAVE, a Mathematica quantum computer simulation update
Tabakin, Frank
2011-01-01
This Mathematica 7.0/8.0 package upgrades and extends the quantum computer simulation code called QDENSITY. Use of the density matrix was emphasized in QDENSITY, although that code was also applicable to a quantum state description. In the present version, the quantum state version is stressed and made amenable to future extensions to parallel computer simulations. The add-on QCWAVE extends QDENSITY in several ways. The first way is to describe the action of one, two and three- qubit quantum gates as a set of small ($2 \\times 2, 4\\times 4$ or $8\\times 8$) matrices acting on the $2^{n_q}$ amplitudes for a system of $n_q$ qubits. This procedure was described in our parallel computer simulation QCMPI and is reviewed here. The advantage is that smaller storage demands are made, without loss of speed, and that the procedure can take advantage of message passing interface (MPI) techniques, which will hopefully be generally available in future Mathematica versions. Another extension of QDENSITY provided here is a mu...
Simulating Boolean circuits on a DNA computer
Energy Technology Data Exchange (ETDEWEB)
Ogihara, Mitsunori; Ray, A. [Univ. of Rochester, NY (United States)
1997-12-01
We demonstrate that DNA computers can simulate Boolean circuits with a small overhead. Boolean circuits embody the notion of massively parallel signal processing and are frequently encountered in many parallel algorithms. Many important problems such as sorting, integer arithmetic, and matrix multiplication are known to be computable by small size Boolean circuits much faster than by ordinary sequential digital computers. This paper shows that DNA chemistry allows one to simulate large semi-unbounded fan-in Boolean circuits with a logarithmic slowdown in computation time. Also, for the class NC{sup 1}, the slowdown can be reduced to a constant. In this algorithm we have encoded the inputs, the Boolean AND gates, and the OR gates to DNA oligonucleotide sequences. We operate on the gates and the inputs by standard molecular techniques of sequence-specific annealing, ligation, separation by size, amplification, sequence-specific cleavage, and detection by size. Additional steps of amplification are not necessary for NC{sup 1} circuits. Preliminary biochemical experiments on a small test circuit have produced encouraging results. Further confirmatory experiments are in progress. 19 refs., 3 figs., 1 tab.
Computational fluid dynamics in oil burner design
Energy Technology Data Exchange (ETDEWEB)
Butcher, T.A. [Brookhaven National Labs., Upton, NY (United States)
1997-09-01
In Computational Fluid Dynamics, the differential equations which describe flow, heat transfer, and mass transfer are approximately solved using a very laborious numerical procedure. Flows of practical interest to burner designs are always turbulent, adding to the complexity of requiring a turbulence model. This paper presents a model for burner design.
Engineering applications of computational fluid dynamics
Awang, Mokhtar
2015-01-01
This volume presents the results of Computational Fluid Dynamics (CFD) analysis that can be used for conceptual studies of product design, detail product development, process troubleshooting. It demonstrates the benefit of CFD modeling as a cost saving, timely, safe and easy to scale-up methodology.
From Cnn Dynamics to Cellular Wave Computers
Roska, Tamas
2013-01-01
Embedded in a historical overview, the development of the Cellular Wave Computing paradigm is presented, starting from the standard CNN dynamics. The theoretical aspects, the physical implementation, the innovation process, as well as the biological relevance are discussed in details. Finally, the latest developments, the physical versus virtual cellular machines, as well as some open questions are presented.
The status of Computational Fluis Dynamics
DEFF Research Database (Denmark)
Nielsen, Peter Vilhelm; Liu, Li; Peng, Lei
2016-01-01
Computational fluid dynamics (CFD) was first introduced in the building ventilation industry in the 1970s. Since then, it has been increasingly used as testified by the growth of the number of peer-reviewed articles, which was less than 10 per year in the 1990s and 60 to 70 per year in the recent...
Computational Fluid Dynamics in Ventilation Design
DEFF Research Database (Denmark)
Nielsen, Peter V.
