A hybrid parallel architecture for electrostatic interactions in the simulation of dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Yang, Sheng-Chun; Lu, Zhong-Yuan; Qian, Hu-Jun; Wang, Yong-Lei; Han, Jie-Ping

2017-11-01

In this work, we upgraded the electrostatic interaction method of CU-ENUF (Yang, et al., 2016) which first applied CUNFFT (nonequispaced Fourier transforms based on CUDA) to the reciprocal-space electrostatic computation and made the computation of electrostatic interaction done thoroughly in GPU. The upgraded edition of CU-ENUF runs concurrently in a hybrid parallel way that enables the computation parallelizing on multiple computer nodes firstly, then further on the installed GPU in each computer. By this parallel strategy, the size of simulation system will be never restricted to the throughput of a single CPU or GPU. The most critical technical problem is how to parallelize a CUNFFT in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Furthermore, the upgraded method is capable of computing electrostatic interactions for both the atomistic molecular dynamics (MD) and the dissipative particle dynamics (DPD). Finally, the benchmarks conducted for validation and performance indicate that the upgraded method is able to not only present a good precision when setting suitable parameters, but also give an efficient way to compute electrostatic interactions for huge simulation systems. Program Files doi:http://dx.doi.org/10.17632/zncf24fhpv.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: C, C++, and CUDA C Supplementary material: The program is designed for effective electrostatic interactions of large-scale simulation systems, which runs on particular computers equipped with NVIDIA GPUs. It has been tested on (a) single computer node with Intel(R) Core(TM) i7-3770@ 3.40 GHz (CPU) and GTX 980 Ti (GPU), and (b) MPI parallel computer nodes with the same configurations. Nature of problem: For molecular dynamics simulation, the electrostatic interaction is the most time-consuming computation because of its long-range feature and slow convergence in simulation space, which approximately take up most of the total simulation time. Although the parallel method CU-ENUF (Yang et al., 2016) based on GPU has achieved a qualitative leap compared with previous methods in electrostatic interactions computation, the computation capability is limited to the throughput capacity of a single GPU for super-scale simulation system. Therefore, we should look for an effective method to handle the calculation of electrostatic interactions efficiently for a simulation system with super-scale size. Solution method: We constructed a hybrid parallel architecture, in which CPU and GPU are combined to accelerate the electrostatic computation effectively. Firstly, the simulation system is divided into many subtasks via domain-decomposition method. Then MPI (Message Passing Interface) is used to implement the CPU-parallel computation with each computer node corresponding to a particular subtask, and furthermore each subtask in one computer node will be executed in GPU in parallel efficiently. In this hybrid parallel method, the most critical technical problem is how to parallelize a CUNFFT (nonequispaced fast Fourier transform based on CUDA) in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Restrictions: The HP-ENUF is mainly oriented to super-scale system simulations, in which the performance superiority is shown adequately. However, for a small simulation system containing less than 106 particles, the mode of multiple computer nodes has no apparent efficiency advantage or even lower efficiency due to the serious network delay among computer nodes, than the mode of single computer node. References: (1) S.-C. Yang, H.-J. Qian, Z.-Y. Lu, Appl. Comput. Harmon. Anal. 2016, http://dx.doi.org/10.1016/j.acha.2016.04.009. (2) S.-C. Yang, Y.-L. Wang, G.-S. Jiao, H.-J. Qian, Z.-Y. Lu, J. Comput. Chem. 37 (2016) 378. (3) S.-C. Yang, Y.-L. Zhu, H.-J. Qian, Z.-Y. Lu, Appl. Chem. Res. Chin. Univ., 2017, http://dx.doi.org/10.1007/s40242-016-6354-5. (4) Y.-L. Zhu, H. Liu, Z.-W. Li, H.-J. Qian, G. Milano, Z.-Y. Lu, J. Comput. Chem. 34 (2013) 2197.

Computer-aided Instructional System for Transmission Line Simulation.

ERIC Educational Resources Information Center

Reinhard, Erwin A.; Roth, Charles H., Jr.

A computer-aided instructional system has been developed which utilizes dynamic computer-controlled graphic displays and which requires student interaction with a computer simulation in an instructional mode. A numerical scheme has been developed for digital simulation of a uniform, distortionless transmission line with resistive terminations and…

A Multiple-Sessions Interactive Computer-Based Learning Tool for Ability Cultivation in Circuit Simulation

ERIC Educational Resources Information Center

Xu, Q.; Lai, L. L.; Tse, N. C. F.; Ichiyanagi, K.

2011-01-01

An interactive computer-based learning tool with multiple sessions is proposed in this paper, which teaches students to think and helps them recognize the merits and limitations of simulation tools so as to improve their practical abilities in electrical circuit simulation based on the case of a power converter with progressive problems. The…

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.

PubMed

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2016-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.

The Impact of Computer Simulations as Interactive Demonstration Tools on the Performance of Grade 11 Learners in Electromagnetism

ERIC Educational Resources Information Center

Kotoka, Jonas; Kriek, Jeanne

2014-01-01

The impact of computer simulations on the performance of 65 grade 11 learners in electromagnetism in a South African high school in the Mpumalanga province is investigated. Learners did not use the simulations individually, but teachers used them as an interactive demonstration tool. Basic concepts in electromagnetism are difficult to understand…

An Interactive Computer Program for Simulating the Effects of Olivine Fractionation from Basaltic and Ultrabasic Liquids.

ERIC Educational Resources Information Center

Pearce, Thomas H.

1983-01-01

Describes interactive computer program (listing available from author) which simulates olivine fractionation from basaltic/ultrabasic liquid. The menu-driven nature of the program (for Apple II microcomputer) allows students to select ideal Rayleigh fractionation or equilibrium crystallization. (JN)

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

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. PMID:25100924

Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models.

PubMed

Saglam, Ali S; Chong, Lillian T

2016-01-14

An essential baseline for determining the extent to which electrostatic interactions enhance the kinetics of protein-protein association is the "basal" kon, which is the rate constant for association in the absence of electrostatic interactions. However, since such association events are beyond the milliseconds time scale, it has not been practical to compute the basal kon by directly simulating the association with flexible models. Here, we computed the basal kon for barnase and barstar, two of the most rapidly associating proteins, using highly efficient, flexible molecular simulations. These simulations involved (a) pseudoatomic protein models that reproduce the molecular shapes, electrostatic, and diffusion properties of all-atom models, and (b) application of the weighted ensemble path sampling strategy, which enhanced the efficiency of generating association events by >130-fold. We also examined the extent to which the computed basal kon is affected by inclusion of intermolecular hydrodynamic interactions in the simulations.

A cis-regulatory logic simulator.

PubMed

Zeigler, Robert D; Gertz, Jason; Cohen, Barak A

2007-07-27

A major goal of computational studies of gene regulation is to accurately predict the expression of genes based on the cis-regulatory content of their promoters. The development of computational methods to decode the interactions among cis-regulatory elements has been slow, in part, because it is difficult to know, without extensive experimental validation, whether a particular method identifies the correct cis-regulatory interactions that underlie a given set of expression data. There is an urgent need for test expression data in which the interactions among cis-regulatory sites that produce the data are known. The ability to rapidly generate such data sets would facilitate the development and comparison of computational methods that predict gene expression patterns from promoter sequence. We developed a gene expression simulator which generates expression data using user-defined interactions between cis-regulatory sites. The simulator can incorporate additive, cooperative, competitive, and synergistic interactions between regulatory elements. Constraints on the spacing, distance, and orientation of regulatory elements and their interactions may also be defined and Gaussian noise can be added to the expression values. The simulator allows for a data transformation that simulates the sigmoid shape of expression levels from real promoters. We found good agreement between sets of simulated promoters and predicted regulatory modules from real expression data. We present several data sets that may be useful for testing new methodologies for predicting gene expression from promoter sequence. We developed a flexible gene expression simulator that rapidly generates large numbers of simulated promoters and their corresponding transcriptional output based on specified interactions between cis-regulatory sites. When appropriate rule sets are used, the data generated by our simulator faithfully reproduces experimentally derived data sets. We anticipate that using simulated gene expression data sets will facilitate the direct comparison of computational strategies to predict gene expression from promoter sequence. The source code is available online and as additional material. The test sets are available as additional material.

Interactional Personality, Mathematical Simulation, and Prediction of Interpersonal Compatability.

ERIC Educational Resources Information Center

Kunce, Joseph T.; And Others

1981-01-01

Used a mathematical simulation procedure adaptable to an interactional concept of personality to predict the interpersonal compatibility of couples. Strife scores derived from computer simulation of interactional personality data correlated significantly with partner ratings for the quality and the stability of their relationship. Significance…

Development of hardware accelerator for molecular dynamics simulations: a computation board that calculates nonbonded interactions in cooperation with fast multipole method.

PubMed

Amisaki, Takashi; Toyoda, Shinjiro; Miyagawa, Hiroh; Kitamura, Kunihiro

2003-04-15

Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle-particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation ("particle processor") are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein-water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 582-592, 2003

CPU SIM: A Computer Simulator for Use in an Introductory Computer Organization-Architecture Class.

ERIC Educational Resources Information Center

Skrein, Dale

1994-01-01

CPU SIM, an interactive low-level computer simulation package that runs on the Macintosh computer, is described. The program is designed for instructional use in the first or second year of undergraduate computer science, to teach various features of typical computer organization through hands-on exercises. (MSE)

A new strategic neurosurgical planning tool for brainstem cavernous malformations using interactive computer graphics with multimodal fusion images.

PubMed

Kin, Taichi; Nakatomi, Hirofumi; Shojima, Masaaki; Tanaka, Minoru; Ino, Kenji; Mori, Harushi; Kunimatsu, Akira; Oyama, Hiroshi; Saito, Nobuhito

2012-07-01

In this study, the authors used preoperative simulation employing 3D computer graphics (interactive computer graphics) to fuse all imaging data for brainstem cavernous malformations. The authors evaluated whether interactive computer graphics or 2D imaging correlated better with the actual operative field, particularly in identifying a developmental venous anomaly (DVA). The study population consisted of 10 patients scheduled for surgical treatment of brainstem cavernous malformations. Data from preoperative imaging (MRI, CT, and 3D rotational angiography) were automatically fused using a normalized mutual information method, and then reconstructed by a hybrid method combining surface rendering and volume rendering methods. With surface rendering, multimodality and multithreshold techniques for 1 tissue were applied. The completed interactive computer graphics were used for simulation of surgical approaches and assumed surgical fields. Preoperative diagnostic rates for a DVA associated with brainstem cavernous malformation were compared between conventional 2D imaging and interactive computer graphics employing receiver operating characteristic (ROC) analysis. The time required for reconstruction of 3D images was 3-6 hours for interactive computer graphics. Observation in interactive mode required approximately 15 minutes. Detailed anatomical information for operative procedures, from the craniotomy to microsurgical operations, could be visualized and simulated three-dimensionally as 1 computer graphic using interactive computer graphics. Virtual surgical views were consistent with actual operative views. This technique was very useful for examining various surgical approaches. Mean (±SEM) area under the ROC curve for rate of DVA diagnosis was significantly better for interactive computer graphics (1.000±0.000) than for 2D imaging (0.766±0.091; p<0.001, Mann-Whitney U-test). The authors report a new method for automatic registration of preoperative imaging data from CT, MRI, and 3D rotational angiography for reconstruction into 1 computer graphic. The diagnostic rate of DVA associated with brainstem cavernous malformation was significantly better using interactive computer graphics than with 2D images. Interactive computer graphics was also useful in helping to plan the surgical access corridor.

Advanced computational simulations of water waves interacting with wave energy converters

NASA Astrophysics Data System (ADS)

Pathak, Ashish; Freniere, Cole; Raessi, Mehdi

2017-03-01

Wave energy converter (WEC) devices harness the renewable ocean wave energy and convert it into useful forms of energy, e.g. mechanical or electrical. This paper presents an advanced 3D computational framework to study the interaction between water waves and WEC devices. The computational tool solves the full Navier-Stokes equations and considers all important effects impacting the device performance. To enable large-scale simulations in fast turnaround times, the computational solver was developed in an MPI parallel framework. A fast multigrid preconditioned solver is introduced to solve the computationally expensive pressure Poisson equation. The computational solver was applied to two surface-piercing WEC geometries: bottom-hinged cylinder and flap. Their numerically simulated response was validated against experimental data. Additional simulations were conducted to investigate the applicability of Froude scaling in predicting full-scale WEC response from the model experiments.

A heterogeneous system based on GPU and multi-core CPU for real-time fluid and rigid body simulation

NASA Astrophysics Data System (ADS)

da Silva Junior, José Ricardo; Gonzalez Clua, Esteban W.; Montenegro, Anselmo; Lage, Marcos; Dreux, Marcelo de Andrade; Joselli, Mark; Pagliosa, Paulo A.; Kuryla, Christine Lucille

2012-03-01

Computational fluid dynamics in simulation has become an important field not only for physics and engineering areas but also for simulation, computer graphics, virtual reality and even video game development. Many efficient models have been developed over the years, but when many contact interactions must be processed, most models present difficulties or cannot achieve real-time results when executed. The advent of parallel computing has enabled the development of many strategies for accelerating the simulations. Our work proposes a new system which uses some successful algorithms already proposed, as well as a data structure organisation based on a heterogeneous architecture using CPUs and GPUs, in order to process the simulation of the interaction of fluids and rigid bodies. This successfully results in a two-way interaction between them and their surrounding objects. As far as we know, this is the first work that presents a computational collaborative environment which makes use of two different paradigms of hardware architecture for this specific kind of problem. Since our method achieves real-time results, it is suitable for virtual reality, simulation and video game fluid simulation problems.

NASA's Information Power Grid: Large Scale Distributed Computing and Data Management

NASA Technical Reports Server (NTRS)

Johnston, William E.; Vaziri, Arsi; Hinke, Tom; Tanner, Leigh Ann; Feiereisen, William J.; Thigpen, William; Tang, Harry (Technical Monitor)

2001-01-01

Large-scale science and engineering are done through the interaction of people, heterogeneous computing resources, information systems, and instruments, all of which are geographically and organizationally dispersed. The overall motivation for Grids is to facilitate the routine interactions of these resources in order to support large-scale science and engineering. Multi-disciplinary simulations provide a good example of a class of applications that are very likely to require aggregation of widely distributed computing, data, and intellectual resources. Such simulations - e.g. whole system aircraft simulation and whole system living cell simulation - require integrating applications and data that are developed by different teams of researchers frequently in different locations. The research team's are the only ones that have the expertise to maintain and improve the simulation code and/or the body of experimental data that drives the simulations. This results in an inherently distributed computing and data management environment.

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME

PubMed Central

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2017-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments. PMID:28190948

Modeling cation/anion-water interactions in functional aluminosilicate structures.

PubMed

Richards, A J; Barnes, P; Collins, D R; Christodoulos, F; Clark, S M

1995-02-01

A need for the computer simulation of hydration/dehydration processes in functional aluminosilicate structures has been noted. Full and realistic simulations of these systems can be somewhat ambitious and require the aid of interactive computer graphics to identify key structural/chemical units, both in the devising of suitable water-ion simulation potentials and in the analysis of hydrogen-bonding schemes in the subsequent simulation studies. In this article, the former is demonstrated by the assembling of a range of essential water-ion potentials. These span the range of formal charges from +4e to -2e, and are evaluated in the context of three types of structure: a porous zeolite, calcium silicate cement, and layered clay. As an example of the latter, the computer graphics output from Monte Carlo computer simulation studies of hydration/dehydration in calcium-zeolite A is presented.

A Comparison of Four Simulation and Instructional Methods for Endodontic Review.

ERIC Educational Resources Information Center

Sandoval, Victor A.; And Others

1987-01-01

The effects of four different endodontic self-instructional review formats (slide-tape, latent-image simulation, computer text simulation, and computer-assisted video interactive simulation) on senior clinical endodontic performance are compared. Student evaluations, as well as comparative developmental expenditures, are discussed. (Author/MLW)

Interactive Computer Simulation and Animation for Improving Student Learning of Particle Kinetics

ERIC Educational Resources Information Center

Fang, N.; Guo, Y.

2016-01-01

Computer simulation and animation (CSA) has been receiving growing attention and wide application in engineering education in recent years. A new interactive CSA module was developed in the present study to improve student learning of particle kinetics in an undergraduate engineering dynamics course. The unique feature of this CSA module is that…

Computer Simulations as an Integral Part of Intermediate Macroeconomics.

ERIC Educational Resources Information Center

Millerd, Frank W.; Robertson, Alastair R.

1987-01-01

Describes the development of two interactive computer simulations which were fully integrated with other course materials. The simulations illustrate the effects of various real and monetary "demand shocks" on aggregate income, interest rates, and components of spending and economic output. Includes an evaluation of the simulations'…

The Impact of Learner's Prior Knowledge on Their Use of Chemistry Computer Simulations: A Case Study

ERIC Educational Resources Information Center

Liu, Han-Chin; Andre, Thomas; Greenbowe, Thomas

2008-01-01

It is complicated to design a computer simulation that adapts to students with different characteristics. This study documented cases that show how college students' prior chemistry knowledge level affected their interaction with peers and their approach to solving problems with the use of computer simulations that were designed to learn…

Simulation of flexible appendage interactions with Mariner Venus/Mercury attitude control and science platform pointing

NASA Technical Reports Server (NTRS)

Fleischer, G. E.

1973-01-01

A new computer subroutine, which solves the attitude equations of motion for any vehicle idealized as a topological tree of hinge-connected rigid bodies, is used to simulate and analyze science instrument pointing control interaction with a flexible Mariner Venus/Mercury (MVM) spacecraft. The subroutine's user options include linearized or partially linearized hinge-connected models whose computational advantages are demonstrated for the MVM problem. Results of the pointing control/flexible vehicle interaction simulations, including imaging experiment pointing accuracy predictions and implications for MVM science sequence planning, are described in detail.

Cyberpsychology: a human-interaction perspective based on cognitive modeling.

PubMed

Emond, Bruno; West, Robert L

2003-10-01

This paper argues for the relevance of cognitive modeling and cognitive architectures to cyberpsychology. From a human-computer interaction point of view, cognitive modeling can have benefits both for theory and model building, and for the design and evaluation of sociotechnical systems usability. Cognitive modeling research applied to human-computer interaction has two complimentary objectives: (1) to develop theories and computational models of human interactive behavior with information and collaborative technologies, and (2) to use the computational models as building blocks for the design, implementation, and evaluation of interactive technologies. From the perspective of building theories and models, cognitive modeling offers the possibility to anchor cyberpsychology theories and models into cognitive architectures. From the perspective of the design and evaluation of socio-technical systems, cognitive models can provide the basis for simulated users, which can play an important role in usability testing. As an example of application of cognitive modeling to technology design, the paper presents a simulation of interactive behavior with five different adaptive menu algorithms: random, fixed, stacked, frequency based, and activation based. Results of the simulation indicate that fixed menu positions seem to offer the best support for classification like tasks such as filing e-mails. This research is part of the Human-Computer Interaction, and the Broadband Visual Communication research programs at the National Research Council of Canada, in collaboration with the Carleton Cognitive Modeling Lab at Carleton University.