2008-01-01
This paper is based on the new REHVA Guidebook Computational Fluid Dynamics in Ventilation Design (Nielsen et al. 2007) written by Peter V. Nielsen, Francis(Nielsen 2007) written by Peter V. Nielsen, Francis Allard, Hazim B. Awbi, Lars Davidson and Alois Schälin. The guidebook is made for people...
Computational Fluid Dynamics and Ventilation Airflow
DEFF Research Database (Denmark)
Nielsen, Peter Vilhelm
2014-01-01
Computational fluid dynamics (CFD) was first introduced in the ventilation industry in the 1970s. CFD has been increasingly used since then, as testified by the number of peer-reviewed articles, which was less than 10 per year in the 1990s, and which is now 60 to 70 per year. This article discusses...
Molecular dynamics simulations through GPU video games technologies
Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia
2016-01-01
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251
Computer simulation in nuclear science and engineering
Energy Technology Data Exchange (ETDEWEB)
Akiyama, Mamoru; Miya, Kenzo; Iwata, Shuichi; Yagawa, Genki; Kondo, Shusuke (Tokyo Univ. (Japan)); Hoshino, Tsutomu; Shimizu, Akinao; Takahashi, Hiroshi; Nakagawa, Masatoshi
1992-03-01
The numerical simulation technology used for the design of nuclear reactors includes the scientific fields of wide range, and is the cultivated technology which grew in the steady efforts to high calculation accuracy through safety examination, reliability verification test, the assessment of operation results and so on. Taking the opportunity of putting numerical simulation to practical use in wide fields, the numerical simulation of five basic equations which describe the natural world and the progress of its related technologies are reviewed. It is expected that numerical simulation technology contributes to not only the means of design study but also the progress of science and technology such as the construction of new innovative concept, the exploration of new mechanisms and substances, of which the models do not exist in the natural world. The development of atomic energy and the progress of computers, Boltzmann's transport equation and its periphery, Navier-Stokes' equation and its periphery, Maxwell's electromagnetic field equation and its periphery, Schroedinger wave equation and its periphery, computational solid mechanics and its periphery, and probabilistic risk assessment and its periphery are described. (K.I.).
Computer Simulations of the Fatigue Crack Propagation
Directory of Open Access Journals (Sweden)
A. Materna
2000-01-01
Full Text Available The following hypothesis for design of structures based on the damage tolerance philosophy is laid down: the perpendicular fatigue crack growth rate v in a certain point of a curved crack front is given by the local value of stress intensity factor per unit of nominal stress K' and the local triaxiality T which describes the constraint. The relationship v = f (K', T is supposed to be typical for a given loading spectrum and material. Such relationship for a 2024 Al alloy and the flight-simulation spectrum was derived from the fatigue test of the rectangular panel with the central hole and used for three-dimensional simulation of the corner fatigue crack propagation in the model of the wing spar flangeplate. Finite element and boundary element methods were used for these computations. The results of the simulation are in good agreement with the experiment.
Cichero, Elena; D'Ursi, Pasqualina; Moscatelli, Marco; Bruno, Olga; Orro, Alessandro; Rotolo, Chiara; Milanesi, Luciano; Fossa, Paola
2013-12-01
Phosphodiesterase 11 (PDE11) is the latest isoform of the PDEs family to be identified, acting on both cyclic adenosine monophosphate and cyclic guanosine monophosphate. The initial reports of PDE11 found evidence for PDE11 expression in skeletal muscle, prostate, testis, and salivary glands; however, the tissue distribution of PDE11 still remains a topic of active study and some controversy. Given the sequence similarity between PDE11 and PDE5, several PDE5 inhibitors have been shown to cross-react with PDE11. Accordingly, many non-selective inhibitors, such as IBMX, zaprinast, sildenafil, and dipyridamole, have been documented to inhibit PDE11. Only recently, a series of dihydrothieno[3,2-d]pyrimidin-4(3H)-one derivatives proved to be selective toward the PDE11 isoform. In the absence of experimental data about PDE11 X-ray structures, we found interesting to gain a better understanding of the enzyme-inhibitor interactions using in silico simulations. In this work, we describe a computational approach based on homology modeling, docking, and molecular dynamics simulation to derive a predictive 3D model of PDE11. Using a Graphical Processing Unit architecture, it is possible to perform long simulations, find stable interactions involved in the complex, and finally to suggest guideline for the identification and synthesis of potent and selective inhibitors.
Computing Optimal Stochastic Portfolio Execution Strategies: A Parametric Approach Using Simulations
Moazeni, Somayeh; Coleman, Thomas F.; Li, Yuying
2010-09-01
Computing optimal stochastic portfolio execution strategies under appropriate risk consideration presents great computational challenge. We investigate a parametric approach for computing optimal stochastic strategies using Monte Carlo simulations. This approach allows reduction in computational complexity by computing coefficients for a parametric representation of a stochastic dynamic strategy based on static optimization. Using this technique, constraints can be similarly handled using appropriate penalty functions. We illustrate the proposed approach to minimize the expected execution cost and Conditional Value-at-Risk (CVaR).
Strong Analog Classical Simulation of Coherent Quantum Dynamics
Wang, Dong-Sheng
2017-02-01
A strong analog classical simulation of general quantum evolution is proposed, which serves as a novel scheme in quantum computation and simulation. The scheme employs the approach of geometric quantum mechanics and quantum informational technique of quantum tomography, which applies broadly to cases of mixed states, nonunitary evolution, and infinite dimensional systems. The simulation provides an intriguing classical picture to probe quantum phenomena, namely, a coherent quantum dynamics can be viewed as a globally constrained classical Hamiltonian dynamics of a collection of coupled particles or strings. Efficiency analysis reveals a fundamental difference between the locality in real space and locality in Hilbert space, the latter enables efficient strong analog classical simulations. Examples are also studied to highlight the differences and gaps among various simulation methods. Funding support from NSERC of Canada and a research fellowship at Department of Physics and Astronomy, University of British Columbia are acknowledged
3D vesicle dynamics simulations with a linearly triangulated surface
Boedec, G.; Leonetti, M.; Jaeger, M.
2011-02-01
Simulations of biomembranes have gained an increasing interest in the past years. Specificities of these membranes propose new challenges for the numerics. In particular, vesicle dynamics are governed by bending forces as well as a surface incompressibility constraint. A method to compute the bending force density resultant onto piecewise linearly triangulated surface meshes is described. This method is coupled with a boundary element method solver for inner and outer fluids, to compute vesicle dynamics under external flows. The surface incompressibility constraint is satisfied by the construction of a projection operator.
Computational Methods in Stochastic Dynamics Volume 2
Stefanou, George; Papadopoulos, Vissarion
2013-01-01
The considerable influence of inherent uncertainties on structural behavior has led the engineering community to recognize the importance of a stochastic approach to structural problems. Issues related to uncertainty quantification and its influence on the reliability of the computational models are continuously gaining in significance. In particular, the problems of dynamic response analysis and reliability assessment of structures with uncertain system and excitation parameters have been the subject of continuous research over the last two decades as a result of the increasing availability of powerful computing resources and technology. This book is a follow up of a previous book with the same subject (ISBN 978-90-481-9986-0) and focuses on advanced computational methods and software tools which can highly assist in tackling complex problems in stochastic dynamic/seismic analysis and design of structures. The selected chapters are authored by some of the most active scholars in their respective areas and...
BeeSim: Leveraging Wearable Computers in Participatory Simulations with Young Children
Peppler, Kylie; Danish, Joshua; Zaitlen, Benjamin; Glosson, Diane; Jacobs, Alexander; Phelps, David
2010-01-01
New technologies have enabled students to become active participants in computational simulations of dynamic and complex systems (called Participatory Simulations), providing a "first-person"perspective on complex systems. However, most existing Participatory Simulations have targeted older children, teens, and adults assuming that such concepts…
Dynamic traffic assignment on parallel computers
Energy Technology Data Exchange (ETDEWEB)
Nagel, K.; Frye, R.; Jakob, R.; Rickert, M.; Stretz, P.