Tools for 3D scientific visualization in computational aerodynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

The purpose is to describe the tools and techniques in use at the NASA Ames Research Center for performing visualization of computational aerodynamics, for example visualization of flow fields from computer simulations of fluid dynamics about vehicles such as the Space Shuttle. The hardware used for visualization is a high-performance graphics workstation connected to a super computer with a high speed channel. At present, the workstation is a Silicon Graphics IRIS 3130, the supercomputer is a CRAY2, and the high speed channel is a hyperchannel. The three techniques used for visualization are post-processing, tracking, and steering. Post-processing analysis is done after the simulation. Tracking analysis is done during a simulation but is not interactive, whereas steering analysis involves modifying the simulation interactively during the simulation. Using post-processing methods, a flow simulation is executed on a supercomputer and, after the simulation is complete, the results of the simulation are processed for viewing. The software in use and under development at NASA Ames Research Center for performing these types of tasks in computational aerodynamics is described. Workstation performance issues, benchmarking, and high-performance networks for this purpose are also discussed as well as descriptions of other hardware for digital video and film recording.

Interactive Simulated Patient: Experiences with Collaborative E-Learning in Medicine

ERIC Educational Resources Information Center

Bergin, Rolf; Youngblood, Patricia; Ayers, Mary K.; Boberg, Jonas; Bolander, Klara; Courteille, Olivier; Dev, Parvati; Hindbeck, Hans; Edward, Leonard E., II; Stringer, Jennifer R.; Thalme, Anders; Fors, Uno G. H.

2003-01-01

Interactive Simulated Patient (ISP) is a computer-based simulation tool designed to provide medical students with the opportunity to practice their clinical problem solving skills. The ISP system allows students to perform most clinical decision-making procedures in a simulated environment, including history taking in natural language, many…

Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.

NASA Astrophysics Data System (ADS)

Elliott, William Dewey

1995-01-01

A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over several simulation timesteps. One MD application described here highlights the utility of including long range contributions to Lennard-Jones potential in constant pressure simulations. Another application shows the time dependence of long range forces in a multiple time step MD simulation.

Interacting with a Computer-Simulated Pet: Factors Influencing Children's Humane Attitudes and Empathy

ERIC Educational Resources Information Center

Tsai, Yueh-Feng; Kaufman, David

2014-01-01

Previous research by Tsai and Kaufman (2010a, 2010b) has suggested that computer-simulated virtual pet dogs can be used as a potential medium to enhance children's development of empathy and humane attitudes toward animals. To gain a deeper understanding of how and why interacting with a virtual pet dog might influence children's social and…

Simulation of Robot Kinematics Using Interactive Computer Graphics.

ERIC Educational Resources Information Center

Leu, M. C.; Mahajan, R.

1984-01-01

Development of a robot simulation program based on geometric transformation softwares available in most computer graphics systems and program features are described. The program can be extended to simulate robots coordinating with external devices (such as tools, fixtures, conveyors) using geometric transformations to describe the…

Exploring Biomolecular Recognition by Modeling and Simulation

NASA Astrophysics Data System (ADS)

Wade, Rebecca

2007-12-01

Biomolecular recognition is complex. The balance between the different molecular properties that contribute to molecular recognition, such as shape, electrostatics, dynamics and entropy, varies from case to case. This, along with the extent of experimental characterization, influences the choice of appropriate computational approaches to study biomolecular interactions. I will present computational studies in which we aim to make concerted use of bioinformatics, biochemical network modeling and molecular simulation techniques to study protein-protein and protein-small molecule interactions and to facilitate computer-aided drug design.

A High Performance Computing Approach to the Simulation of Fluid Solid Interaction Problems with Rigid and Flexible Components (Open Access Publisher’s Version)

DTIC Science & Technology

2014-08-01

performance computing, smoothed particle hydrodynamics, rigid body dynamics, flexible body dynamics ARMAN PAZOUKI ∗, RADU SERBAN ∗, DAN NEGRUT ∗ A...HIGH PERFORMANCE COMPUTING APPROACH TO THE SIMULATION OF FLUID-SOLID INTERACTION PROBLEMS WITH RIGID AND FLEXIBLE COMPONENTS This work outlines a unified...are implemented to model rigid and flexible multibody dynamics. The two- way coupling of the fluid and solid phases is supported through use of

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

PubMed Central

Ando, Tadashi; Chow, Edmond; Saad, Yousef; Skolnick, Jeffrey

2012-01-01

Hydrodynamic interactions play an important role in the dynamics of macromolecules. The most common way to take into account hydrodynamic effects in molecular simulations is in the context of a Brownian dynamics simulation. However, the calculation of correlated Brownian noise vectors in these simulations is computationally very demanding and alternative methods are desirable. This paper studies methods based on Krylov subspaces for computing Brownian noise vectors. These methods are related to Chebyshev polynomial approximations, but do not require eigenvalue estimates. We show that only low accuracy is required in the Brownian noise vectors to accurately compute values of dynamic and static properties of polymer and monodisperse suspension models. With this level of accuracy, the computational time of Krylov subspace methods scales very nearly as O(N2) for the number of particles N up to 10 000, which was the limit tested. The performance of the Krylov subspace methods, especially the “block” version, is slightly better than that of the Chebyshev method, even without taking into account the additional cost of eigenvalue estimates required by the latter. Furthermore, at N = 10 000, the Krylov subspace method is 13 times faster than the exact Cholesky method. Thus, Krylov subspace methods are recommended for performing large-scale Brownian dynamics simulations with hydrodynamic interactions. PMID:22897254

VASA: Interactive Computational Steering of Large Asynchronous Simulation Pipelines for Societal Infrastructure.

PubMed

Ko, Sungahn; Zhao, Jieqiong; Xia, Jing; Afzal, Shehzad; Wang, Xiaoyu; Abram, Greg; Elmqvist, Niklas; Kne, Len; Van Riper, David; Gaither, Kelly; Kennedy, Shaun; Tolone, William; Ribarsky, William; Ebert, David S

2014-12-01

We present VASA, a visual analytics platform consisting of a desktop application, a component model, and a suite of distributed simulation components for modeling the impact of societal threats such as weather, food contamination, and traffic on critical infrastructure such as supply chains, road networks, and power grids. Each component encapsulates a high-fidelity simulation model that together form an asynchronous simulation pipeline: a system of systems of individual simulations with a common data and parameter exchange format. At the heart of VASA is the Workbench, a visual analytics application providing three distinct features: (1) low-fidelity approximations of the distributed simulation components using local simulation proxies to enable analysts to interactively configure a simulation run; (2) computational steering mechanisms to manage the execution of individual simulation components; and (3) spatiotemporal and interactive methods to explore the combined results of a simulation run. We showcase the utility of the platform using examples involving supply chains during a hurricane as well as food contamination in a fast food restaurant chain.

Experiment and simulation for CSI: What are the missing links?

NASA Technical Reports Server (NTRS)

Belvin, W. Keith; Park, K. C.

1989-01-01

Viewgraphs on experiment and simulation for control structure interaction (CSI) are presented. Topics covered include: control structure interaction; typical control/structure interaction system; CSI problem classification; actuator/sensor models; modeling uncertainty; noise models; real-time computations; and discrete versus continuous.

A Turing Machine Simulator.

ERIC Educational Resources Information Center

Navarro, Aaron B.

1981-01-01

Presents a program in Level II BASIC for a TRS-80 computer that simulates a Turing machine and discusses the nature of the device. The program is run interactively and is designed to be used as an educational tool by computer science or mathematics students studying computational or automata theory. (MP)

Simulating complex intracellular processes using object-oriented computational modelling.

PubMed

Johnson, Colin G; Goldman, Jacki P; Gullick, William J

2004-11-01

The aim of this paper is to give an overview of computer modelling and simulation in cellular biology, in particular as applied to complex biochemical processes within the cell. This is illustrated by the use of the techniques of object-oriented modelling, where the computer is used to construct abstractions of objects in the domain being modelled, and these objects then interact within the computer to simulate the system and allow emergent properties to be observed. The paper also discusses the role of computer simulation in understanding complexity in biological systems, and the kinds of information which can be obtained about biology via simulation.

Interactions of Organics within Hydrated Selective Layer of Reverse Osmosis Desalination Membrane: A Combined Experimental and Computational Study.

PubMed

Ghoufi, Aziz; Dražević, Emil; Szymczyk, Anthony

2017-03-07

In this work we have examined a computational approach in predicting the interactions between uncharged organic solutes and polyamide membranes. We used three model organic molecules with identical molecular weights (100.1 g/mol), 4-aminopiperidine, 3,3-dimethyl-2-butanone (pinacolone) and methylisobutyl ketone for which we obtained experimental data on partitioning, diffusion and separation on a typical seawater reverse osmosis (RO) membrane. The interaction energy between the solutes and the membrane phase (fully aromatic polyamide) was computed from molecular dynamics (MD) simulations and the resulting sequence was found to correlate well with the experimental rejections and sorption data. Sorption of the different organic solutes within the membrane skin layer determined from attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) nicely agreed with interaction energies computed from molecular simulations. Qualitative information about solute diffusivity inside the membrane was also extracted from MD simulations while ATR-FTIR experiments indicated strongly hindered diffusion with diffusion coefficients in the membrane about 10 -15 m 2 /s. The computational approach presented here could be a first step toward predicting rejections trends of, for example, hormones and pharmaceuticals by RO dense membranes.

Computing fluid-particle interaction forces for nano-suspension droplet spreading: molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zhou, Weizhou; Shi, Baiou; Webb, Edmund

2017-11-01

Recently, there are many experimental and theoretical studies to understand and control the dynamic spreading of nano-suspension droplets on solid surfaces. However, fundamental understanding of driving forces dictating the kinetics of nano-suspension wetting and spreading, especially capillary forces that manifest during the process, is lacking. Here, we present results from atomic scale simulations that were used to compute forces between suspended particles and advancing liquid fronts. The role of nano-particle size, particle loading, and interaction strength on forces computed from simulations will be discussed. Results demonstrate that increasing the particle size dramatically changes observed wetting behavior from depinning to pinning. From simulations on varying particle size, a relationship between computed forces and particle size is advanced and compared to existing expressions in the literature. High particle loading significantly slowed spreading kinetics, by introducing tortuous transport paths for liquid delivery to the advancing contact line. Lastly, we show how weakening the interaction between the particle and the underlying substrate can change a system from exhibiting pinning behavior to de-pinning.

A Novel Use of Computer Simulation in an Applied Pharmacokinetics Course.

ERIC Educational Resources Information Center

Sullivan, Timothy J.

1982-01-01

The use of a package of interactive computer programs designed to simulate pharmacokinetic monitoring of drug therapy in a required undergraduate applied pharmacokinetics course is described. Students were assigned the problem of maintaining therapeutic drug concentrations in a computer generated "patient" as an adjunct to classroom instruction.…

FACE computer simulation. [Flexible Arm Controls Experiment

NASA Technical Reports Server (NTRS)

Sadeh, Willy Z.; Szmyd, Jeffrey A.

1990-01-01

A computer simulation of the FACE (Flexible Arm Controls Experiment) was conducted to assess its design for use in the Space Shuttle. The FACE is supposed to be a 14-ft long articulate structure with 4 degrees of freedom, consisting of shoulder pitch and yaw, elbow pitch, and wrist pitch. Kinematics of the FACE was simulated to obtain data on arm operation, function, workspace and interaction. Payload capture ability was modeled. The simulation indicates the capability for detailed kinematic simulation and payload capture ability analysis, and the feasibility of real-time simulation was determined. In addition, the potential for interactive real-time training through integration of the simulation with various interface controllers was revealed. At this stage, the flexibility of the arm was not yet considered.

A Computer Simulation of the Trophic Dynamics of an Aquatic System.

ERIC Educational Resources Information Center

Bowker, D. W.; Randerson, P. F.

1989-01-01

Described is a computer program, AQUASIM, which simulates interaction between environmental factors, phytoplankton, zooplankton, and fish in an aquatic ecosystem. The conceptual flow, equations, variables, rate processes, and parameter manipulations are discussed. (CW)

Augmented Reality Simulations on Handheld Computers

ERIC Educational Resources Information Center

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…

Analyzing Robotic Kinematics Via Computed Simulations

NASA Technical Reports Server (NTRS)

Carnahan, Timothy M.

1992-01-01

Computing system assists in evaluation of kinematics of conceptual robot. Displays positions and motions of robotic manipulator within work cell. Also displays interactions between robotic manipulator and other objects. Results of simulation displayed on graphical computer workstation. System includes both off-the-shelf software originally developed for automotive industry and specially developed software. Simulation system also used to design human-equivalent hand, to model optical train in infrared system, and to develop graphical interface for teleoperator simulation system.

Numerical propulsion system simulation

NASA Technical Reports Server (NTRS)

Lytle, John K.; Remaklus, David A.; Nichols, Lester D.

1990-01-01

The cost of implementing new technology in aerospace propulsion systems is becoming prohibitively expensive. One of the major contributors to the high cost is the need to perform many large scale system tests. Extensive testing is used to capture the complex interactions among the multiple disciplines and the multiple components inherent in complex systems. The objective of the Numerical Propulsion System Simulation (NPSS) is to provide insight into these complex interactions through computational simulations. This will allow for comprehensive evaluation of new concepts early in the design phase before a commitment to hardware is made. It will also allow for rapid assessment of field-related problems, particularly in cases where operational problems were encountered during conditions that would be difficult to simulate experimentally. The tremendous progress taking place in computational engineering and the rapid increase in computing power expected through parallel processing make this concept feasible within the near future. However it is critical that the framework for such simulations be put in place now to serve as a focal point for the continued developments in computational engineering and computing hardware and software. The NPSS concept which is described will provide that framework.

Analysis, preliminary design and simulation systems for control-structure interaction problems

NASA Technical Reports Server (NTRS)

Park, K. C.; Alvin, Kenneth F.

1991-01-01

Software aspects of control-structure interaction (CSI) analysis are discussed. The following subject areas are covered: (1) implementation of a partitioned algorithm for simulation of large CSI problems; (2) second-order discrete Kalman filtering equations for CSI simulations; and (3) parallel computations and control of adaptive structures.

High-performance biocomputing for simulating the spread of contagion over large contact networks

PubMed Central

2012-01-01

Background Many important biological problems can be modeled as contagion diffusion processes over interaction networks. This article shows how the EpiSimdemics interaction-based simulation system can be applied to the general contagion diffusion problem. Two specific problems, computational epidemiology and human immune system modeling, are given as examples. We then show how the graphics processing unit (GPU) within each compute node of a cluster can effectively be used to speed-up the execution of these types of problems. Results We show that a single GPU can accelerate the EpiSimdemics computation kernel by a factor of 6 and the entire application by a factor of 3.3, compared to the execution time on a single core. When 8 CPU cores and 2 GPU devices are utilized, the speed-up of the computational kernel increases to 9.5. When combined with effective techniques for inter-node communication, excellent scalability can be achieved without significant loss of accuracy in the results. Conclusions We show that interaction-based simulation systems can be used to model disparate and highly relevant problems in biology. We also show that offloading some of the work to GPUs in distributed interaction-based simulations can be an effective way to achieve increased intra-node efficiency. PMID:22537298

Enhancing Tele-robotics with Immersive Virtual Reality

DTIC Science & Technology

2017-11-03

graduate and undergraduate students within the Digital Gaming and Simulation, Computer Science, and psychology programs have actively collaborated...investigates the use of artificial intelligence and visual computing. Numerous fields across the human-computer interaction and gaming research areas...invested in digital gaming and simulation to cognitively stimulate humans by computers, forming a $10.5B industry [1]. On the other hand, cognitive

Environments for online maritime simulators with cloud computing capabilities

NASA Astrophysics Data System (ADS)

Raicu, Gabriel; Raicu, Alexandra

2016-12-01

This paper presents the cloud computing environments, network principles and methods for graphical development in realistic naval simulation, naval robotics and virtual interactions. The aim of this approach is to achieve a good simulation quality in large networked environments using open source solutions designed for educational purposes. Realistic rendering of maritime environments requires near real-time frameworks with enhanced computing capabilities during distance interactions. E-Navigation concepts coupled with the last achievements in virtual and augmented reality will enhance the overall experience leading to new developments and innovations. We have to deal with a multiprocessing situation using advanced technologies and distributed applications using remote ship scenario and automation of ship operations.

Proton Upset Monte Carlo Simulation

NASA Technical Reports Server (NTRS)

O'Neill, Patrick M.; Kouba, Coy K.; Foster, Charles C.

2009-01-01

The Proton Upset Monte Carlo Simulation (PROPSET) program calculates the frequency of on-orbit upsets in computer chips (for given orbits such as Low Earth Orbit, Lunar Orbit, and the like) from proton bombardment based on the results of heavy ion testing alone. The software simulates the bombardment of modern microelectronic components (computer chips) with high-energy (.200 MeV) protons. The nuclear interaction of the proton with the silicon of the chip is modeled and nuclear fragments from this interaction are tracked using Monte Carlo techniques to produce statistically accurate predictions.

How Science Students Can Learn about Unobservable Phenomena Using Computer-Based Analogies

ERIC Educational Resources Information Center

Trey, L.; Khan, S.

2008-01-01

A novel instructional computer simulation that incorporates a dynamic analogy to represent Le Chatelier's Principle was designed to investigate the contribution of this feature to students' understanding. Two groups of 12th grade Chemistry students (n=15) interacted with the computer simulation during the study. Both groups did the same…

Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation

NASA Technical Reports Server (NTRS)

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.

Learning English with "The Sims": Exploiting Authentic Computer Simulation Games for L2 Learning

ERIC Educational Resources Information Center

Ranalli, Jim

2008-01-01

With their realistic animation, complex scenarios and impressive interactivity, computer simulation games might be able to provide context-rich, cognitively engaging virtual environments for language learning. However, simulation games designed for L2 learners are in short supply. As an alternative, could games designed for the mass-market be…

YASS: A System Simulator for Operating System and Computer Architecture Teaching and Learning

ERIC Educational Resources Information Center

Mustafa, Besim

2013-01-01

A highly interactive, integrated and multi-level simulator has been developed specifically to support both the teachers and the learners of modern computer technologies at undergraduate level. The simulator provides a highly visual and user configurable environment with many pedagogical features aimed at facilitating deep understanding of concepts…

Construction of Interaction Layer on Socio-Environmental Simulation

NASA Astrophysics Data System (ADS)

Torii, Daisuke; Ishida, Toru

In this study, we propose a method to construct a system based on a legacy socio-environmental simulator which enables to design more realistic interaction models in socio-environmetal simulations. First, to provide a computational model suitable for agent interactions, an interaction layer is constructed and connected from outside of a legacy socio-environmental simulator. Next, to configure the agents interacting ability, connection description for controlling the flow of information in the connection area is provided. As a concrete example, we realized an interaction layer by Q which is a scenario description language and connected it to CORMAS, a socio-envirionmental simulator. Finally, we discuss the capability of our method, using the system, in the Fire-Fighter domain.

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Modeling of Tool-Tissue Interactions for Computer-Based Surgical Simulation: A Literature Review

PubMed Central

Misra, Sarthak; Ramesh, K. T.; Okamura, Allison M.

2009-01-01

Surgical simulators present a safe and potentially effective method for surgical training, and can also be used in robot-assisted surgery for pre- and intra-operative planning. Accurate modeling of the interaction between surgical instruments and organs has been recognized as a key requirement in the development of high-fidelity surgical simulators. Researchers have attempted to model tool-tissue interactions in a wide variety of ways, which can be broadly classified as (1) linear elasticity-based, (2) nonlinear (hyperelastic) elasticity-based finite element (FE) methods, and (3) other techniques that not based on FE methods or continuum mechanics. Realistic modeling of organ deformation requires populating the model with real tissue data (which are difficult to acquire in vivo) and simulating organ response in real time (which is computationally expensive). Further, it is challenging to account for connective tissue supporting the organ, friction, and topological changes resulting from tool-tissue interactions during invasive surgical procedures. Overcoming such obstacles will not only help us to model tool-tissue interactions in real time, but also enable realistic force feedback to the user during surgical simulation. This review paper classifies the existing research on tool-tissue interactions for surgical simulators specifically based on the modeling techniques employed and the kind of surgical operation being simulated, in order to inform and motivate future research on improved tool-tissue interaction models. PMID:20119508

Methods for simulation-based analysis of fluid-structure interaction.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barone, Matthew Franklin; Payne, Jeffrey L.

2005-10-01

Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonalmore » decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.« less

Computers for Interactive Learning.

ERIC Educational Resources Information Center

Grabowski, Barbara; Aggen, William

1984-01-01

Analyzes features of computer-based interactive video including sophisticated answer judging, diagnostic feedback, simulation, animation, audible tones, touch sensitive screen, function keys, and video enhancements, and matches these to the characteristics and pedagogical styles of learners. The learner characteristics discussed include internal…

Understanding Emergency Care Delivery Through Computer Simulation Modeling.

PubMed

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

2018-02-01

In 2017, Academic Emergency Medicine convened a consensus conference entitled, "Catalyzing System Change through Health Care Simulation: Systems, Competency, and Outcomes." This article, 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 article 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 article, our goal is to enhance adoption of computer simulation, a set of methods that hold great promise in addressing emergency care organization and design challenges. © 2017 by the Society for Academic Emergency Medicine.

Simulation System for Training in Laparoscopic Surgery

NASA Technical Reports Server (NTRS)

Basdogan, Cagatay; Ho, Chih-Hao

2003-01-01

A computer-based simulation system creates a visual and haptic virtual environment for training a medical practitioner in laparoscopic surgery. Heretofore, it has been common practice to perform training in partial laparoscopic surgical procedures by use of a laparoscopic training box that encloses a pair of laparoscopic tools, objects to be manipulated by the tools, and an endoscopic video camera. However, the surgical procedures simulated by use of a training box are usually poor imitations of the actual ones. The present computer-based system improves training by presenting a more realistic simulated environment to the trainee. The system includes a computer monitor that displays a real-time image of the affected interior region of the patient, showing laparoscopic instruments interacting with organs and tissues, as would be viewed by use of an endoscopic video camera and displayed to a surgeon during a laparoscopic operation. The system also includes laparoscopic tools that the trainee manipulates while observing the image on the computer monitor (see figure). The instrumentation on the tools consists of (1) position and orientation sensors that provide input data for the simulation and (2) actuators that provide force feedback to simulate the contact forces between the tools and tissues. The simulation software includes components that model the geometries of surgical tools, components that model the geometries and physical behaviors of soft tissues, and components that detect collisions between them. Using the measured positions and orientations of the tools, the software detects whether they are in contact with tissues. In the event of contact, the deformations of the tissues and contact forces are computed by use of the geometric and physical models. The image on the computer screen shows tissues deformed accordingly, while the actuators apply the corresponding forces to the distal ends of the tools. For the purpose of demonstration, the system has been set up to simulate the insertion of a flexible catheter in a bile duct. [As thus configured, the system can also be used to simulate other endoscopic procedures (e.g., bronchoscopy and colonoscopy) that include the insertion of flexible tubes into flexible ducts.] A hybrid approach has been followed in developing the software for real-time simulation of the visual and haptic interactions (1) between forceps and the catheter, (2) between the forceps and the duct, and (3) between the catheter and the duct. The deformations of the duct are simulated by finite-element and modalanalysis procedures, using only the most significant vibration modes of the duct for computing deformations and interaction forces. The catheter is modeled as a set of virtual particles uniformly distributed along the center line of the catheter and connected to each other via linear and torsional springs and damping elements. The interactions between the forceps and the duct as well as the catheter are simulated by use of a ray-based haptic-interaction- simulating technique in which the forceps are modeled as connected line segments.

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu

2015-12-07

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence ofmore » a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.« less

Project ITCH: Interactive Digital Simulation in Electrical Engineering Education.

ERIC Educational Resources Information Center

Bailey, F. N.; Kain, R. Y.

A two-stage project is investigating the educational potential of a low-cost time-sharing system used as a simulation tool in Electrical Engineering (EE) education. Phase I involves a pilot study and Phase II a full integration. The system employs interactive computer simulation to teach engineering concepts which are not well handled by…

First Steps towards an Interactive Real-Time Hazard Management Simulation

ERIC Educational Resources Information Center

Gemmell, Alastair M. D.; Finlayson, Ian G.; Marston, Philip G.

2010-01-01

This paper reports on the construction and initial testing of a computer-based interactive flood hazard management simulation, designed for undergraduates taking an applied geomorphology course. Details of the authoring interface utilized to create the simulation are presented. Students act as the managers of civil defence utilities in a fictional…

Numerical propulsion system simulation: An interdisciplinary approach

NASA Technical Reports Server (NTRS)

Nichols, Lester D.; Chamis, Christos C.

1991-01-01

The tremendous progress being made in computational engineering and the rapid growth in computing power that is resulting from parallel processing now make it feasible to consider the use of computer simulations to gain insights into the complex interactions in aerospace propulsion systems and to evaluate new concepts early in the design process before a commitment to hardware is made. Described here is a NASA initiative to develop a Numerical Propulsion System Simulation (NPSS) capability.

Numerical propulsion system simulation - An interdisciplinary approach

NASA Technical Reports Server (NTRS)

Nichols, Lester D.; Chamis, Christos C.

1991-01-01

The tremendous progress being made in computational engineering and the rapid growth in computing power that is resulting from parallel processing now make it feasible to consider the use of computer simulations to gain insights into the complex interactions in aerospace propulsion systems and to evaluate new concepts early in the design process before a commitment to hardware is made. Described here is a NASA initiative to develop a Numerical Propulsion System Simulation (NPSS) capability.

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

NASA Astrophysics Data System (ADS)

Miao, Linling; Young, Charles D.; Sing, Charles E.

2017-07-01

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.

The Benefits & Drawbacks of Integrating Cloud Computing and Interactive Whiteboards in Teacher Preparation

ERIC Educational Resources Information Center

Blue, Elfreda; Tirotta, Rose

2011-01-01

Twenty-first century technology has changed the way tools are used to support and enhance learning and instruction. Cloud computing and interactive white boards, make it possible for learners to interact, simulate, collaborate, and document learning experiences and real world problem-solving. This article discusses how various technologies (blogs,…

Physics Computing '92: Proceedings of the 4th International Conference

NASA Astrophysics Data System (ADS)

de Groot, Robert A.; Nadrchal, Jaroslav

1993-04-01

The Table of Contents for the book is as follows: * Preface * INVITED PAPERS * Ab Initio Theoretical Approaches to the Structural, Electronic and Vibrational Properties of Small Clusters and Fullerenes: The State of the Art * Neural Multigrid Methods for Gauge Theories and Other Disordered Systems * Multicanonical Monte Carlo Simulations * On the Use of the Symbolic Language Maple in Physics and Chemistry: Several Examples * Nonequilibrium Phase Transitions in Catalysis and Population Models * Computer Algebra, Symmetry Analysis and Integrability of Nonlinear Evolution Equations * The Path-Integral Quantum Simulation of Hydrogen in Metals * Digital Optical Computing: A New Approach of Systolic Arrays Based on Coherence Modulation of Light and Integrated Optics Technology * Molecular Dynamics Simulations of Granular Materials * Numerical Implementation of a K.A.M. Algorithm * Quasi-Monte Carlo, Quasi-Random Numbers and Quasi-Error Estimates * What Can We Learn from QMC Simulations * Physics of Fluctuating Membranes * Plato, Apollonius, and Klein: Playing with Spheres * Steady States in Nonequilibrium Lattice Systems * CONVODE: A REDUCE Package for Differential Equations * Chaos in Coupled Rotators * Symplectic Numerical Methods for Hamiltonian Problems * Computer Simulations of Surfactant Self Assembly * High-dimensional and Very Large Cellular Automata for Immunological Shape Space * A Review of the Lattice Boltzmann Method * Electronic Structure of Solids in the Self-interaction Corrected Local-spin-density Approximation * Dedicated Computers for Lattice Gauge Theory Simulations * Physics Education: A Survey of Problems and Possible Solutions * Parallel Computing and Electronic-Structure Theory * High Precision Simulation Techniques for Lattice Field Theory * CONTRIBUTED PAPERS * Case Study of Microscale Hydrodynamics Using Molecular Dynamics and Lattice Gas Methods * Computer Modelling of the Structural and Electronic Properties of the Supported Metal Catalysis * Ordered Particle Simulations for Serial and MIMD Parallel Computers * "NOLP" -- Program Package for Laser Plasma Nonlinear Optics * Algorithms to Solve Nonlinear Least Square Problems * Distribution of Hydrogen Atoms in Pd-H Computed by Molecular Dynamics * A Ray Tracing of Optical System for Protein Crystallography Beamline at Storage Ring-SIBERIA-2 * Vibrational Properties of a Pseudobinary Linear Chain with Correlated Substitutional Disorder * Application of the Software Package Mathematica in Generalized Master Equation Method * Linelist: An Interactive Program for Analysing Beam-foil Spectra * GROMACS: A Parallel Computer for Molecular Dynamics Simulations * GROMACS Method of Virial Calculation Using a Single Sum * The Interactive Program for the Solution of the Laplace Equation with the Elimination of Singularities for Boundary Functions * Random-Number Generators: Testing Procedures and Comparison of RNG Algorithms * Micro-TOPIC: A Tokamak Plasma Impurities Code * Rotational Molecular Scattering Calculations * Orthonormal Polynomial Method for Calibrating of Cryogenic Temperature Sensors * Frame-based System Representing Basis of Physics * The Role of Massively Data-parallel Computers in Large Scale Molecular Dynamics Simulations * Short-range Molecular Dynamics on a Network of Processors and Workstations * An Algorithm for Higher-order Perturbation Theory in Radiative Transfer Computations * Hydrostochastics: The Master Equation Formulation of Fluid Dynamics * HPP Lattice Gas on Transputers and Networked Workstations * Study on the Hysteresis Cycle Simulation Using Modeling with Different Functions on Intervals * Refined Pruning Techniques for Feed-forward Neural Networks * Random Walk Simulation of the Motion of Transient Charges in Photoconductors * The Optical Hysteresis in Hydrogenated Amorphous Silicon * Diffusion Monte Carlo Analysis of Modern Interatomic Potentials for He * A Parallel Strategy for Molecular Dynamics Simulations of Polar Liquids on Transputer Arrays * Distribution of Ions Reflected on Rough Surfaces * The Study of Step Density Distribution During Molecular Beam Epitaxy Growth: Monte Carlo Computer Simulation * Towards a Formal Approach to the Construction of Large-scale Scientific Applications Software * Correlated Random Walk and Discrete Modelling of Propagation through Inhomogeneous Media * Teaching Plasma Physics Simulation * A Theoretical Determination of the Au-Ni Phase Diagram * Boson and Fermion Kinetics in One-dimensional Lattices * Computational Physics Course on the Technical University * Symbolic Computations in Simulation Code Development and Femtosecond-pulse Laser-plasma Interaction Studies * Computer Algebra and Integrated Computing Systems in Education of Physical Sciences * Coordinated System of Programs for Undergraduate Physics Instruction * Program Package MIRIAM and Atomic Physics of Extreme Systems * High Energy Physics Simulation on the T_Node * The Chapman-Kolmogorov Equation as Representation of Huygens' Principle and the Monolithic Self-consistent Numerical Modelling of Lasers * Authoring System for Simulation Developments * Molecular Dynamics Study of Ion Charge Effects in the Structure of Ionic Crystals * A Computational Physics Introductory Course * Computer Calculation of Substrate Temperature Field in MBE System * Multimagnetical Simulation of the Ising Model in Two and Three Dimensions * Failure of the CTRW Treatment of the Quasicoherent Excitation Transfer * Implementation of a Parallel Conjugate Gradient Method for Simulation of Elastic Light Scattering * Algorithms for Study of Thin Film Growth * Algorithms and Programs for Physics Teaching in Romanian Technical Universities * Multicanonical Simulation of 1st order Transitions: Interface Tension of the 2D 7-State Potts Model * Two Numerical Methods for the Calculation of Periodic Orbits in Hamiltonian Systems * Chaotic Behavior in a Probabilistic Cellular Automata? * Wave Optics Computing by a Networked-based Vector Wave Automaton * Tensor Manipulation Package in REDUCE * Propagation of Electromagnetic Pulses in Stratified Media * The Simple Molecular Dynamics Model for the Study of Thermalization of the Hot Nucleon Gas * Electron Spin Polarization in PdCo Alloys Calculated by KKR-CPA-LSD Method * Simulation Studies of Microscopic Droplet Spreading * A Vectorizable Algorithm for the Multicolor Successive Overrelaxation Method * Tetragonality of the CuAu I Lattice and Its Relation to Electronic Specific Heat and Spin Susceptibility * Computer Simulation of the Formation of Metallic Aggregates Produced by Chemical Reactions in Aqueous Solution * Scaling in Growth Models with Diffusion: A Monte Carlo Study * The Nucleus as the Mesoscopic System * Neural Network Computation as Dynamic System Simulation * First-principles Theory of Surface Segregation in Binary Alloys * Data Smooth Approximation Algorithm for Estimating the Temperature Dependence of the Ice Nucleation Rate * Genetic Algorithms in Optical Design * Application of 2D-FFT in the Study of Molecular Exchange Processes by NMR * Advanced Mobility Model for Electron Transport in P-Si Inversion Layers * Computer Simulation for Film Surfaces and its Fractal Dimension * Parallel Computation Techniques and the Structure of Catalyst Surfaces * Educational SW to Teach Digital Electronics and the Corresponding Text Book * Primitive Trinomials (Mod 2) Whose Degree is a Mersenne Exponent * Stochastic Modelisation and Parallel Computing * Remarks on the Hybrid Monte Carlo Algorithm for the ∫4 Model * An Experimental Computer Assisted Workbench for Physics Teaching * A Fully Implicit Code to Model Tokamak Plasma Edge Transport * EXPFIT: An Interactive Program for Automatic Beam-foil Decay Curve Analysis * Mapping Technique for Solving General, 1-D Hamiltonian Systems * Freeway Traffic, Cellular Automata, and Some (Self-Organizing) Criticality * Photonuclear Yield Analysis by Dynamic Programming * Incremental Representation of the Simply Connected Planar Curves * Self-convergence in Monte Carlo Methods * Adaptive Mesh Technique for Shock Wave Propagation * Simulation of Supersonic Coronal Streams and Their Interaction with the Solar Wind * The Nature of Chaos in Two Systems of Ordinary Nonlinear Differential Equations * Considerations of a Window-shopper * Interpretation of Data Obtained by RTP 4-Channel Pulsed Radar Reflectometer Using a Multi Layer Perceptron * Statistics of Lattice Bosons for Finite Systems * Fractal Based Image Compression with Affine Transformations * Algorithmic Studies on Simulation Codes for Heavy-ion Reactions * An Energy-Wise Computer Simulation of DNA-Ion-Water Interactions Explains the Abnormal Structure of Poly[d(A)]:Poly[d(T)] * Computer Simulation Study of Kosterlitz-Thouless-Like Transitions * Problem-oriented Software Package GUN-EBT for Computer Simulation of Beam Formation and Transport in Technological Electron-Optical Systems * Parallelization of a Boundary Value Solver and its Application in Nonlinear Dynamics * The Symbolic Classification of Real Four-dimensional Lie Algebras * Short, Singular Pulses Generation by a Dye Laser at Two Wavelengths Simultaneously * Quantum Monte Carlo Simulations of the Apex-Oxygen-Model * Approximation Procedures for the Axial Symmetric Static Einstein-Maxwell-Higgs Theory * Crystallization on a Sphere: Parallel Simulation on a Transputer Network * FAMULUS: A Software Product (also) for Physics Education * MathCAD vs. FAMULUS -- A Brief Comparison * First-principles Dynamics Used to Study Dissociative Chemisorption * A Computer Controlled System for Crystal Growth from Melt * A Time Resolved Spectroscopic Method for Short Pulsed Particle Emission * Green's Function Computation in Radiative Transfer Theory * Random Search Optimization Technique for One-criteria and Multi-criteria Problems * Hartley Transform Applications to Thermal Drift Elimination in Scanning Tunneling Microscopy * Algorithms of Measuring, Processing and Interpretation of Experimental Data Obtained with Scanning Tunneling Microscope * Time-dependent Atom-surface Interactions * Local and Global Minima on Molecular Potential Energy Surfaces: An Example of N3 Radical * Computation of Bifurcation Surfaces * Symbolic Computations in Quantum Mechanics: Energies in Next-to-solvable Systems * A Tool for RTP Reactor and Lamp Field Design * Modelling of Particle Spectra for the Analysis of Solid State Surface * List of Participants

Spatial interpretation of NASA's Marshall Space Flight Center Payload Operations Control Center using virtual reality technology

NASA Technical Reports Server (NTRS)

Lindsey, Patricia F.

1993-01-01

In its search for higher level computer interfaces and more realistic electronic simulations for measurement and spatial analysis in human factors design, NASA at MSFC is evaluating the functionality of virtual reality (VR) technology. Virtual reality simulation generates a three dimensional environment in which the participant appears to be enveloped. It is a type of interactive simulation in which humans are not only involved, but included. Virtual reality technology is still in the experimental phase, but it appears to be the next logical step after computer aided three-dimensional animation in transferring the viewer from a passive to an active role in experiencing and evaluating an environment. There is great potential for using this new technology when designing environments for more successful interaction, both with the environment and with another participant in a remote location. At the University of North Carolina, a VR simulation of a the planned Sitterson Hall, revealed a flaw in the building's design that had not been observed during examination of the more traditional building plan simulation methods on paper and on computer aided design (CAD) work station. The virtual environment enables multiple participants in remote locations to come together and interact with one another and with the environment. Each participant is capable of seeing herself and the other participants and of interacting with them within the simulated environment.

Thermodynamic and transport properties of nitrogen fluid: Molecular theory and computer simulations

NASA Astrophysics Data System (ADS)

Eskandari Nasrabad, A.; Laghaei, R.

2018-04-01

Computer simulations and various theories are applied to compute the thermodynamic and transport properties of nitrogen fluid. To model the nitrogen interaction, an existing potential in the literature is modified to obtain a close agreement between the simulation results and experimental data for the orthobaric densities. We use the Generic van der Waals theory to calculate the mean free volume and apply the results within the modified Cohen-Turnbull relation to obtain the self-diffusion coefficient. Compared to experimental data, excellent results are obtained via computer simulations for the orthobaric densities, the vapor pressure, the equation of state, and the shear viscosity. We analyze the results of the theory and computer simulations for the various thermophysical properties.

Learner Perceptions of Realism and Magic in Computer Simulations.

ERIC Educational Resources Information Center

Hennessy, Sara; O'Shea, Tim

1993-01-01

Discusses the possible lack of credibility in educational interactive computer simulations. Topics addressed include "Shopping on Mars," a collaborative adventure game for arithmetic calculation that uses direct manipulation in the microworld; the Alternative Reality Kit, a graphical animated environment for creating interactive…

Computer Simulation for Pain Management Education: A Pilot Study.