1998-12-01
The authors describe part of the current framework of the TRANSIMS traffic research project at the Los Alamos National Laboratory. It includes parallel implementations of a route planner and a microscopic traffic simulation model. They present performance figures and results of an offline load-balancing scheme used in one of the iterative re-planning runs required for dynamic route assignment.
Dynamic Simulation for Missile Erection System
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
In order to study the dynamic characteristics of the missile erection system, it can be considered as a rigid-flexible coupling multi-body system. Firstly, the actual system is abstracted as an equal and simplified one and then the forces applied to it are analyzed. Secondly, the rigid-flexible coupling dynamic simulation for erection system is accomplished by use of the system simulation software, for example Pro/E, ADAMS, ANSYS, MATLAB/Simulink, etc. Finally, having the aid of simulation results, the kinetic and dynamic characteristics of the flexible bodies in erection system are analyzed.The simulation considering the erection system as a rigid-flexible coupling system can provide valuable results to the research of its kinetic, dynamic and vibrational characteristics.
Use of computational fluid dynamics in respiratory medicine.
Fernández Tena, Ana; Casan Clarà, Pere
2015-06-01
Computational Fluid Dynamics (CFD) is a computer-based tool for simulating fluid movement. The main advantages of CFD over other fluid mechanics studies include: substantial savings in time and cost, the analysis of systems or conditions that are very difficult to simulate experimentally (as is the case of the airways), and a practically unlimited level of detail. We used the Ansys-Fluent CFD program to develop a conducting airway model to simulate different inspiratory flow rates and the deposition of inhaled particles of varying diameters, obtaining results consistent with those reported in the literature using other procedures. We hope this approach will enable clinicians to further individualize the treatment of different respiratory diseases.
Type II Quantum Computing Algorithm For Computational Fluid Dynamics
2006-03-01
Hall/CRC (2003) 30. Gilbert Strang, Linear Algebra and its Applications. Thompson Learning, Inc (1988) 31. George Arfken and Hans Weber, Mathematical ... method is called ensemble Figure 3. Ensemble measurement averages the measurement results of N identical quantum computers to obtain the magnitude of...the lattice Boltzmann equation. There are two methods of modeling this mesoscopic equation. The first approach is to directly simulate the
Simulation of stochastic network dynamics via entropic matching.
Ramalho, Tiago; Selig, Marco; Gerland, Ulrich; Ensslin, Torsten A
2013-02-01
The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a model's dynamics over a large parameter space renders full-fledged stochastic simulations impractical, motivating approximation schemes. Here we propose an approximation scheme which improves upon the standard linear noise approximation while retaining similar computational complexity. The underlying idea is to minimize, at each time step, the Kullback-Leibler divergence between the true time evolved probability distribution and a Gaussian approximation (entropic matching). This condition leads to ordinary differential equations for the mean and the covariance matrix of the Gaussian. For cases of weak nonlinearity, the method is more accurate than the linear method when both are compared to stochastic simulations.
Computational simulation of wave propagation problems in infinite domains
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
This paper deals with the computational simulation of both scalar wave and vector wave propagation problems in infinite domains. Due to its advantages in simulating complicated geometry and complex material properties, the finite element method is used to simulate the near field of a wave propagation problem involving an infinite domain. To avoid wave reflection and refraction at the common boundary between the near field and the far field of an infinite domain, we have to use some special treatments to this boundary. For a wave radiation problem, a wave absorbing boundary can be applied to the common boundary between the near field and the far field of an infinite domain, while for a wave scattering problem, the dynamic infinite element can be used to propagate the incident wave from the near field to the far field of the infinite domain. For the sake of illustrating how these two different approaches are used to simulate the effect of the far field, a mathematical expression for a wave absorbing boundary of high-order accuracy is derived from a two-dimensional scalar wave radiation problem in an infinite domain, while the detailed mathematical formulation of the dynamic infinite element is derived from a two-dimensional vector wave scattering problem in an infinite domain. Finally, the coupled method of finite elements and dynamic infinite elements is used to investigate the effects of topographical conditions on the free field motion along the surface of a canyon.