PubMed

Allred, Kelly; Gerardi, Nicole

2017-10-01

Effective pain management is an elusive concept in acute care. Inadequate knowledge has been identified as a barrier to providing optimal pain management. This study aimed to determine student perceptions of an interactive computer simulation as a potential method for learning pain management, as a motivator to read and learn more about pain management, preference over traditional lecture, and its potential to change nursing practice. A post-computer simulation survey with a mixed-methods descriptive design was used in this study. A college of nursing in a large metropolitan university in the Southeast United States. A convenience sample of 30 nursing students in a Bachelor of Science nursing program. An interactive computer simulation was developed as a potential alternative method of teaching pain management to nursing students. Increases in educational gain as well as its potential to change practice were explored. Each participant was asked to complete a survey consisting of 10 standard 5-point Likert scale items and 5 open-ended questions. The survey was used to evaluate the students' perception of the simulation, specifically related to educational benefit, preference compared with traditional teaching methods, and perceived potential to change nursing practice. Data provided descriptive statistics for initial evaluation of the computer simulation. The responses on the survey suggest nursing students perceive the computer simulation to be entertaining, fun, educational, occasionally preferred over regular lecture, and with potential to change practice. Preliminary data support the use of computer simulation in educating nursing students about pain management. Copyright © 2017 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.

Computational Analysis and Simulation of Empathic Behaviors: a Survey of Empathy Modeling with Behavioral Signal Processing Framework.

PubMed

Xiao, Bo; Imel, Zac E; Georgiou, Panayiotis; Atkins, David C; Narayanan, Shrikanth S

2016-05-01

Empathy is an important psychological process that facilitates human communication and interaction. Enhancement of empathy has profound significance in a range of applications. In this paper, we review emerging directions of research on computational analysis of empathy expression and perception as well as empathic interactions, including their simulation. We summarize the work on empathic expression analysis by the targeted signal modalities (e.g., text, audio, and facial expressions). We categorize empathy simulation studies into theory-based emotion space modeling or application-driven user and context modeling. We summarize challenges in computational study of empathy including conceptual framing and understanding of empathy, data availability, appropriate use and validation of machine learning techniques, and behavior signal processing. Finally, we propose a unified view of empathy computation and offer a series of open problems for future research.

Simulating Microbial Community Patterning Using Biocellion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Seung-Hwa; Kahan, Simon H.; Momeni, Babak

2014-04-17

Mathematical modeling and computer simulation are important tools for understanding complex interactions between cells and their biotic and abiotic environment: similarities and differences between modeled and observed behavior provide the basis for hypothesis forma- tion. Momeni et al. [5] investigated pattern formation in communities of yeast strains engaging in different types of ecological interactions, comparing the predictions of mathematical modeling and simulation to actual patterns observed in wet-lab experiments. However, simu- lations of millions of cells in a three-dimensional community are ex- tremely time-consuming. One simulation run in MATLAB may take a week or longer, inhibiting exploration of the vastmore » space of parameter combinations and assumptions. Improving the speed, scale, and accu- racy of such simulations facilitates hypothesis formation and expedites discovery. Biocellion is a high performance software framework for ac- celerating discrete agent-based simulation of biological systems with millions to trillions of cells. Simulations of comparable scale and accu- racy to those taking a week of computer time using MATLAB require just hours using Biocellion on a multicore workstation. Biocellion fur- ther accelerates large scale, high resolution simulations using cluster computers by partitioning the work to run on multiple compute nodes. Biocellion targets computational biologists who have mathematical modeling backgrounds and basic C++ programming skills. This chap- ter describes the necessary steps to adapt the original Momeni et al.'s model to the Biocellion framework as a case study.« less

Optimization Model for Web Based Multimodal Interactive Simulations.

PubMed

Halic, Tansel; Ahn, Woojin; De, Suvranu

2015-07-15

This paper presents a technique for optimizing the performance of web based multimodal interactive simulations. For such applications where visual quality and the performance of simulations directly influence user experience, overloading of hardware resources may result in unsatisfactory reduction in the quality of the simulation and user satisfaction. However, optimization of simulation performance on individual hardware platforms is not practical. Hence, we present a mixed integer programming model to optimize the performance of graphical rendering and simulation performance while satisfying application specific constraints. Our approach includes three distinct phases: identification, optimization and update . In the identification phase, the computing and rendering capabilities of the client device are evaluated using an exploratory proxy code. This data is utilized in conjunction with user specified design requirements in the optimization phase to ensure best possible computational resource allocation. The optimum solution is used for rendering (e.g. texture size, canvas resolution) and simulation parameters (e.g. simulation domain) in the update phase. Test results are presented on multiple hardware platforms with diverse computing and graphics capabilities to demonstrate the effectiveness of our approach.

Optimization Model for Web Based Multimodal Interactive Simulations

PubMed Central

Halic, Tansel; Ahn, Woojin; De, Suvranu

2015-01-01

This paper presents a technique for optimizing the performance of web based multimodal interactive simulations. For such applications where visual quality and the performance of simulations directly influence user experience, overloading of hardware resources may result in unsatisfactory reduction in the quality of the simulation and user satisfaction. However, optimization of simulation performance on individual hardware platforms is not practical. Hence, we present a mixed integer programming model to optimize the performance of graphical rendering and simulation performance while satisfying application specific constraints. Our approach includes three distinct phases: identification, optimization and update. In the identification phase, the computing and rendering capabilities of the client device are evaluated using an exploratory proxy code. This data is utilized in conjunction with user specified design requirements in the optimization phase to ensure best possible computational resource allocation. The optimum solution is used for rendering (e.g. texture size, canvas resolution) and simulation parameters (e.g. simulation domain) in the update phase. Test results are presented on multiple hardware platforms with diverse computing and graphics capabilities to demonstrate the effectiveness of our approach. PMID:26085713

A parallel interaction potential approach coupled with the immersed boundary method for fully resolved simulations of deformable interfaces and membranes

NASA Astrophysics Data System (ADS)

Spandan, Vamsi; Meschini, Valentina; Ostilla-Mónico, Rodolfo; Lohse, Detlef; Querzoli, Giorgio; de Tullio, Marco D.; Verzicco, Roberto

2017-11-01

In this paper we show and discuss how the deformation dynamics of closed liquid-liquid interfaces (for example drops and bubbles) can be replicated with use of a phenomenological interaction potential model. This new approach to simulate liquid-liquid interfaces is based on the fundamental principle of minimum potential energy where the total potential energy depends on the extent of deformation of a spring network distributed on the surface of the immersed drop or bubble. Simulating liquid-liquid interfaces using this model require computing ad-hoc elastic constants which is done through a reverse-engineered approach. The results from our simulations agree very well with previous studies on the deformation of drops in standard flow configurations such as a deforming drop in a shear flow or cross flow. The interaction potential model is highly versatile, computationally efficient and can be easily incorporated into generic single phase fluid solvers to also simulate complex fluid-structure interaction problems. This is shown by simulating flow in the left ventricle of the heart with mechanical and natural mitral valves where the imposed flow, motion of ventricle and valves dynamically govern the behaviour of each other. Results from these simulations are compared with ad-hoc in-house experimental measurements. Finally, we present a simple and easy to implement parallelisation scheme, as high performance computing is unavoidable when studying large scale problems involving several thousands of simultaneously deforming bodies in highly turbulent flows.

Efficient coarse simulation of a growing avascular tumor

PubMed Central

Kavousanakis, Michail E.; Liu, Ping; Boudouvis, Andreas G.; Lowengrub, John; Kevrekidis, Ioannis G.

2013-01-01

The subject of this work is the development and implementation of algorithms which accelerate the simulation of early stage tumor growth models. Among the different computational approaches used for the simulation of tumor progression, discrete stochastic models (e.g., cellular automata) have been widely used to describe processes occurring at the cell and subcell scales (e.g., cell-cell interactions and signaling processes). To describe macroscopic characteristics (e.g., morphology) of growing tumors, large numbers of interacting cells must be simulated. However, the high computational demands of stochastic models make the simulation of large-scale systems impractical. Alternatively, continuum models, which can describe behavior at the tumor scale, often rely on phenomenological assumptions in place of rigorous upscaling of microscopic models. This limits their predictive power. In this work, we circumvent the derivation of closed macroscopic equations for the growing cancer cell populations; instead, we construct, based on the so-called “equation-free” framework, a computational superstructure, which wraps around the individual-based cell-level simulator and accelerates the computations required for the study of the long-time behavior of systems involving many interacting cells. The microscopic model, e.g., a cellular automaton, which simulates the evolution of cancer cell populations, is executed for relatively short time intervals, at the end of which coarse-scale information is obtained. These coarse variables evolve on slower time scales than each individual cell in the population, enabling the application of forward projection schemes, which extrapolate their values at later times. This technique is referred to as coarse projective integration. Increasing the ratio of projection times to microscopic simulator execution times enhances the computational savings. Crucial accuracy issues arising for growing tumors with radial symmetry are addressed by applying the coarse projective integration scheme in a cotraveling (cogrowing) frame. As a proof of principle, we demonstrate that the application of this scheme yields highly accurate solutions, while preserving the computational savings of coarse projective integration. PMID:22587128

On the concept of the interactive information and simulation system for gas dynamics and multiphysics problems

NASA Astrophysics Data System (ADS)

Bessonov, O.; Silvestrov, P.

2017-02-01

This paper describes the general idea and the first implementation of the Interactive information and simulation system - an integrated environment that combines computational modules for modeling the aerodynamics and aerothermodynamics of re-entry space vehicles with the large collection of different information materials on this topic. The internal organization and the composition of the system are described and illustrated. Examples of the computational and information output are presented. The system has the unified implementation for Windows and Linux operation systems and can be deployed on any modern high-performance personal computer.

Simulation of hypersonic shock wave - laminar boundary layer interactions

NASA Astrophysics Data System (ADS)

Kianvashrad, N.; Knight, D.

2017-06-01

The capability of the Navier-Stokes equations with a perfect gas model for simulation of hypersonic shock wave - laminar boundary layer interactions is assessed. The configuration is a hollow cylinder flare. The experimental data were obtained by Calspan-University of Buffalo (CUBRC) for total enthalpies ranging from 5.07 to 21.85 MJ/kg. Comparison of the computed and experimental surface pressure and heat transfer is performed and the computed §ow¦eld structure is analyzed.

MUSIDH, multiple use of simulated demographic histories, a novel method to reduce computation time in microsimulation models of infectious diseases.

PubMed

Fischer, E A J; De Vlas, S J; Richardus, J H; Habbema, J D F

2008-09-01

Microsimulation of infectious diseases requires simulation of many life histories of interacting individuals. In particular, relatively rare infections such as leprosy need to be studied in very large populations. Computation time increases disproportionally with the size of the simulated population. We present a novel method, MUSIDH, an acronym for multiple use of simulated demographic histories, to reduce computation time. Demographic history refers to the processes of birth, death and all other demographic events that should be unrelated to the natural course of an infection, thus non-fatal infections. MUSIDH attaches a fixed number of infection histories to each demographic history, and these infection histories interact as if being the infection history of separate individuals. With two examples, mumps and leprosy, we show that the method can give a factor 50 reduction in computation time at the cost of a small loss in precision. The largest reductions are obtained for rare infections with complex demographic histories.

A Physics-driven Neural Networks-based Simulation System (PhyNNeSS) for multimodal interactive virtual environments involving nonlinear deformable objects

PubMed Central

De, Suvranu; Deo, Dhannanjay; Sankaranarayanan, Ganesh; Arikatla, Venkata S.

2012-01-01

Background While an update rate of 30 Hz is considered adequate for real time graphics, a much higher update rate of about 1 kHz is necessary for haptics. Physics-based modeling of deformable objects, especially when large nonlinear deformations and complex nonlinear material properties are involved, at these very high rates is one of the most challenging tasks in the development of real time simulation systems. While some specialized solutions exist, there is no general solution for arbitrary nonlinearities. Methods In this work we present PhyNNeSS - a Physics-driven Neural Networks-based Simulation System - to address this long-standing technical challenge. The first step is an off-line pre-computation step in which a database is generated by applying carefully prescribed displacements to each node of the finite element models of the deformable objects. In the next step, the data is condensed into a set of coefficients describing neurons of a Radial Basis Function network (RBFN). During real-time computation, these neural networks are used to reconstruct the deformation fields as well as the interaction forces. Results We present realistic simulation examples from interactive surgical simulation with real time force feedback. As an example, we have developed a deformable human stomach model and a Penrose-drain model used in the Fundamentals of Laparoscopic Surgery (FLS) training tool box. Conclusions A unique computational modeling system has been developed that is capable of simulating the response of nonlinear deformable objects in real time. The method distinguishes itself from previous efforts in that a systematic physics-based pre-computational step allows training of neural networks which may be used in real time simulations. We show, through careful error analysis, that the scheme is scalable, with the accuracy being controlled by the number of neurons used in the simulation. PhyNNeSS has been integrated into SoFMIS (Software Framework for Multimodal Interactive Simulation) for general use. PMID:22629108

Investigation of Carbohydrate Recognition via Computer Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Quentin R.; Lindsay, Richard J.; Petridis, Loukas

Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. Here, we focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We reviewmore » the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.« less

Investigation of Carbohydrate Recognition via Computer Simulation

DOE PAGES

Johnson, Quentin R.; Lindsay, Richard J.; Petridis, Loukas; ...

2015-04-28

Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. Here, we focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We reviewmore » the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.« less

Improvements to information management systems simulator

NASA Technical Reports Server (NTRS)

Bilek, R. W.

1972-01-01

The performance of personnel in the augmentation and improvement of the interactive IMSIM information management simulation model is summarized. With this augmented model, NASA now has even greater capabilities for the simulation of computer system configurations, data processing loads imposed on these configurations, and executive software to control system operations. Through these simulations, NASA has an extremely cost effective capability for the design and analysis of computer-based data management systems.

Design and Application of Interactive Simulations in Problem-Solving in University-Level Physics Education

ERIC Educational Resources Information Center

Ceberio, Mikel; Almudí, José Manuel; Franco, Ángel

2016-01-01

In recent years, interactive computer simulations have been progressively integrated in the teaching of the sciences and have contributed significant improvements in the teaching-learning process. Practicing problem-solving is a key factor in science and engineering education. The aim of this study was to design simulation-based problem-solving…

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors.

PubMed

Glowacki, David R; O'Connor, Michael; Calabró, Gaetano; Price, James; Tew, Philip; Mitchell, Thomas; Hyde, Joseph; Tew, David P; Coughtrie, David J; McIntosh-Smith, Simon

2014-01-01

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude.

Fluid-Structure Interaction in Composite Structures

DTIC Science & Technology

2014-03-01

polymer composite structures. Some previous experimental observations were confirmed using the results from the computer simulations , which also...computer simulations , which also enhanced understanding the effect of FSI on dynamic responses of composite structures. vi THIS PAGE INTENTIONALLY...forces) are applied. A great amount of research has been made using the FEM to study and simulate the cases when the structures are surrounded by

Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

PubMed

Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

2014-12-18

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

PubMed Central

Doblack, Benjamin N.; Allis, Tim; Dávila, Lilian P.

2014-01-01

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced. PMID:25549300

Implementation and performance of FDPS: a framework for developing parallel particle simulation codes

NASA Astrophysics Data System (ADS)

Iwasawa, Masaki; Tanikawa, Ataru; Hosono, Natsuki; Nitadori, Keigo; Muranushi, Takayuki; Makino, Junichiro

2016-08-01

We present the basic idea, implementation, measured performance, and performance model of FDPS (Framework for Developing Particle Simulators). FDPS is an application-development framework which helps researchers to develop simulation programs using particle methods for large-scale distributed-memory parallel supercomputers. A particle-based simulation program for distributed-memory parallel computers needs to perform domain decomposition, exchange of particles which are not in the domain of each computing node, and gathering of the particle information in other nodes which are necessary for interaction calculation. Also, even if distributed-memory parallel computers are not used, in order to reduce the amount of computation, algorithms such as the Barnes-Hut tree algorithm or the Fast Multipole Method should be used in the case of long-range interactions. For short-range interactions, some methods to limit the calculation to neighbor particles are required. FDPS provides all of these functions which are necessary for efficient parallel execution of particle-based simulations as "templates," which are independent of the actual data structure of particles and the functional form of the particle-particle interaction. By using FDPS, researchers can write their programs with the amount of work necessary to write a simple, sequential and unoptimized program of O(N2) calculation cost, and yet the program, once compiled with FDPS, will run efficiently on large-scale parallel supercomputers. A simple gravitational N-body program can be written in around 120 lines. We report the actual performance of these programs and the performance model. The weak scaling performance is very good, and almost linear speed-up was obtained for up to the full system of the K computer. The minimum calculation time per timestep is in the range of 30 ms (N = 107) to 300 ms (N = 109). These are currently limited by the time for the calculation of the domain decomposition and communication necessary for the interaction calculation. We discuss how we can overcome these bottlenecks.

Zonal methods for the parallel execution of range-limited N-body simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowers, Kevin J.; Dror, Ron O.; Shaw, David E.

2007-01-20

Particle simulations in fields ranging from biochemistry to astrophysics require the evaluation of interactions between all pairs of particles separated by less than some fixed interaction radius. The applicability of such simulations is often limited by the time required for calculation, but the use of massive parallelism to accelerate these computations is typically limited by inter-processor communication requirements. Recently, Snir [M. Snir, A note on N-body computations with cutoffs, Theor. Comput. Syst. 37 (2004) 295-318] and Shaw [D.E. Shaw, A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions, J. Comput. Chem. 26 (2005) 1318-1328] independently introducedmore » two distinct methods that offer asymptotic reductions in the amount of data transferred between processors. In the present paper, we show that these schemes represent special cases of a more general class of methods, and introduce several new algorithms in this class that offer practical advantages over all previously described methods for a wide range of problem parameters. We also show that several of these algorithms approach an approximate lower bound on inter-processor data transfer.« less

Numerical simulation of NQR/NMR: Applications in quantum computing.

PubMed

Possa, Denimar; Gaudio, Anderson C; Freitas, Jair C C

2011-04-01

A numerical simulation program able to simulate nuclear quadrupole resonance (NQR) as well as nuclear magnetic resonance (NMR) experiments is presented, written using the Mathematica package, aiming especially applications in quantum computing. The program makes use of the interaction picture to compute the effect of the relevant nuclear spin interactions, without any assumption about the relative size of each interaction. This makes the program flexible and versatile, being useful in a wide range of experimental situations, going from NQR (at zero or under small applied magnetic field) to high-field NMR experiments. Some conditions specifically required for quantum computing applications are implemented in the program, such as the possibility of use of elliptically polarized radiofrequency and the inclusion of first- and second-order terms in the average Hamiltonian expansion. A number of examples dealing with simple NQR and quadrupole-perturbed NMR experiments are presented, along with the proposal of experiments to create quantum pseudopure states and logic gates using NQR. The program and the various application examples are freely available through the link http://www.profanderson.net/files/nmr_nqr.php. Copyright © 2011 Elsevier Inc. All rights reserved.

Application of foam-extend on turbulent fluid-structure interaction

NASA Astrophysics Data System (ADS)

Rege, K.; Hjertager, B. H.

2017-12-01

Turbulent flow around flexible structures is likely to induce structural vibrations which may eventually lead to fatigue failure. In order to assess the fatigue life of these structures, it is necessary to take the action of the flow on the structure into account, but also the influence of the vibrating structure on the fluid flow. This is achieved by performing fluid-structure interaction (FSI) simulations. In this work, we have investigated the capability of a FSI toolkit for the finite volume computational fluid dynamics software foam-extend to simulate turbulence-induced vibrations of a flexible structure. A large-eddy simulation (LES) turbulence model has been implemented to a basic FSI problem of a flexible wall which is placed in a confined, turbulent flow. This problem was simulated for 2.32 seconds. This short simulation required over 200 computation hours, using 20 processor cores. Thereby, it has been shown that the simulation of FSI with LES is possible, but also computationally demanding. In order to make turbulent FSI simulations with foam-extend more applicable, more sophisticated turbulence models and/or faster FSI iteration schemes should be applied.

Dynamic Interactions for Network Visualization and Simulation

DTIC Science & Technology

2009-03-01

projects.htm, Site accessed January 5, 2009. 12. John S. Weir, Major, USAF, Mediated User-Simulator Interactive Command with Visualization ( MUSIC -V). Master’s...Computing Sciences in Colleges, December 2005). 14. Enrique Campos -Nanez, “nscript user manual,” Department of System Engineer- ing University of

Interactive Heat Transfer Simulations for Everyone

ERIC Educational Resources Information Center

Xie, Charles

2012-01-01

Heat transfer is widely taught in secondary Earth science and physics. Researchers have identified many misconceptions related to heat and temperature. These misconceptions primarily stem from hunches developed in everyday life (though the confusions in terminology often worsen them). Interactive computer simulations that visualize thermal energy,…

Engaging Undergraduate Math Majors in Geoscience Research using Interactive Simulations and Computer Art

NASA Astrophysics Data System (ADS)

Matott, L. S.; Hymiak, B.; Reslink, C. F.; Baxter, C.; Aziz, S.

2012-12-01

As part of the NSF-sponsored 'URGE (Undergraduate Research Group Experiences) to Compute' program, Dr. Matott has been collaborating with talented Math majors to explore the design of cost-effective systems to safeguard groundwater supplies from contaminated sites. Such activity is aided by a combination of groundwater modeling, simulation-based optimization, and high-performance computing - disciplines largely unfamiliar to the students at the outset of the program. To help train and engage the students, a number of interactive and graphical software packages were utilized. Examples include: (1) a tutorial for exploring the behavior of evolutionary algorithms and other heuristic optimizers commonly used in simulation-based optimization; (2) an interactive groundwater modeling package for exploring alternative pump-and-treat containment scenarios at a contaminated site in Billings, Montana; (3) the R software package for visualizing various concepts related to subsurface hydrology; and (4) a job visualization tool for exploring the behavior of numerical experiments run on a large distributed computing cluster. Further engagement and excitement in the program was fostered by entering (and winning) a computer art competition run by the Coalition for Academic Scientific Computation (CASC). The winning submission visualizes an exhaustively mapped optimization cost surface and dramatically illustrates the phenomena of artificial minima - valley locations that correspond to designs whose costs are only partially optimal.

Computational Analysis and Simulation of Empathic Behaviors: A Survey of Empathy Modeling with Behavioral Signal Processing Framework

PubMed Central

Xiao, Bo; Imel, Zac E.; Georgiou, Panayiotis; Atkins, David C.; Narayanan, Shrikanth S.

2017-01-01

Empathy is an important psychological process that facilitates human communication and interaction. Enhancement of empathy has profound significance in a range of applications. In this paper, we review emerging directions of research on computational analysis of empathy expression and perception as well as empathic interactions, including their simulation. We summarize the work on empathic expression analysis by the targeted signal modalities (e.g., text, audio, facial expressions). We categorize empathy simulation studies into theory-based emotion space modeling or application-driven user and context modeling. We summarize challenges in computational study of empathy including conceptual framing and understanding of empathy, data availability, appropriate use and validation of machine learning techniques, and behavior signal processing. Finally, we propose a unified view of empathy computation, and offer a series of open problems for future research. PMID:27017830

The design and implementation of CRT displays in the TCV real-time simulation

NASA Technical Reports Server (NTRS)

Leavitt, J. B.; Tariq, S. I.; Steinmetz, G. G.

1975-01-01

The design and application of computer graphics to the Terminal Configured Vehicle (TCV) program were described. A Boeing 737-100 series aircraft was modified with a second flight deck and several computers installed in the passenger cabin. One of the elements in support of the TCV program is a sophisticated simulation system developed to duplicate the operation of the aft flight deck. This facility consists of an aft flight deck simulator, equipped with realistic flight instrumentation, a CDC 6600 computer, and an Adage graphics terminal; this terminal presents to the simulator pilot displays similar to those used on the aircraft with equivalent man-machine interactions. These two displays form the primary flight instrumentation for the pilot and are dynamic images depicting critical flight information. The graphics terminal is a high speed interactive refresh-type graphics system. To support the cockpit display, two remote CRT's were wired in parallel with two of the Adage scopes.

Investigation of prescribed movement in fluid–structure interaction simulation for the human phonation process☆

PubMed Central

Zörner, S.; Kaltenbacher, M.; Döllinger, M.

2013-01-01

In a partitioned approach for computational fluid–structure interaction (FSI) the coupling between fluid and structure causes substantial computational resources. Therefore, a convenient alternative is to reduce the problem to a pure flow simulation with preset movement and applying appropriate boundary conditions. This work investigates the impact of replacing the fully-coupled interface condition with a one-way coupling. To continue to capture structural movement and its effect onto the flow field, prescribed wall movements from separate simulations and/or measurements are used. As an appropriate test case, we apply the different coupling strategies to the human phonation process, which is a highly complex interaction of airflow through the larynx and structural vibration of the vocal folds (VF). We obtain vocal fold vibrations from a fully-coupled simulation and use them as input data for the simplified simulation, i.e. just solving the fluid flow. All computations are performed with our research code CFS++, which is based on the finite element (FE) method. The presented results show that a pure fluid simulation with prescribed structural movement can substitute the fully-coupled approach. However, caution must be used to ensure accurate boundary conditions on the interface, and we found that only a pressure driven flow correctly responds to the physical effects when using specified motion. PMID:24204083

Shock Interaction with Random Spherical Particle Beds

NASA Astrophysics Data System (ADS)

Neal, Chris; Mehta, Yash; Salari, Kambiz; Jackson, Thomas L.; Balachandar, S. "Bala"; Thakur, Siddharth

2016-11-01

In this talk we present results on fully resolved simulations of shock interaction with randomly distributed bed of particles. Multiple simulations were carried out by varying the number of particles to isolate the effect of volume fraction. Major focus of these simulations was to understand 1) the effect of the shockwave and volume fraction on the forces experienced by the particles, 2) the effect of particles on the shock wave, and 3) fluid mediated particle-particle interactions. Peak drag force for particles at different volume fractions show a downward trend as the depth of the bed increased. This can be attributed to dissipation of energy as the shockwave travels through the bed of particles. One of the fascinating observations from these simulations was the fluctuations in different quantities due to presence of multiple particles and their random distribution. These are large simulations with hundreds of particles resulting in large amount of data. We present statistical analysis of the data and make relevant observations. Average pressure in the computational domain is computed to characterize the strengths of the reflected and transmitted waves. We also present flow field contour plots to support our observations. U.S. Department of Energy, National Nuclear Security Administration, Advanced Simulation and Computing Program, as a Cooperative Agreement under the Predictive Science Academic Alliance Program, under Contract No. DE-NA0002378.

A Pilot Study of Computer-Based Simulation Training for Enhancing Family Medicine Residents' Competence in Computerized Settings.

PubMed

Shachak, Aviv; Domb, Sharon; Borycki, Elizabeth; Fong, Nancy; Skyrme, Alison; Kushniruk, Andre; Reis, Shmuel; Ziv, Amitai

2015-01-01

We previously developed a prototype computer-based simulation to teach residents how to integrate better EMR use in the patient-physician interaction. To evaluate the prototype, we conducted usability tests with three non-clinician students, followed by a pilot study with 16 family medicine residents. The pilot study included pre- and post-test surveys of competencies and attitudes related to using the EMR in the consultation and the acceptability of the simulation, as well as 'think aloud' observations. After using the simulation prototypes, the mean scores for competencies and attitudes improved from 14.88/20 to 15.63/20 and from 22.25/30 to 23.13/30, respectively; however, only the difference for competencies was significant (paired t-test; t=-2.535, p=0.023). Mean scores for perceived usefulness and ease of use of the simulation were good (3.81 and 4.10 on a 5-point scale, respectively). Issues identified in usability testing include confusing interaction with some features, preferences for a more interactive representation of the EMR, and more options for shared decision making. In conclusion, computer-based simulation may be an effective and acceptable tool for teaching residents how to better use EMRs in clinical encounters.

Evacuation simulation using Hybrid Space Discretisation and Application to Large Underground Rail Tunnel Station

NASA Astrophysics Data System (ADS)

Chooramun, N.; Lawrence, P. J.; Galea, E. R.

2017-08-01

In all evacuation simulation tools, the space through which agents navigate and interact is represented by one the following methods, namely Coarse regions, Fine nodes and Continuous regions. Each of the spatial representation methods has its benefits and limitations. For instance, the Coarse approach allows simulations to be processed very rapidly, but is unable to represent the interactions of the agents from an individual perspective; the Continuous approach provides a detailed representation of agent movement and interaction but suffers from relatively poor computational performance. The Fine nodal approach presents a compromise between the Continuous and Coarse approaches such that it allows agent interaction to be modelled while providing good computational performance. Our approach for representing space in an evacuation simulation tool differs such that it allows evacuation simulations to be run using a combination of Coarse regions, Fine nodes and Continuous regions. This approach, which we call Hybrid Spatial Discretisation (HSD), is implemented within the buildingEXODUS evacuation simulation software. The HSD incorporates the benefits of each of the spatial representation methods whilst providing an optimal environment for representing agent movement and interaction. In this work, we demonstrate the effectiveness of the HSD through its application to a moderately large case comprising of an underground rail tunnel station with a population of 2,000 agents.

Interactive physically-based sound simulation

NASA Astrophysics Data System (ADS)

Raghuvanshi, Nikunj

The realization of interactive, immersive virtual worlds requires the ability to present a realistic audio experience that convincingly compliments their visual rendering. Physical simulation is a natural way to achieve such realism, enabling deeply immersive virtual worlds. However, physically-based sound simulation is very computationally expensive owing to the high-frequency, transient oscillations underlying audible sounds. The increasing computational power of desktop computers has served to reduce the gap between required and available computation, and it has become possible to bridge this gap further by using a combination of algorithmic improvements that exploit the physical, as well as perceptual properties of audible sounds. My thesis is a step in this direction. My dissertation concentrates on developing real-time techniques for both sub-problems of sound simulation: synthesis and propagation. Sound synthesis is concerned with generating the sounds produced by objects due to elastic surface vibrations upon interaction with the environment, such as collisions. I present novel techniques that exploit human auditory perception to simulate scenes with hundreds of sounding objects undergoing impact and rolling in real time. Sound propagation is the complementary problem of modeling the high-order scattering and diffraction of sound in an environment as it travels from source to listener. I discuss my work on a novel numerical acoustic simulator (ARD) that is hundred times faster and consumes ten times less memory than a high-accuracy finite-difference technique, allowing acoustic simulations on previously-intractable spaces, such as a cathedral, on a desktop computer. Lastly, I present my work on interactive sound propagation that leverages my ARD simulator to render the acoustics of arbitrary static scenes for multiple moving sources and listener in real time, while accounting for scene-dependent effects such as low-pass filtering and smooth attenuation behind obstructions, reverberation, scattering from complex geometry and sound focusing. This is enabled by a novel compact representation that takes a thousand times less memory than a direct scheme, thus reducing memory footprints to fit within available main memory. To the best of my knowledge, this is the only technique and system in existence to demonstrate auralization of physical wave-based effects in real-time on large, complex 3D scenes.

Computational simulation of the creep-rupture process in filamentary composite materials

NASA Technical Reports Server (NTRS)

Slattery, Kerry T.; Hackett, Robert M.

1991-01-01

A computational simulation of the internal damage accumulation which causes the creep-rupture phenomenon in filamentary composite materials is developed. The creep-rupture process involves complex interactions between several damage mechanisms. A statistically-based computational simulation using a time-differencing approach is employed to model these progressive interactions. The finite element method is used to calculate the internal stresses. The fibers are modeled as a series of bar elements which are connected transversely by matrix elements. Flaws are distributed randomly throughout the elements in the model. Load is applied, and the properties of the individual elements are updated at the end of each time step as a function of the stress history. The simulation is continued until failure occurs. Several cases, with different initial flaw dispersions, are run to establish a statistical distribution of the time-to-failure. The calculations are performed on a supercomputer. The simulation results compare favorably with the results of creep-rupture experiments conducted at the Lawrence Livermore National Laboratory.

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Decision Making in Computer-Simulated Experiments.

ERIC Educational Resources Information Center

Suits, J. P.; Lagowski, J. J.

A set of interactive, computer-simulated experiments was designed to respond to the large range of individual differences in aptitude and reasoning ability generally exhibited by students enrolled in first-semester general chemistry. These experiments give students direct experience in the type of decision making needed in an experimental setting.…

Factors Promoting Engaged Exploration with Computer Simulations

ERIC Educational Resources Information Center

Podolefsky, Noah S.; Perkins, Katherine K.; Adams, Wendy K.

2010-01-01

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…

Designing Online Scaffolds for Interactive Computer Simulation

ERIC Educational Resources Information Center

Chen, Ching-Huei; Wu, I-Chia; Jen, Fen-Lan

2013-01-01

The purpose of this study was to examine the effectiveness of online scaffolds in computer simulation to facilitate students' science learning. We first introduced online scaffolds to assist and model students' science learning and to demonstrate how a system embedded with online scaffolds can be designed and implemented to help high school…

Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions.

PubMed

Isele-Holder, Rolf E; Mitchell, Wayne; Ismail, Ahmed E

2012-11-07

For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation of these contributions, we have implemented a particle-particle particle-mesh Ewald solver for dispersion (r(-6)) interactions into the LAMMPS molecular dynamics package. We demonstrate that the solver's O(N log N) scaling behavior allows its application to large-scale simulations. We carefully determine a set of parameters for the solver that provides accurate results and efficient computation. We perform a series of simulations with Lennard-Jones particles, SPC/E water, and hexane to show that with our choice of parameters the dependence of physical results on the chosen cutoff radius is removed. Physical results and computation time of these simulations are compared to results obtained using either a plain cutoff or a traditional Ewald sum for dispersion.

A collision scheme for hybrid fluid-particle simulation of plasmas

NASA Astrophysics Data System (ADS)

Nguyen, Christine; Lim, Chul-Hyun; Verboncoeur, John

2006-10-01

Desorption phenomena at the wall of a tokamak can lead to the introduction of impurities at the edge of a thermonuclear plasma. In particular, the use of carbon as a constituent of the tokamak wall, as planned for ITER, requires the study of carbon and hydrocarbon transport in the plasma, including understanding of collisional interaction with the plasma. These collisions can result in new hydrocarbons, hydrogen, secondary electrons and so on. Computational modeling is a primary tool for studying these phenomena. XOOPIC [1] and OOPD1 are widely used computer modeling tools for the simulation of plasmas. Both are particle type codes. Particle simulation gives more kinetic information than fluid simulation, but more computation time is required. In order to reduce this disadvantage, hybrid simulation has been developed, and applied to the modeling of collisions. Present particle simulation tools such as XOOPIC and OODP1 employ a Monte Carlo model for the collisions between particle species and a neutral background gas defined by its temperature and pressure. In fluid-particle hybrid plasma models, collisions include combinations of particle and fluid interactions categorized by projectile-target pairing: particle-particle, particle-fluid, and fluid-fluid. For verification of this hybrid collision scheme, we compare simulation results to analytic solutions for classical plasma models. [1] Verboncoeur et al. Comput. Phys. Comm. 87, 199 (1995).

QCE: A Simulator for Quantum Computer Hardware

NASA Astrophysics Data System (ADS)

Michielsen, Kristel; de Raedt, Hans

2003-09-01

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. QCE runs in a Windows 98/NT/2000/ME/XP environment. It can be used to validate designs of physically realizable quantum processors and as an interactive educational tool to learn about quantum computers and quantum algorithms. A detailed exposition is given of the implementation of the CNOT and the Toffoli gate, the quantum Fourier transform, Grover's database search algorithm, an order finding algorithm, Shor's algorithm, a three-input adder and a number partitioning algorithm. We also review the results of simulations of an NMR-like quantum computer.

Analyzing Conflict Dynamics with the Aid of an Interactive Microworld Simulator of a Fishing Dispute

ERIC Educational Resources Information Center

Kuperman, Ranan D.

2010-01-01

This article presents findings from a research project that uses an interactive simulator of an imaginary fishing dispute. Subjects operating the simulator play the role of a state leader, while the computer program controls the behavior of a contending state as well as provides all the environmental data associated with the conflict. The…

Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals

NASA Astrophysics Data System (ADS)

Patriarca, M.; Kuronen, A.; Robles, M.; Kaski, K.

2007-01-01

The study of crystal defects and the complex processes underlying their formation and time evolution has motivated the development of the program ALINE for interactive molecular dynamics experiments. This program couples a molecular dynamics code to a Graphical User Interface and runs on a UNIX-X11 Window System platform with the MOTIF library, which is contained in many standard Linux releases. ALINE is written in C, thus giving the user the possibility to modify the source code, and, at the same time, provides an effective and user-friendly framework for numerical experiments, in which the main parameters can be interactively varied and the system visualized in various ways. We illustrate the main features of the program through some examples of detection and dynamical tracking of point-defects, linear defects, and planar defects, such as stacking faults in lattice-mismatched heterostructures. Program summaryTitle of program:ALINE Catalogue identifier:ADYJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYJ_v1_0 Program obtainable from: CPC Program Library, Queen University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers:DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers Installations:Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland Operating systems under which the program has been tested:True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4 Programming language used:Standard C and MOTIF libraries Memory required to execute with typical data:6 Mbytes but may be larger depending on the system size No. of lines in distributed program, including test data, etc.:16 901 No. of bytes in distributed program, including test data, etc.:449 559 Distribution format:tar.gz Nature of physical problem:Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are difficult to detect and track even within numerical experiments, especially when one is interested in studying their dynamical properties and time evolution. Furthermore, traditional simulation methods require the storage of a huge amount of data which in turn may imply a long work for their analysis. Method of solution:Simplifications of the simulation work described above strongly depend also on the computer performance. It has now become possible to realize some of such simplifications thanks to the real possibility of using interactive programs. The solution proposed here is based on the development of an interactive graphical simulation program both for avoiding large storage of data and the subsequent elaboration and analysis as well as for visualizing and tracking many phenomena inside three-dimensional samples. However, the full computational power of traditional simulation programs may not be available in general in programs with graphical user interfaces, due to their interactive nature. Nevertheless interactive programs can still be very useful for detecting processes difficult to visualize, restricting the range or making a fine tuning of the parameters, and tailoring the faster programs toward precise targets. Restrictions on the complexity of the problem:The restrictions on the applicability of the program are related to the computer resources available. The graphical interface and interactivity demand computational resources that depend on the particular numerical simulation to be performed. To preserve a balance between speed and resources, the choice of the number of atoms to be simulated is critical. With an average current computer, simulations of systems with more than 10 5 atoms may not be easily feasible on an interactive scheme. Another restriction is related to the fact that the program was originally designed to simulate systems in the solid phase, so that problems in the simulation may occur if some particular physical quantities are computed beyond the melting point. Typical running time:It depends on the machine architecture, system size, and user needs. Unusual features of the program:In the program, besides the window in which the system is represented in real space, an additional graphical window presenting the real time distribution histogram for different physical variables (such as kinetic or potential energy) is included. Such tool is very interesting for making demonstrative numerical experiments for teaching purposes as well as for research, e.g., for detecting and tracking crystal defects. The program includes: an initial condition builder, an interactive display of the simulation, a set of tools which allow the user to filter through different physical quantities the information—either displayed in real time or printed in the output files—and to perform an efficient search of the interesting regions of parameter space.