Computational Fluid Dynamics In GARUDA Grid Environment
Roy, Chandra Bhushan
2011-01-01
GARUDA Grid developed on NKN (National Knowledge Network) network by Centre for Development of Advanced Computing (C-DAC) hubs High Performance Computing (HPC) Clusters which are geographically separated all over India. C-DAC has been associated with development of HPC infrastructure since its establishment in year 1988. The Grid infrastructure provides a secure and efficient way of accessing heterogeneous resource . Enabling scientific applications on Grid has been researched for some time now. In this regard we have successfully enabled Computational Fluid Dynamics (CFD) application which can help CFD community as a whole in effective manner to carry out computational research which requires huge compuational resource beyond once in house capability. This work is part of current on-going project Grid GARUDA funded by Department of Information Technology.
Dynamical electron backscatter diffraction patterns. Part I: pattern simulations.
Callahan, Patrick G; De Graef, Marc
2013-10-01
A new approach for the simulation of dynamic electron backscatter diffraction (EBSD) patterns is introduced. The computational approach merges deterministic dynamic electron-scattering computations based on Bloch waves with a stochastic Monte Carlo (MC) simulation of the energy, depth, and directional distributions of the backscattered electrons (BSEs). An efficient numerical scheme is introduced, based on a modified Lambert projection, for the computation of the scintillator electron count as a function of the position and orientation of the EBSD detector; the approach allows for the rapid computation of an individual EBSD pattern by bi-linear interpolation of a master EBSD pattern. The master pattern stores the BSE yield as a function of the electron exit direction and exit energy and is used along with weight factors extracted from the MC simulation to obtain energy-weighted simulated EBSD patterns. Example simulations for nickel yield realistic patterns and energy-dependent trends in pattern blurring versus filter window energies are in agreement with experimental energy-filtered EBSD observations reported in the literature.
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.
Dynamic Process Simulation for Analysis and Design.
Nuttall, Herbert E., Jr.; Himmelblau, David M.
A computer program for the simulation of complex continuous process in real-time in an interactive mode is described. The program is user oriented, flexible, and provides both numerical and graphic output. The program has been used in classroom teaching and computer aided design. Typical input and output are illustrated for a sample problem to…
New Computer Simulations of Macular Neural Functioning
Ross, Muriel D.; Doshay, D.; Linton, S.; Parnas, B.; Montgomery, K.; Chimento, T.
1994-01-01
We use high performance graphics workstations and supercomputers to study the functional significance of the three-dimensional (3-D) organization of gravity sensors. These sensors have a prototypic architecture foreshadowing more complex systems. Scaled-down simulations run on a Silicon Graphics workstation and scaled-up, 3-D versions run on a Cray Y-MP supercomputer. A semi-automated method of reconstruction of neural tissue from serial sections studied in a transmission electron microscope has been developed to eliminate tedious conventional photography. The reconstructions use a mesh as a step in generating a neural surface for visualization. Two meshes are required to model calyx surfaces. The meshes are connected and the resulting prisms represent the cytoplasm and the bounding membranes. A finite volume analysis method is employed to simulate voltage changes along the calyx in response to synapse activation on the calyx or on calyceal processes. The finite volume method insures that charge is conserved at the calyx-process junction. These and other models indicate that efferent processes act as voltage followers, and that the morphology of some afferent processes affects their functioning. In a final application, morphological information is symbolically represented in three dimensions in a computer. The possible functioning of the connectivities is tested using mathematical interpretations of physiological parameters taken from the literature. Symbolic, 3-D simulations are in progress to probe the functional significance of the connectivities. This research is expected to advance computer-based studies of macular functioning and of synaptic plasticity.