Novel systems and methods for quantum communication, quantum computation, and quantum simulation

NASA Astrophysics Data System (ADS)

Gorshkov, Alexey Vyacheslavovich

Precise control over quantum systems can enable the realization of fascinating applications such as powerful computers, secure communication devices, and simulators that can elucidate the physics of complex condensed matter systems. However, the fragility of quantum effects makes it very difficult to harness the power of quantum mechanics. In this thesis, we present novel systems and tools for gaining fundamental insights into the complex quantum world and for bringing practical applications of quantum mechanics closer to reality. We first optimize and show equivalence between a wide range of techniques for storage of photons in atomic ensembles. We describe experiments demonstrating the potential of our optimization algorithms for quantum communication and computation applications. Next, we combine the technique of photon storage with strong atom-atom interactions to propose a robust protocol for implementing the two-qubit photonic phase gate, which is an important ingredient in many quantum computation and communication tasks. In contrast to photon storage, many quantum computation and simulation applications require individual addressing of closely-spaced atoms, ions, quantum dots, or solid state defects. To meet this requirement, we propose a method for coherent optical far-field manipulation of quantum systems with a resolution that is not limited by the wavelength of radiation. While alkali atoms are currently the system of choice for photon storage and many other applications, we develop new methods for quantum information processing and quantum simulation with ultracold alkaline-earth atoms in optical lattices. We show how multiple qubits can be encoded in individual alkaline-earth atoms and harnessed for quantum computing and precision measurements applications. We also demonstrate that alkaline-earth atoms can be used to simulate highly symmetric systems exhibiting spin-orbital interactions and capable of providing valuable insights into strongly correlated physics of transition metal oxides, heavy fermion materials, and spin liquid phases. While ultracold atoms typically exhibit only short-range interactions, numerous exotic phenomena and practical applications require long-range interactions, which can be achieved with ultracold polar molecules. We demonstrate the possibility to engineer a repulsive interaction between polar molecules, which allows for the suppression of inelastic collisions, efficient evaporative cooling, and the creation of novel phases of polar molecules.

Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

PubMed

Bryce, Richard A

2011-04-01

The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

PubMed

Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

2018-02-01

Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field

PubMed Central

Stark, Austin C.; Andrews, Casey T.

2013-01-01

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods – especially with regard to using them to model, for example, intracellular environments – is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields. PMID:24223529

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

PubMed

Stark, Austin C; Andrews, Casey T; Elcock, Adrian H

2013-09-10

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

Computational simulations of the interaction of water waves with pitching flap-type ocean wave energy converters

NASA Astrophysics Data System (ADS)

Pathak, Ashish; Raessi, Mehdi

2016-11-01

Using an in-house computational framework, we have studied the interaction of water waves with pitching flap-type ocean wave energy converters (WECs). The computational framework solves the full 3D Navier-Stokes equations and captures important effects, including the fluid-solid interaction, the nonlinear and viscous effects. The results of the computational tool, is first compared against the experimental data on the response of a flap-type WEC in a wave tank, and excellent agreement is demonstrated. Further simulations at the model and prototype scales are presented to assess the validity of the Froude scaling. The simulations are used to address some important questions, such as the validity range of common WEC modeling approaches that rely heavily on the Froude scaling and the inviscid potential flow theory. Additionally, the simulations examine the role of the Keulegan-Carpenter (KC) number, which is often used as a measure of relative importance of viscous drag on bodies exposed to oscillating flows. The performance of the flap-type WECs is investigated at various KC numbers to establish the relationship between the viscous drag and KC number for such geometry. That is of significant importance because such relationship only exists for simple geometries, e.g., a cylinder. Support from the National Science Foundation is gratefully acknowledged.

Investigations in Computer-Aided Instruction and Computer-Aided Controls. Final Report.

ERIC Educational Resources Information Center

Rosenberg, R.C.; And Others

These research projects, designed to delve into certain relationships between humans and computers, are focused on computer-assisted instruction and on man-computer interaction. One study demonstrates that within the limits of formal engineering theory, a computer simulated laboratory (Dynamic Systems Laboratory) can be built in which freshmen…

Documentation and user guides for SPBLOB: a computer simulation model of the join population dynamics for loblolly pine and the southern pine beetle

Treesearch

John Bishir; James Roberds; Brian Strom; Xiaohai Wan

2009-01-01

SPLOB is a computer simulation model for the interaction between loblolly pine (Pinus taeda L.), the economically most important forest crop in the United States, and the southern pine beetle (SPB: Dendroctonus frontalis Zimm.), the major insect pest for this species. The model simulates loblolly pine stands from time of planting...

ESIM_DSN Web-Enabled Distributed Simulation Network

NASA Technical Reports Server (NTRS)

Bedrossian, Nazareth; Novotny, John

2002-01-01

In this paper, the eSim(sup DSN) approach to achieve distributed simulation capability using the Internet is presented. With this approach a complete simulation can be assembled from component subsystems that run on different computers. The subsystems interact with each other via the Internet The distributed simulation uses a hub-and-spoke type network topology. It provides the ability to dynamically link simulation subsystem models to different computers as well as the ability to assign a particular model to each computer. A proof-of-concept demonstrator is also presented. The eSim(sup DSN) demonstrator can be accessed at http://www.jsc.draper.com/esim which hosts various examples of Web enabled simulations.

CFD simulation of flow through heart: a perspective review.

PubMed

Khalafvand, S S; Ng, E Y K; Zhong, L

2011-01-01

The heart is an organ which pumps blood around the body by contraction of muscular wall. There is a coupled system in the heart containing the motion of wall and the motion of blood fluid; both motions must be computed simultaneously, which make biological computational fluid dynamics (CFD) difficult. The wall of the heart is not rigid and hence proper boundary conditions are essential for CFD modelling. Fluid-wall interaction is very important for real CFD modelling. There are many assumptions for CFD simulation of the heart that make it far from a real model. A realistic fluid-structure interaction modelling the structure by the finite element method and the fluid flow by CFD use more realistic coupling algorithms. This type of method is very powerful to solve the complex properties of the cardiac structure and the sensitive interaction of fluid and structure. The final goal of heart modelling is to simulate the total heart function by integrating cardiac anatomy, electrical activation, mechanics, metabolism and fluid mechanics together, as in the computational framework.

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

PubMed

Mereghetti, Paolo; Wade, Rebecca C

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Cyber-Ed.

ERIC Educational Resources Information Center

Ruben, Barbara

1994-01-01

Reviews a number of interactive environmental computer education networks and software packages. Computer networks include National Geographic Kids Network, Global Lab, and Global Rivers Environmental Education Network. Computer software involve environmental decision making, simulation games, tropical rainforests, the ocean, the greenhouse…

KINPLOT: An Interactive Pharmacokinetics Graphics Program for Digital Computers.

ERIC Educational Resources Information Center

Wilson, Robert C.; And Others

1982-01-01

Inability to see the relevance of mathematics to understanding the time course of drugs in the body may discourage interest in pharmacokinetics. A UNC-developed computer graphics simulation program helps visualize the nature of pharmacokinetic-patient interactions, generates classroom handouts, and is used in the pharmaceuticals industry to…

A multilevel-skin neighbor list algorithm for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Chenglong; Zhao, Mingcan; Hou, Chaofeng; Ge, Wei

2018-01-01

Searching of the interaction pairs and organization of the interaction processes are important steps in molecular dynamics (MD) algorithms and are critical to the overall efficiency of the simulation. Neighbor lists are widely used for these steps, where thicker skin can reduce the frequency of list updating but is discounted by more computation in distance check for the particle pairs. In this paper, we propose a new neighbor-list-based algorithm with a precisely designed multilevel skin which can reduce unnecessary computation on inter-particle distances. The performance advantages over traditional methods are then analyzed against the main simulation parameters on Intel CPUs and MICs (many integrated cores), and are clearly demonstrated. The algorithm can be generalized for various discrete simulations using neighbor lists.

A Parallel Sliding Region Algorithm to Make Agent-Based Modeling Possible for a Large-Scale Simulation: Modeling Hepatitis C Epidemics in Canada.

PubMed

Wong, William W L; Feng, Zeny Z; Thein, Hla-Hla

2016-11-01

Agent-based models (ABMs) are computer simulation models that define interactions among agents and simulate emergent behaviors that arise from the ensemble of local decisions. ABMs have been increasingly used to examine trends in infectious disease epidemiology. However, the main limitation of ABMs is the high computational cost for a large-scale simulation. To improve the computational efficiency for large-scale ABM simulations, we built a parallelizable sliding region algorithm (SRA) for ABM and compared it to a nonparallelizable ABM. We developed a complex agent network and performed two simulations to model hepatitis C epidemics based on the real demographic data from Saskatchewan, Canada. The first simulation used the SRA that processed on each postal code subregion subsequently. The second simulation processed the entire population simultaneously. It was concluded that the parallelizable SRA showed computational time saving with comparable results in a province-wide simulation. Using the same method, SRA can be generalized for performing a country-wide simulation. Thus, this parallel algorithm enables the possibility of using ABM for large-scale simulation with limited computational resources.

Simulations of noble gases adsorbed on graphene

NASA Astrophysics Data System (ADS)

Maiga, Sidi; Gatica, Silvina

2014-03-01

We present results of Grand Canonical Monte Carlo simulations of adsorption of Kr, Ar and Xe on a suspended graphene sheet. We compute the adsorbate-adsorbate interaction by a Lennard-Jones potential. We adopt a hybrid model for the graphene-adsorbate force; in the hybrid model, the potential interaction with the nearest carbon atoms (within a distance rnn) is computed with an atomistic pair potential Ua; for the atoms at r>rnn, we compute the interaction energy as a continuous integration over a carbon uniform sheet with the density of graphene. For the atomistic potential Ua, we assume the anisotropic LJ potential adapted from the graphite-He interaction proposed by Cole et.al. This interaction includes the anisotropy of the C atoms on graphene, which originates in the anisotropic π-bonds. The adsorption isotherms, energy and structure of the layer are obtained and compared with experimental results. We also compare with the adsorption on graphite and carbon nanotubes. This research was supported by NSF/PRDM (Howard University) and NSF (DMR 1006010).

A computer simulation of aircraft evacuation with fire

NASA Technical Reports Server (NTRS)

Middleton, V. E.

1983-01-01

A computer simulation was developed to assess passenger survival during the post-crash evacuation of a transport category aircraft when fire is a major threat. The computer code, FIREVAC, computes individual passenger exit paths and times to exit, taking into account delays and congestion caused by the interaction among the passengers and changing cabin conditions. Simple models for the physiological effects of the toxic cabin atmosphere are included with provision for including more sophisticated models as they become available. Both wide-body and standard-body aircraft may be simulated. Passenger characteristics are assigned stochastically from experimentally derived distributions. Results of simulations of evacuation trials and hypothetical evacuations under fire conditions are presented.

Computer simulation of the processes of inactivation of bacterial cells by dynamic low-coherent speckles

NASA Astrophysics Data System (ADS)

Ulianova, Onega V.; Ulyanov, Sergey S.; Sazanova, Elena V.; Zhihong, Zhang; Sibo, Zhou; Luo, Qingming; Zudina, Irina; Bednov, Andrey

2006-05-01

Biochemical, biophysical and optical aspects of interaction of low-coherent light with bacterial cells have been discussed. Influence of low-coherent speckles on the colonies grows is investigated. It has been demonstrated that effects of light on the inhibition of cells (Francisella Tularensis) are connected with speckle dynamics. The regimes of illumination of cell suspension with purpose of devitalization of hazard bacteria, caused very dangerous infections, such as tularemia, are found. Mathematical model of interaction of low-coherent laser radiation with bacteria suspension has been proposed. Computer simulations of the processes of laser-cells interaction have been carried out.

Programming of a flexible computer simulation to visualize pharmacokinetic-pharmacodynamic models.

PubMed

Lötsch, J; Kobal, G; Geisslinger, G

2004-01-01

Teaching pharmacokinetic-pharmacodynamic (PK/PD) models can be made more effective using computer simulations. We propose the programming of educational PK or PK/PD computer simulations as an alternative to the use of pre-built simulation software. This approach has the advantage of adaptability to non-standard or complicated PK or PK/PD models. Simplicity of the programming procedure was achieved by selecting the LabVIEW programming environment. An intuitive user interface to visualize the time courses of drug concentrations or effects can be obtained with pre-built elements. The environment uses a wiring analogy that resembles electrical circuit diagrams rather than abstract programming code. The goal of high interactivity of the simulation was attained by allowing the program to run in continuously repeating loops. This makes the program behave flexibly to the user input. The programming is described with the aid of a 2-compartment PK simulation. Examples of more sophisticated simulation programs are also given where the PK/PD simulation shows drug input, concentrations in plasma, and at effect site and the effects themselves as a function of time. A multi-compartmental model of morphine, including metabolite kinetics and effects is also included. The programs are available for download from the World Wide Web at http:// www. klinik.uni-frankfurt.de/zpharm/klin/ PKPDsimulation/content.html. For pharmacokineticists who only program occasionally, there is the possibility of building the computer simulation, together with the flexible interactive simulation algorithm for clinical pharmacological teaching in the field of PK/PD models.

Quantum Metropolis sampling.

PubMed

Temme, K; Osborne, T J; Vollbrecht, K G; Poulin, D; Verstraete, F

2011-03-03

The original motivation to build a quantum computer came from Feynman, who imagined a machine capable of simulating generic quantum mechanical systems--a task that is believed to be intractable for classical computers. Such a machine could have far-reaching applications in the simulation of many-body quantum physics in condensed-matter, chemical and high-energy systems. Part of Feynman's challenge was met by Lloyd, who showed how to approximately decompose the time evolution operator of interacting quantum particles into a short sequence of elementary gates, suitable for operation on a quantum computer. However, this left open the problem of how to simulate the equilibrium and static properties of quantum systems. This requires the preparation of ground and Gibbs states on a quantum computer. For classical systems, this problem is solved by the ubiquitous Metropolis algorithm, a method that has basically acquired a monopoly on the simulation of interacting particles. Here we demonstrate how to implement a quantum version of the Metropolis algorithm. This algorithm permits sampling directly from the eigenstates of the Hamiltonian, and thus evades the sign problem present in classical simulations. A small-scale implementation of this algorithm should be achievable with today's technology.

A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE

NASA Astrophysics Data System (ADS)

Fukushige, Toshiyuki; Taiji, Makoto; Makino, Junichiro; Ebisuzaki, Toshikazu; Sugimoto, Daiichiro

1996-09-01

We have developed a parallel, pipelined special-purpose computer for N-body simulations, MD-GRAPE (for "GRAvity PipE"). In gravitational N- body simulations, almost all computing time is spent on the calculation of interactions between particles. GRAPE is specialized hardware to calculate these interactions. It is used with a general-purpose front-end computer that performs all calculations other than the force calculation. MD-GRAPE is the first parallel GRAPE that can calculate an arbitrary central force. A force different from a pure 1/r potential is necessary for N-body simulations with periodic boundary conditions using the Ewald or particle-particle/particle-mesh (P^3^M) method. MD-GRAPE accelerates the calculation of particle-particle force for these algorithms. An MD- GRAPE board has four MD chips and its peak performance is 4.2 GFLOPS. On an MD-GRAPE board, a cosmological N-body simulation takes 6O0(N/10^6^)^3/2^ s per step for the Ewald method, where N is the number of particles, and would take 24O(N/10^6^) s per step for the P^3^M method, in a uniform distribution of particles.

Human-computer interaction in multitask situations

NASA Technical Reports Server (NTRS)

Rouse, W. B.

1977-01-01

Human-computer interaction in multitask decisionmaking situations is considered, and it is proposed that humans and computers have overlapping responsibilities. Queueing theory is employed to model this dynamic approach to the allocation of responsibility between human and computer. Results of simulation experiments are used to illustrate the effects of several system variables including number of tasks, mean time between arrivals of action-evoking events, human-computer speed mismatch, probability of computer error, probability of human error, and the level of feedback between human and computer. Current experimental efforts are discussed and the practical issues involved in designing human-computer systems for multitask situations are considered.

Coupling Visualization, Simulation, and Deep Learning for Ensemble Steering of Complex Energy Models: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Potter, Kristin C; Brunhart-Lupo, Nicholas J; Bush, Brian W

We have developed a framework for the exploration, design, and planning of energy systems that combines interactive visualization with machine-learning based approximations of simulations through a general purpose dataflow API. Our system provides a visual inter- face allowing users to explore an ensemble of energy simulations representing a subset of the complex input parameter space, and spawn new simulations to 'fill in' input regions corresponding to new enegery system scenarios. Unfortunately, many energy simula- tions are far too slow to provide interactive responses. To support interactive feedback, we are developing reduced-form models via machine learning techniques, which provide statistically soundmore » esti- mates of the full simulations at a fraction of the computational cost and which are used as proxies for the full-form models. Fast com- putation and an agile dataflow enhance the engagement with energy simulations, and allow researchers to better allocate computational resources to capture informative relationships within the system and provide a low-cost method for validating and quality-checking large-scale modeling efforts.« less

Prediction of Solution Properties of Flexible-Chain Polymers: A Computer Simulation Undergraduate Experiment

ERIC Educational Resources Information Center

de la Torre, Jose Garcia; Cifre, Jose G. Hernandez; Martinez, M. Carmen Lopez

2008-01-01

This paper describes a computational exercise at undergraduate level that demonstrates the employment of Monte Carlo simulation to study the conformational statistics of flexible polymer chains, and to predict solution properties. Three simple chain models, including excluded volume interactions, have been implemented in a public-domain computer…

Exploring Focal and Aberration Properties of Electrostatic Lenses through Computer Simulation

ERIC Educational Resources Information Center

Sise, Omer; Manura, David J.; Dogan, Mevlut

2008-01-01

The interactive nature of computer simulation allows students to develop a deeper understanding of the laws of charged particle optics. Here, the use of commercially available optical design programs is described as a tool to aid in solving charged particle optics problems. We describe simple and practical demonstrations of basic electrostatic…

Shock-Wave/Boundary-Layer Interactions in Hypersonic Low Density Flows

NASA Technical Reports Server (NTRS)

Moss, James N.; Olejniczak, Joseph

2004-01-01

Results of numerical simulations of Mach 10 air flow over a hollow cylinder-flare and a double-cone are presented where viscous effects are significant. The flow phenomena include shock-shock and shock- boundary-layer interactions with accompanying flow separation, recirculation, and reattachment. The purpose of this study is to promote an understanding of the fundamental gas dynamics resulting from such complex interactions and to clarify the requirements for meaningful simulations of such flows when using the direct simulation Monte Carlo (DSMC) method. Particular emphasis is placed on the sensitivity of computed results to grid resolution. Comparisons of the DSMC results for the hollow cylinder-flare (30 deg.) configuration are made with the results of experimental measurements conducted in the ONERA RSCh wind tunnel for heating, pressure, and the extent of separation. Agreement between computations and measurements for various quantities is good except that for pressure. For the same flow conditions, the double- cone geometry (25 deg.- 65 deg.) produces much stronger interactions, and these interactions are investigated numerically using both DSMC and Navier-Stokes codes. For the double-cone computations, a two orders of magnitude variation in free-stream density (with Reynolds numbers from 247 to 24,7 19) is investigated using both computational methods. For this range of flow conditions, the computational results are in qualitative agreement for the extent of separation with the DSMC method always predicting a smaller separation region. Results from the Navier-Stokes calculations suggest that the flow for the highest density double-cone case may be unsteady; however, the DSMC solution does not show evidence of unsteadiness.

Computational Flow Modeling of Human Upper Airway Breathing

NASA Astrophysics Data System (ADS)

Mylavarapu, Goutham

Computational modeling of biological systems have gained a lot of interest in biomedical research, in the recent past. This thesis focuses on the application of computational simulations to study airflow dynamics in human upper respiratory tract. With advancements in medical imaging, patient specific geometries of anatomically accurate respiratory tracts can now be reconstructed from Magnetic Resonance Images (MRI) or Computed Tomography (CT) scans, with better and accurate details than traditional cadaver cast models. Computational studies using these individualized geometrical models have advantages of non-invasiveness, ease, minimum patient interaction, improved accuracy over experimental and clinical studies. Numerical simulations can provide detailed flow fields including velocities, flow rates, airway wall pressure, shear stresses, turbulence in an airway. Interpretation of these physical quantities will enable to develop efficient treatment procedures, medical devices, targeted drug delivery etc. The hypothesis for this research is that computational modeling can predict the outcomes of a surgical intervention or a treatment plan prior to its application and will guide the physician in providing better treatment to the patients. In the current work, three different computational approaches Computational Fluid Dynamics (CFD), Flow-Structure Interaction (FSI) and Particle Flow simulations were used to investigate flow in airway geometries. CFD approach assumes airway wall as rigid, and relatively easy to simulate, compared to the more challenging FSI approach, where interactions of airway wall deformations with flow are also accounted. The CFD methodology using different turbulence models is validated against experimental measurements in an airway phantom. Two case-studies using CFD, to quantify a pre and post-operative airway and another, to perform virtual surgery to determine the best possible surgery in a constricted airway is demonstrated. The unsteady Large Eddy simulations (LES) and a steady Reynolds Averaged Navier Stokes (RANS) approaches in CFD modeling are discussed. The more challenging FSI approach is modeled first in simple two-dimensional anatomical geometry and then extended to simplified three dimensional geometry and finally in three dimensionally accurate geometries. The concepts of virtual surgery and the differences to CFD are discussed. Finally, the influence of various drug delivery parameters on particle deposition efficiency in airway anatomy are investigated through particle-flow simulations in a nasal airway model.

Two Applications of Simulation in the Educational Environment. Tech Memo.

ERIC Educational Resources Information Center

Thomas, David B.

Two educational computer simulations are described in this paper. One of the simulations is STATSIM, a series of exercises applicable to statistical instruction. The content of the other simulation is comprised of mathematical learning models. Student involvement, the interactive nature of the simulations, and terminal display of materials are…

Development of a Prototype Simulation Executive with Zooming in the Numerical Propulsion System Simulation

NASA Technical Reports Server (NTRS)

Reed, John A.; Afjeh, Abdollah A.

1995-01-01

A major difficulty in designing aeropropulsion systems is that of identifying and understanding the interactions between the separate engine components and disciplines (e.g., fluid mechanics, structural mechanics, heat transfer, material properties, etc.). The traditional analysis approach is to decompose the system into separate components with the interaction between components being evaluated by the application of each of the single disciplines in a sequential manner. Here, one discipline uses information from the calculation of another discipline to determine the effects of component coupling. This approach, however, may not properly identify the consequences of these effects during the design phase, leaving the interactions to be discovered and evaluated during engine testing. This contributes to the time and cost of developing new propulsion systems as, typically, several design-build-test cycles are needed to fully identify multidisciplinary effects and reach the desired system performance. The alternative to sequential isolated component analysis is to use multidisciplinary coupling at a more fundamental level. This approach has been made more plausible due to recent advancements in computation simulation along with application of concurrent engineering concepts. Computer simulation systems designed to provide an environment which is capable of integrating the various disciplines into a single simulation system have been proposed and are currently being developed. One such system is being developed by the Numerical Propulsion System Simulation (NPSS) project. The NPSS project, being developed at the Interdisciplinary Technology Office at the NASA Lewis Research Center is a 'numerical test cell' designed to provide for comprehensive computational design and analysis of aerospace propulsion systems. It will provide multi-disciplinary analyses on a variety of computational platforms, and a user-interface consisting of expert systems, data base management and visualization tools, to allow the designer to investigate the complex interactions inherent in these systems. An interactive programming software system, known as the Application Visualization System (AVS), was utilized for the development of the propulsion system simulation. The modularity of this system provides the ability to couple propulsion system components, as well as disciplines, and provides for the ability to integrate existing, well established analysis codes into the overall system simulation. This feature allows the user to customize the simulation model by inserting desired analysis codes. The prototypical simulation environment for multidisciplinary analysis, called Turbofan Engine System Simulation (TESS), which incorporates many of the characteristics of the simulation environment proposed herein, is detailed.

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

NASA Astrophysics Data System (ADS)

Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

2009-10-01

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

Long-ranged contributions to solvation free energies from theory and short-ranged models

PubMed Central

Remsing, Richard C.; Liu, Shule; Weeks, John D.

2016-01-01

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object. PMID:26929375

PROGRAPE-1: A Programmable, Multi-Purpose Computer for Many-Body Simulations

NASA Astrophysics Data System (ADS)

Hamada, Tsuyoshi; Fukushige, Toshiyuki; Kawai, Atsushi; Makino, Junichiro

2000-10-01

We have developed PROGRAPE-1 (PROgrammable GRAPE-1), a programmable multi-purpose computer for many-body simulations. The main difference between PROGRAPE-1 and ``traditional'' GRAPE systems is that the former uses FPGA (Field Programmable Gate Array) chips as the processing elements, while the latter relies on a hardwired pipeline processor specialized to gravitational interactions. Since the logic implemented in FPGA chips can be reconfigured, we can use PROGRAPE-1 to calculate not only gravitational interactions, but also other forms of interactions, such as the van der Waals force, hydro\\-dynamical interactions in the SPHr calculation, and so on. PROGRAPE-1 comprises two Altera EPF10K100 FPGA chips, each of which contains nominally 100000 gates. To evaluate the programmability and performance of PROGRAPE-1, we implemented a pipeline for gravitational interactions similar to that of GRAPE-3. One pipeline is fitted into a single FPGA chip, operated at 16 MHz clock. Thus, for gravitational interactions, PROGRAPE-1 provided a speed of 0.96 Gflops-equivalent. PROGRAPE will prove to be useful for a wide-range of particle-based simulations in which the calculation cost of interactions other than gravity is high, such as the evaluation of SPH interactions.

An adaptive maneuvering logic computer program for the simulation of one-on-one air-to-air combat. Volume 1: General description

NASA Technical Reports Server (NTRS)

Burgin, G. H.; Fogel, L. J.; Phelps, J. P.

1975-01-01

A technique for computer simulation of air combat is described. Volume 1 decribes the computer program and its development in general terms. Two versions of the program exist. Both incorporate a logic for selecting and executing air combat maneuvers with performance models of specific fighter aircraft. In the batch processing version the flight paths of two aircraft engaged in interactive aerial combat and controlled by the same logic are computed. The realtime version permits human pilots to fly air-to-air combat against the adaptive maneuvering logic (AML) in Langley Differential Maneuvering Simulator (DMS). Volume 2 consists of a detailed description of the computer programs.

Natural three-qubit interactions in one-way quantum computing

NASA Astrophysics Data System (ADS)

Tame, M. S.; Paternostro, M.; Kim, M. S.; Vedral, V.

2006-02-01

We address the effects of natural three-qubit interactions on the computational power of one-way quantum computation. A benefit of using more sophisticated entanglement structures is the ability to construct compact and economic simulations of quantum algorithms with limited resources. We show that the features of our study are embodied by suitably prepared optical lattices, where effective three-spin interactions have been theoretically demonstrated. We use this to provide a compact construction for the Toffoli gate. Information flow and two-qubit interactions are also outlined, together with a brief analysis of relevant sources of imperfection.

An Integrated Crustal Dynamics Simulator

NASA Astrophysics Data System (ADS)

Xing, H. L.; Mora, P.

2007-12-01

Numerical modelling offers an outstanding opportunity to gain an understanding of the crustal dynamics and complex crustal system behaviour. This presentation provides our long-term and ongoing effort on finite element based computational model and software development to simulate the interacting fault system for earthquake forecasting. A R-minimum strategy based finite-element computational model and software tool, PANDAS, for modelling 3-dimensional nonlinear frictional contact behaviour between multiple deformable bodies with the arbitrarily-shaped contact element strategy has been developed by the authors, which builds up a virtual laboratory to simulate interacting fault systems including crustal boundary conditions and various nonlinearities (e.g. from frictional contact, materials, geometry and thermal coupling). It has been successfully applied to large scale computing of the complex nonlinear phenomena in the non-continuum media involving the nonlinear frictional instability, multiple material properties and complex geometries on supercomputers, such as the South Australia (SA) interacting fault system, South California fault model and Sumatra subduction model. It has been also extended and to simulate the hot fractured rock (HFR) geothermal reservoir system in collaboration of Geodynamics Ltd which is constructing the first geothermal reservoir system in Australia and to model the tsunami generation induced by earthquakes. Both are supported by Australian Research Council.

Generating Inviscid and Viscous Fluid Flow Simulations over a Surface Using a Quasi-simultaneous Technique

NASA Technical Reports Server (NTRS)

Sturdza, Peter (Inventor); Martins-Rivas, Herve (Inventor); Suzuki, Yoshifumi (Inventor)

2014-01-01

A fluid-flow simulation over a computer-generated surface is generated using a quasi-simultaneous technique. The simulation includes a fluid-flow mesh of inviscid and boundary-layer fluid cells. An initial fluid property for an inviscid fluid cell is determined using an inviscid fluid simulation that does not simulate fluid viscous effects. An initial boundary-layer fluid property a boundary-layer fluid cell is determined using the initial fluid property and a viscous fluid simulation that simulates fluid viscous effects. An updated boundary-layer fluid property is determined for the boundary-layer fluid cell using the initial fluid property, initial boundary-layer fluid property, and an interaction law. The interaction law approximates the inviscid fluid simulation using a matrix of aerodynamic influence coefficients computed using a two-dimensional surface panel technique and a fluid-property vector. An updated fluid property is determined for the inviscid fluid cell using the updated boundary-layer fluid property.

Simulation tools for robotics research and assessment

NASA Astrophysics Data System (ADS)

Fields, MaryAnne; Brewer, Ralph; Edge, Harris L.; Pusey, Jason L.; Weller, Ed; Patel, Dilip G.; DiBerardino, Charles A.

2016-05-01

The Robotics Collaborative Technology Alliance (RCTA) program focuses on four overlapping technology areas: Perception, Intelligence, Human-Robot Interaction (HRI), and Dexterous Manipulation and Unique Mobility (DMUM). In addition, the RCTA program has a requirement to assess progress of this research in standalone as well as integrated form. Since the research is evolving and the robotic platforms with unique mobility and dexterous manipulation are in the early development stage and very expensive, an alternate approach is needed for efficient assessment. Simulation of robotic systems, platforms, sensors, and algorithms, is an attractive alternative to expensive field-based testing. Simulation can provide insight during development and debugging unavailable by many other means. This paper explores the maturity of robotic simulation systems for applications to real-world problems in robotic systems research. Open source (such as Gazebo and Moby), commercial (Simulink, Actin, LMS), government (ANVEL/VANE), and the RCTA-developed RIVET simulation environments are examined with respect to their application in the robotic research domains of Perception, Intelligence, HRI, and DMUM. Tradeoffs for applications to representative problems from each domain are presented, along with known deficiencies and disadvantages. In particular, no single robotic simulation environment adequately covers the needs of the robotic researcher in all of the domains. Simulation for DMUM poses unique constraints on the development of physics-based computational models of the robot, the environment and objects within the environment, and the interactions between them. Most current robot simulations focus on quasi-static systems, but dynamic robotic motion places an increased emphasis on the accuracy of the computational models. In order to understand the interaction of dynamic multi-body systems, such as limbed robots, with the environment, it may be necessary to build component-level computational models to provide the necessary simulation fidelity for accuracy. However, the Perception domain remains the most problematic for adequate simulation performance due to the often cartoon nature of computer rendering and the inability to model realistic electromagnetic radiation effects, such as multiple reflections, in real-time.

Efficient scatter model for simulation of ultrasound images from computed tomography data

NASA Astrophysics Data System (ADS)

D'Amato, J. P.; Lo Vercio, L.; Rubi, P.; Fernandez Vera, E.; Barbuzza, R.; Del Fresno, M.; Larrabide, I.

2015-12-01

Background and motivation: Real-time ultrasound simulation refers to the process of computationally creating fully synthetic ultrasound images instantly. Due to the high value of specialized low cost training for healthcare professionals, there is a growing interest in the use of this technology and the development of high fidelity systems that simulate the acquisitions of echographic images. The objective is to create an efficient and reproducible simulator that can run either on notebooks or desktops using low cost devices. Materials and methods: We present an interactive ultrasound simulator based on CT data. This simulator is based on ray-casting and provides real-time interaction capabilities. The simulation of scattering that is coherent with the transducer position in real time is also introduced. Such noise is produced using a simplified model of multiplicative noise and convolution with point spread functions (PSF) tailored for this purpose. Results: The computational efficiency of scattering maps generation was revised with an improved performance. This allowed a more efficient simulation of coherent scattering in the synthetic echographic images while providing highly realistic result. We describe some quality and performance metrics to validate these results, where a performance of up to 55fps was achieved. Conclusion: The proposed technique for real-time scattering modeling provides realistic yet computationally efficient scatter distributions. The error between the original image and the simulated scattering image was compared for the proposed method and the state-of-the-art, showing negligible differences in its distribution.

LOS selective fading and AN/FRC-170(V) radio hybrid computer simulation phase A report

NASA Astrophysics Data System (ADS)

Klukis, M. K.; Lyon, T. I.; Walker, R.

1981-09-01

This report documents results of the first phase of modeling, simulation and study of the dual diversity AN/FRC-170(V) radio and frequency selective fading line of sight channel. Both hybrid computer and circuit technologies were used to develop a fast, accurate and flexible simulation tool to investigate changes and proposed improvements to the design of the AN/FRC-170(V) radio. In addition to the simulation study, a remote hybrid computer terminal was provided to DCEC for interactive study of the modeled radio and channel. Simulated performance of the radio for Rayleigh, line of sight two ray channels, and additive noise are included in the report.

The effect of denaturant on protein stability: a Monte Carlo lattice simulation

NASA Astrophysics Data System (ADS)

Choi, Ho Sup; Huh, June; Jo, Won Ho

2003-03-01

Denaturants are the reagents that decrease protein stability by interacting with both nonpolar and polar surfaces of protein when added to the aqueous solvent. However, the physical nature of these interactions has not been clearly understood. It is not easy to elucidate the nature of denaturant theoretically or experimentally. Even in computer simulation, the denaturant atoms are unable to be dealt explicitly due to computationally enormous costs. We have used a lattice model of protein and denaturant. By varying concentration of denaturant and interaction energy between protein and denaturant, we have measured the change of stability of the protein. This simple model reflects the experimental observation that the free energy of unfolding is a linear function of denaturant concentration in the transition range. We have also performed a simulation under isotropic perturbation. In this case, denaturant molecules are not included and a biasing potential is introduced in order to increase the radius of gyration of protein, which incorporates the effect of denaturant implicitly. The calculated free energy landscape and conformational ensembles sampled under this condition is very close to those of simulation using denaturant molecules interacting with protein. We have applied this simple approach for simulating the effect of denaturant to real proteins.

Visualization and Tracking of Parallel CFD Simulations

NASA Technical Reports Server (NTRS)

Vaziri, Arsi; Kremenetsky, Mark

1995-01-01

We describe a system for interactive visualization and tracking of a 3-D unsteady computational fluid dynamics (CFD) simulation on a parallel computer. CM/AVS, a distributed, parallel implementation of a visualization environment (AVS) runs on the CM-5 parallel supercomputer. A CFD solver is run as a CM/AVS module on the CM-5. Data communication between the solver, other parallel visualization modules, and a graphics workstation, which is running AVS, are handled by CM/AVS. Partitioning of the visualization task, between CM-5 and the workstation, can be done interactively in the visual programming environment provided by AVS. Flow solver parameters can also be altered by programmable interactive widgets. This system partially removes the requirement of storing large solution files at frequent time steps, a characteristic of the traditional 'simulate (yields) store (yields) visualize' post-processing approach.

Distributed and collaborative synthetic environments

NASA Technical Reports Server (NTRS)

Bajaj, Chandrajit L.; Bernardini, Fausto

1995-01-01

Fast graphics workstations and increased computing power, together with improved interface technologies, have created new and diverse possibilities for developing and interacting with synthetic environments. A synthetic environment system is generally characterized by input/output devices that constitute the interface between the human senses and the synthetic environment generated by the computer; and a computation system running a real-time simulation of the environment. A basic need of a synthetic environment system is that of giving the user a plausible reproduction of the visual aspect of the objects with which he is interacting. The goal of our Shastra research project is to provide a substrate of geometric data structures and algorithms which allow the distributed construction and modification of the environment, efficient querying of objects attributes, collaborative interaction with the environment, fast computation of collision detection and visibility information for efficient dynamic simulation and real-time scene display. In particular, we address the following issues: (1) A geometric framework for modeling and visualizing synthetic environments and interacting with them. We highlight the functions required for the geometric engine of a synthetic environment system. (2) A distribution and collaboration substrate that supports construction, modification, and interaction with synthetic environments on networked desktop machines.

Effective Student Learning of Fractions with an Interactive Simulation

ERIC Educational Resources Information Center

Hensberry, Karina K. R.; Moore, Emily B.; Perkins, Katherine K.

2015-01-01

Computer technology, when coupled with reform-based teaching practices, has been shown to be an effective way to support student learning of mathematics. The quality of the technology itself, as well as how it is used, impacts how much students learn. Interactive simulations are dynamic virtual environments similar to virtual manipulatives that…

An Interactive Simulation System for Modeling Stands, Harvests, and Machines

Treesearch

Jingxin Wang; W. Dale Greene

1999-01-01

A interactive computer simulation program models stands, harvest, and machine factors and evaluates their interatcitons while performing felling, skidding, or fowarding activities. A stand generator allows the user to generate either natural or planted stands. Fellings with chainsaw, drive-to-tree feller-bunchers, or harvesters and extraction with grapple skidders or...

DTkid: Interactive Simulation Software for Training Tutors of Children with Autism

ERIC Educational Resources Information Center

Randell, Tom; Hall, Martin; Bizo, Lewis; Remington, Bob

2007-01-01

Discrete-trial training (DTT) relies critically on implementation by trained tutors. We report three experiments carried out in the development of "DTkid"--interactive computer simulation software that presents "SIMon", a realistic virtual child with whom novice tutors can learn and practise DTT techniques. Experiments 1 and 2 exposed groups of…

Dyadic brain modelling, mirror systems and the ontogenetic ritualization of ape gesture

PubMed Central

Arbib, Michael; Ganesh, Varsha; Gasser, Brad

2014-01-01

The paper introduces dyadic brain modelling, offering both a framework for modelling the brains of interacting agents and a general framework for simulating and visualizing the interactions generated when the brains (and the two bodies) are each coded up in computational detail. It models selected neural mechanisms in ape brains supportive of social interactions, including putative mirror neuron systems inspired by macaque neurophysiology but augmented by increased access to proprioceptive state. Simulation results for a reduced version of the model show ritualized gesture emerging from interactions between a simulated child and mother ape. PMID:24778382

Dyadic brain modelling, mirror systems and the ontogenetic ritualization of ape gesture.