Macromolecular Chain at a Cellular Surface: a Computer Simulation Model
Xie, Jun; Pandey, Ras
2001-06-01
Computer simulations are performed to study conformation and dynamics of relatively large chain macromolecule at the surface of a model cell membrane - a preliminary attempt to ultimately realistic model for protein on a cell membrane. We use a discrete lattice of size Lx × L × L. The chain molecule of length Lc is modelled by consecutive nodes connected by bonds on the trail of a random walk with appropriate constraints such as excluded volume, energy dependent configurational bias, etc. Monte Carlo method is used to move chains via segmental dynamics, i.e., end-move, kink-jump, crank-shaft, reptation, etc. Membrane substrate is designed by an ensemble of short chains on a flat surface. Large chain molecule is then driven toward the membrane by a field. We plan to examine the dynamics of chain macromolecule, spread of its density, and its conformation.
Simulating Flexible-Spacecraft Dynamics and Control
Fedor, Joseph
1987-01-01
Versatile program applies to many types of spacecraft and dynamical problems. Flexible Spacecraft Dynamics and Control program (FSD) developed to aid in simulation of large class of flexible and rigid spacecraft. Extremely versatile and used in attitude dynamics and control analysis as well as in-orbit support of deployment and control of spacecraft. Applicable to inertially oriented spinning, Earth-oriented, or gravity-gradient-stabilized spacecraft. Written in FORTRAN 77.
Molecular dynamics 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.)
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Object Oriented Modelling and Dynamical Simulation
DEFF Research Database (Denmark)
Wagner, Falko Jens; Poulsen, Mikael Zebbelin
1998-01-01
This report with appendix describes the work done in master project at DTU.The goal of the project was to develop a concept for simulation of dynamical systems based on object oriented methods.The result was a library of C++-classes, for use when both building componentbased models and when...... onduction simulation experiments....
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Multiscale Model Approach for Magnetization Dynamics Simulations
De Lucia, Andrea; Tretiakov, Oleg A; Kläui, Mathias
2016-01-01
Simulations of magnetization dynamics in a multiscale environment enable rapid evaluation of the Landau-Lifshitz-Gilbert equation in a mesoscopic sample with nanoscopic accuracy in areas where such accuracy is required. We have developed a multiscale magnetization dynamics simulation approach that can be applied to large systems with spin structures that vary locally on small length scales. To implement this, the conventional micromagnetic simulation framework has been expanded to include a multiscale solving routine. The software selectively simulates different regions of a ferromagnetic sample according to the spin structures located within in order to employ a suitable discretization and use either a micromagnetic or an atomistic model. To demonstrate the validity of the multiscale approach, we simulate the spin wave transmission across the regions simulated with the two different models and different discretizations. We find that the interface between the regions is fully transparent for spin waves with f...
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... an improved stability with a factor of , but the overhead of computer time is a factor of at least two. The conclusion is that the second-order “Verlet”-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated...
Dynamic 3D computed tomography scanner for vascular imaging
Lee, Mark K.; Holdsworth, David W.; Fenster, Aaron
2000-04-01
A 3D dynamic computed-tomography (CT) scanner was developed for imaging objects undergoing periodic motion. The scanner system has high spatial and sufficient temporal resolution to produce quantitative tomographic/volume images of objects such as excised arterial samples perfused under physiological pressure conditions and enables the measurements of the local dynamic elastic modulus (Edyn) of the arteries in the axial and longitudinal directions. The system was comprised of a high resolution modified x-ray image intensifier (XRII) based computed tomographic system and a computer-controlled cardiac flow simulator. A standard NTSC CCD camera with a macro lens was coupled to the electro-optically zoomed XRII to acquire dynamic volumetric images. Through prospective cardiac gating and computer synchronized control, a time-resolved sequence of 20 mm thick high resolution volume images of porcine aortic specimens during one simulated cardiac cycle were obtained. Performance evaluation of the scanners illustrated that tomographic images can be obtained with resolution as high as 3.2 mm-1 with only a 9% decrease in the resolution for objects moving at velocities of 1 cm/s in 2D mode and static spatial resolution of 3.55 mm-1 with only a 14% decrease in the resolution in 3D mode for objects moving at a velocity of 10 cm/s. Application of the system for imaging of intact excised arterial specimens under simulated physiological flow/pressure conditions enabled measurements of the Edyn of the arteries with a precision of +/- kPa for the 3D scanner. Evaluation of the Edyn in the axial and longitudinal direction produced values of 428 +/- 35 kPa and 728 +/- 71 kPa, demonstrating the isotropic and homogeneous viscoelastic nature of the vascular specimens. These values obtained from the Dynamic CT systems were not statistically different (p less than 0.05) from the values obtained by standard uniaxial tensile testing and volumetric measurements.
Parallel Computational Fluid Dynamics: Current Status and Future Requirements
Simon, Horst D.; VanDalsem, William R.; Dagum, Leonardo; Kutler, Paul (Technical Monitor)
1994-01-01
One or the key objectives of the Applied Research Branch in the Numerical Aerodynamic Simulation (NAS) Systems Division at NASA Allies Research Center is the accelerated introduction of highly parallel machines into a full operational environment. In this report we discuss the performance results obtained from the implementation of some computational fluid dynamics (CFD) applications on the Connection Machine CM-2 and the Intel iPSC/860. We summarize some of the experiences made so far with the parallel testbed machines at the NAS Applied Research Branch. Then we discuss the long term computational requirements for accomplishing some of the grand challenge problems in computational aerosciences. We argue that only massively parallel machines will be able to meet these grand challenge requirements, and we outline the computer science and algorithm research challenges ahead.
Computational physics simulation of classical and quantum systems
Scherer, Philipp O J
2017-01-01
This textbook presents basic numerical methods and applies them to a large variety of physical models in multiple computer experiments. Classical algorithms and more recent methods are explained. Partial differential equations are treated generally comparing important methods, and equations of motion are solved by a large number of simple as well as more sophisticated methods. Several modern algorithms for quantum wavepacket motion are compared. The first part of the book discusses the basic numerical methods, while the second part simulates classical and quantum systems. Simple but non-trivial examples from a broad range of physical topics offer readers insights into the numerical treatment but also the simulated problems. Rotational motion is studied in detail, as are simple quantum systems. A two-level system in an external field demonstrates elementary principles from quantum optics and simulation of a quantum bit. Principles of molecular dynamics are shown. Modern bounda ry element methods are presented ...
The Brain Dynamics of Linguistic Computation
Directory of Open Access Journals (Sweden)
Elliot eMurphy
2015-10-01
Full Text Available Neural oscillations at distinct frequencies are increasingly being related to a number of basic and higher cognitive faculties. Oscillations enable the construction of coherently organised neuronal assemblies through establishing transitory temporal correlations. By exploring the elementary operations of the language faculty – labeling, concatenation, cyclic transfer – alongside neural dynamics, a new model of linguistic computation is proposed. It is argued that the universality of language, and the true biological source of Universal Grammar, is not to be found purely in the genome as has long been suggested, but more specifically within the extraordinarily preserved nature of mammalian brain rhythms employed in the computation of linguistic structures. Computational-representational theories are used as a guide in investigating the neurobiological foundations of the human ‘cognome’ – the set of computations performed by the nervous system – and new directions are suggested for how the dynamics of brain (the ‘dynome’ operates and execute linguistic operations. The extent to which brain rhythms are the suitable neuronal processes which can capture the computational properties of the human language faculty is considered against a backdrop of existing cartographic research into the localisation of linguistic interpretation. Particular focus is placed on labeling, the operation elsewhere argued to be species-specific. A Basic Label model of the human cognome-dynome is proposed, leading to clear, causally-addressable empirical predictions, to be investigated by a suggested research program, Dynamic Cognomics. In addition, a distinction between minimal and maximal degrees of explanation is introduced to differentiate between the depth of analysis provided by cartographic, rhythmic, neurochemical and other approaches to computation.