PubMed

Arbib, Michael; Ganesh, Varsha; Gasser, Brad

2014-01-01

The paper introduces dyadic brain modelling, offering both a framework for modelling the brains of interacting agents and a general framework for simulating and visualizing the interactions generated when the brains (and the two bodies) are each coded up in computational detail. It models selected neural mechanisms in ape brains supportive of social interactions, including putative mirror neuron systems inspired by macaque neurophysiology but augmented by increased access to proprioceptive state. Simulation results for a reduced version of the model show ritualized gesture emerging from interactions between a simulated child and mother ape.

Computational fluid dynamics uses in fluid dynamics/aerodynamics education

NASA Technical Reports Server (NTRS)

Holst, Terry L.

1994-01-01

The field of computational fluid dynamics (CFD) has advanced to the point where it can now be used for the purpose of fluid dynamics physics education. Because of the tremendous wealth of information available from numerical simulation, certain fundamental concepts can be efficiently communicated using an interactive graphical interrogation of the appropriate numerical simulation data base. In other situations, a large amount of aerodynamic information can be communicated to the student by interactive use of simple CFD tools on a workstation or even in a personal computer environment. The emphasis in this presentation is to discuss ideas for how this process might be implemented. Specific examples, taken from previous publications, will be used to highlight the presentation.

A digital computer program for the dynamic interaction simulation of controls and structure (DISCOS), volume 1

NASA Technical Reports Server (NTRS)

Bodley, C. S.; Devers, A. D.; Park, A. C.; Frisch, H. P.

1978-01-01

A theoretical development and associated digital computer program system for the dynamic simulation and stability analysis of passive and actively controlled spacecraft are 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 is 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. In addition, the program system is used for designing attitude control systems and for evaluating total dynamic system performance, including time domain response and frequency domain stability analyses.

Interactive 3D display simulator for autostereoscopic smart pad

NASA Astrophysics Data System (ADS)

Choe, Yeong-Seon; Lee, Ho-Dong; Park, Min-Chul; Son, Jung-Young; Park, Gwi-Tae

2012-06-01

There is growing interest of displaying 3D images on a smart pad for entertainments and information services. Designing and realizing various types of 3D displays on the smart pad is not easy for costs and given time. Software simulation can be an alternative method to save and shorten the development. In this paper, we propose a 3D display simulator for autostereoscopic smart pad. It simulates light intensity of each view and crosstalk for smart pad display panels. Designers of 3D display for smart pad can interactively simulate many kinds of autostereoscopic displays interactively by changing parameters required for panel design. Crosstalk to reduce leakage of one eye's image into the image of the other eye, and light intensity for computing visual comfort zone are important factors in designing autostereoscopic display for smart pad. Interaction enables intuitive designs. This paper describes an interactive 3D display simulator for autostereoscopic smart pad.

Interactive Electronic Circuit Simulation on Small Computer Systems

DTIC Science & Technology

1979-11-01

longer needed. Do not return it to the originator. UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE (Whan Dots Entered) REPORT DOCUMENTATION PAGE... CLASSIFICATION OF THIS PAGE(H7i»n Data Entend) Interactive-mode circuit simulation and batch-mode circuit simulation on minicomputers are compared...on the circuit Q. For circuits with Q less than 1, this ratio is typically 10:1. UNCLASSIFIED 2 SECURITY CLASSIFICATION OF THIS PAGEflWiim Data

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

PubMed Central

Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

2013-01-01

Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules. As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.g., in cells. Stokesian dynamics (SD) is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. This algorithm traditionally involves an O(N3) operation to compute Brownian forces at each time step, although asymptotically faster but more complex SD methods are now available. Motivated by the idea of hydrodynamic screening, the far-field part of the hydrodynamic matrix in SD may be approximated by a diagonal matrix, which is equivalent to assuming that long range hydrodynamic interactions are completely screened. This approximation allows sparse matrix methods to be used, which can reduce the apparent computational scaling to O(N). Previously there were several simulation studies using this approximation for monodisperse suspensions. Here, we employ newly designed preconditioned iterative methods for both the computation of Brownian forces and the solution of linear systems, and consider the validity of this approximation in polydisperse suspensions. We evaluate the accuracy of the diagonal approximation method using an intracellular-like suspension. The diffusivities of particles obtained with this approximation are close to those with the original method. However, this approximation underestimates intermolecular correlated motions, which is a trade-off between accuracy and computing efficiency. The new method makes it possible to perform large-scale and long-time simulation with an approximate accounting of hydrodynamic interactions. PMID:24089734

RESTSIM: A Simulation Model That Highlights Decision Making under Conditions of Uncertainty.

ERIC Educational Resources Information Center

Zinkhan, George M.; Taylor, James R.

1983-01-01

Describes RESTSIM, an interactive computer simulation program for graduate and upper-level undergraduate management, marketing, and retailing courses, which introduces naive users to simulation as a decision support technique, and provides a vehicle for studying various statistical procedures for evaluating simulation output. (MBR)

NON-SPATIAL CALIBRATIONS OF A GENERAL UNIT MODEL FOR ECOSYSTEM SIMULATIONS. (R825792)

EPA Science Inventory

General Unit Models simulate system interactions aggregated within one spatial unit of resolution. For unit models to be applicable to spatial computer simulations, they must be formulated generally enough to simulate all habitat elements within the landscape. We present the d...

NON-SPATIAL CALIBRATIONS OF A GENERAL UNIT MODEL FOR ECOSYSTEM SIMULATIONS. (R827169)

EPA Science Inventory

General Unit Models simulate system interactions aggregated within one spatial unit of resolution. For unit models to be applicable to spatial computer simulations, they must be formulated generally enough to simulate all habitat elements within the landscape. We present the d...

Local rules simulation of the kinetics of virus capsid self-assembly.

PubMed

Schwartz, R; Shor, P W; Prevelige, P E; Berger, B

1998-12-01

A computer model is described for studying the kinetics of the self-assembly of icosahedral viral capsids. Solution of this problem is crucial to an understanding of the viral life cycle, which currently cannot be adequately addressed through laboratory techniques. The abstract simulation model employed to address this is based on the local rules theory of. Proc. Natl. Acad. Sci. USA. 91:7732-7736). It is shown that the principle of local rules, generalized with a model of kinetics and other extensions, can be used to simulate complicated problems in self-assembly. This approach allows for a computationally tractable molecular dynamics-like simulation of coat protein interactions while retaining many relevant features of capsid self-assembly. Three simple simulation experiments are presented to illustrate the use of this model. These show the dependence of growth and malformation rates on the energetics of binding interactions, the tolerance of errors in binding positions, and the concentration of subunits in the examples. These experiments demonstrate a tradeoff within the model between growth rate and fidelity of assembly for the three parameters. A detailed discussion of the computational model is also provided.

3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model.

PubMed

Spühler, Jeannette H; Jansson, Johan; Jansson, Niclas; Hoffman, Johan

2018-01-01

Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework.

3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model

PubMed Central

Spühler, Jeannette H.; Jansson, Johan; Jansson, Niclas; Hoffman, Johan

2018-01-01

Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework. PMID:29713288

Large-Eddy/Lattice Boltzmann Simulations of Micro-blowing Strategies for Subsonic and Supersonic Drag Control

NASA Technical Reports Server (NTRS)

Menon, Suresh

2003-01-01

This report summarizes the progress made in the first 8 to 9 months of this research. The Lattice Boltzmann Equation (LBE) methodology for Large-eddy Simulations (LES) of microblowing has been validated using a jet-in-crossflow test configuration. In this study, the flow intake is also simulated to allow the interaction to occur naturally. The Lattice Boltzmann Equation Large-eddy Simulations (LBELES) approach is capable of capturing not only the flow features associated with the flow, such as hairpin vortices and recirculation behind the jet, but also is able to show better agreement with experiments when compared to previous RANS predictions. The LBELES is shown to be computationally very efficient and therefore, a viable method for simulating the injection process. Two strategies have been developed to simulate multi-hole injection process as in the experiment. In order to allow natural interaction between the injected fluid and the primary stream, the flow intakes for all the holes have to be simulated. The LBE method is computationally efficient but is still 3D in nature and therefore, there may be some computational penalty. In order to study a large number or holes, a new 1D subgrid model has been developed that will simulate a reduced form of the Navier-Stokes equation in these holes.

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

PubMed Central

Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

2013-01-01

This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. PMID:23913979

PyFly: A fast, portable aerodynamics simulator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia, Daniel; Ghommem, M.; Collier, Nathaniel O.

Here, we present a fast, user-friendly implementation of a potential flow solver based on the unsteady vortex lattice method (UVLM), namely PyFly. UVLM computes the aerodynamic loads applied on lifting surfaces while capturing the unsteady effects such as the added mass forces, the growth of bound circulation, and the wake while assuming that the flow separation location is known a priori. This method is based on discretizing the body surface into a lattice of vortex rings and relies on the Biot–Savart law to construct the velocity field at every point in the simulated domain. We introduce the pointwise approximation approachmore » to simulate the interactions of the far-field vortices to overcome the computational burden associated with the classical implementation of UVLM. The computational framework uses the Python programming language to provide an easy to handle user interface while the computational kernels are written in Fortran. The mixed language approach enables high performance regarding solution time and great flexibility concerning easiness of code adaptation to different system configurations and applications. The computational tool predicts the unsteady aerodynamic behavior of multiple moving bodies (e.g., flapping wings, rotating blades, suspension bridges) subject to incoming air. The aerodynamic simulator can also deal with enclosure effects, multi-body interactions, and B-spline representation of body shapes. Finally, we simulate different aerodynamic problems to illustrate the usefulness and effectiveness of PyFly.« less

PyFly: A fast, portable aerodynamics simulator

DOE PAGES

Garcia, Daniel; Ghommem, M.; Collier, Nathaniel O.; ...

2018-03-14

Here, we present a fast, user-friendly implementation of a potential flow solver based on the unsteady vortex lattice method (UVLM), namely PyFly. UVLM computes the aerodynamic loads applied on lifting surfaces while capturing the unsteady effects such as the added mass forces, the growth of bound circulation, and the wake while assuming that the flow separation location is known a priori. This method is based on discretizing the body surface into a lattice of vortex rings and relies on the Biot–Savart law to construct the velocity field at every point in the simulated domain. We introduce the pointwise approximation approachmore » to simulate the interactions of the far-field vortices to overcome the computational burden associated with the classical implementation of UVLM. The computational framework uses the Python programming language to provide an easy to handle user interface while the computational kernels are written in Fortran. The mixed language approach enables high performance regarding solution time and great flexibility concerning easiness of code adaptation to different system configurations and applications. The computational tool predicts the unsteady aerodynamic behavior of multiple moving bodies (e.g., flapping wings, rotating blades, suspension bridges) subject to incoming air. The aerodynamic simulator can also deal with enclosure effects, multi-body interactions, and B-spline representation of body shapes. Finally, we simulate different aerodynamic problems to illustrate the usefulness and effectiveness of PyFly.« less

Interactive computer simulations of knee-replacement surgery.

PubMed

Gunther, Stephen B; Soto, Gabriel E; Colman, William W

2002-07-01

Current surgical training programs in the United States are based on an apprenticeship model. This model is outdated because it does not provide conceptual scaffolding, promote collaborative learning, or offer constructive reinforcement. Our objective was to create a more useful approach by preparing students and residents for operative cases using interactive computer simulations of surgery. Total-knee-replacement surgery (TKR) is an ideal procedure to model on the computer because there is a systematic protocol for the procedure. Also, this protocol is difficult to learn by the apprenticeship model because of the multiple instruments that must be used in a specific order. We designed an interactive computer tutorial to teach medical students and residents how to perform knee-replacement surgery. We also aimed to reinforce the specific protocol of the operative procedure. Our final goal was to provide immediate, constructive feedback. We created a computer tutorial by generating three-dimensional wire-frame models of the surgical instruments. Next, we applied a surface to the wire-frame models using three-dimensional modeling. Finally, the three-dimensional models were animated to simulate the motions of an actual TKR. The tutorial is a step-by-step tutorial that teaches and tests the correct sequence of steps in a TKR. The student or resident must select the correct instruments in the correct order. The learner is encouraged to learn the stepwise surgical protocol through repetitive use of the computer simulation. Constructive feedback is acquired through a grading system, which rates the student's or resident's ability to perform the task in the correct order. The grading system also accounts for the time required to perform the simulated procedure. We evaluated the efficacy of this teaching technique by testing medical students who learned by the computer simulation and those who learned by reading the surgical protocol manual. Both groups then performed TKR on manufactured bone models using real instruments. Their technique was graded with the standard protocol. The students who learned on the computer simulation performed the task in a shorter time and with fewer errors than the control group. They were also more engaged in the learning process. Surgical training programs generally lack a consistent approach to preoperative education related to surgical procedures. This interactive computer tutorial has allowed us to make a quantum leap in medical student and resident teaching in our orthopedic department because the students actually participate in the entire process. Our technique provides a linear, sequential method of skill acquisition and direct feedback, which is ideally suited for learning stepwise surgical protocols. Since our initial evaluation has shown the efficacy of this program, we have implemented this teaching tool into our orthopedic curriculum. Our plans for future work with this simulator include modeling procedures involving other anatomic areas of interest, such as the hip and shoulder.

Computer Instructional Aids for Undergraduate Control Education.

ERIC Educational Resources Information Center

Volz, Richard A.; And Others

Engineering is coming to rely more and more heavily upon the computer for computations, analyses, and graphic displays which aid the design process. A general purpose simulation system, the Time-shared Automatic Control Laboratory (TACL), and a set of computer-aided design programs, Control Oriented Interactive Graphic Analysis and Design…

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

DOE PAGES

Song, Lingshuang; Yang, Lin; Meng, Jie; ...

2016-12-29

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostlymore » in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.« less

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Lingshuang; Yang, Lin; Meng, Jie

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostlymore » in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.« less

Computational examination of utility scale wind turbine wake interactions

DOE PAGES

Okosun, Tyamo; Zhou, Chenn Q.

2015-07-14

We performed numerical simulations of small, utility scale wind turbine groupings to determine how wakes generated by upstream turbines affect the performance of the small turbine group as a whole. Specifically, various wind turbine arrangements were simulated to better understand how turbine location influences small group wake interactions. The minimization of power losses due to wake interactions certainly plays a significant role in the optimization of wind farms. Since wind turbines extract kinetic energy from the wind, the air passing through a wind turbine decreases in velocity, and turbines downstream of the initial turbine experience flows of lower energy, resultingmore » in reduced power output. Our study proposes two arrangements of turbines that could generate more power by exploiting the momentum of the wind to increase velocity at downstream turbines, while maintaining low wake interactions at the same time. Furthermore, simulations using Computational Fluid Dynamics are used to obtain results much more quickly than methods requiring wind tunnel models or a large scale experimental test.« less

Modified Monte Carlo method for study of electron transport in degenerate electron gas in the presence of electron-electron interactions, application to graphene

NASA Astrophysics Data System (ADS)

Borowik, Piotr; Thobel, Jean-Luc; Adamowicz, Leszek

2017-07-01

Standard computational methods used to take account of the Pauli Exclusion Principle into Monte Carlo (MC) simulations of electron transport in semiconductors may give unphysical results in low field regime, where obtained electron distribution function takes values exceeding unity. Modified algorithms were already proposed and allow to correctly account for electron scattering on phonons or impurities. Present paper extends this approach and proposes improved simulation scheme allowing including Pauli exclusion principle for electron-electron (e-e) scattering into MC simulations. Simulations with significantly reduced computational cost recreate correct values of the electron distribution function. Proposed algorithm is applied to study transport properties of degenerate electrons in graphene with e-e interactions. This required adapting the treatment of e-e scattering in the case of linear band dispersion relation. Hence, this part of the simulation algorithm is described in details.

The effects of computer simulation versus hands-on dissection and the placement of computer simulation within the learning cycle on student achievement and attitude

NASA Astrophysics Data System (ADS)

Hopkins, Kathryn Susan

The value of dissection as an instructional strategy has been debated, but not evidenced in research literature. The purpose of this study was to examine the efficacy of using computer simulated frog dissection as a substitute for traditional hands-on frog dissection and to examine the possible enhancement of achievement by combining the two strategies in a specific sequence. In this study, 134 biology students at two Central Texas schools were divided into the five following treatment groups: computer simulation of frog dissection, computer simulation before dissection, traditional hands-on frog dissection, dissection before computer simulation, and textual worksheet materials. The effects on achievement were evaluated by labeling 10 structures on three diagrams, identifying 11 pinned structures on a prosected frog, and answering 9 multiple-choice questions over the dissection process. Attitude was evaluated using a thirty item survey with a five-point Likert scale. The quasi-experimental design was pretest/post-test/post-test nonequivalent group for both control and experimental groups, a 2 x 2 x 5 completely randomized factorial design (gender, school, five treatments). The pretest/post-test design was incorporated to control for prior knowledge using analysis of covariance. The dissection only group evidenced a significantly higher performance than all other treatments except dissection-then-computer on the post-test segment requiring students to label pinned anatomical parts on a prosected frog. Interactions between treatment and school in addition to interaction between treatment and gender were found to be significant. The diagram and attitude post-tests evidenced no significant difference. Results on the nine multiple-choice questions about dissection procedures indicated a significant difference between schools. The interaction between treatment and school was also found to be significant. On a delayed post-test, a significant difference in gender was found on the diagram labeling segment of the post-test. Males were reported to have the higher score. Since existing research conflicts with this study's results, additional research using authentic assessment is recommended. Instruction should be aligned with dissection content and process objectives for each treatment group, and the teacher variable should be controlled.

Aortic dissection simulation models for clinical support: fluid-structure interaction vs. rigid wall models.

PubMed

Alimohammadi, Mona; Sherwood, Joseph M; Karimpour, Morad; Agu, Obiekezie; Balabani, Stavroula; Díaz-Zuccarini, Vanessa

2015-04-15

The management and prognosis of aortic dissection (AD) is often challenging and the use of personalised computational models is being explored as a tool to improve clinical outcome. Including vessel wall motion in such simulations can provide more realistic and potentially accurate results, but requires significant additional computational resources, as well as expertise. With clinical translation as the final aim, trade-offs between complexity, speed and accuracy are inevitable. The present study explores whether modelling wall motion is worth the additional expense in the case of AD, by carrying out fluid-structure interaction (FSI) simulations based on a sample patient case. Patient-specific anatomical details were extracted from computed tomography images to provide the fluid domain, from which the vessel wall was extrapolated. Two-way fluid-structure interaction simulations were performed, with coupled Windkessel boundary conditions and hyperelastic wall properties. The blood was modelled using the Carreau-Yasuda viscosity model and turbulence was accounted for via a shear stress transport model. A simulation without wall motion (rigid wall) was carried out for comparison purposes. The displacement of the vessel wall was comparable to reports from imaging studies in terms of intimal flap motion and contraction of the true lumen. Analysis of the haemodynamics around the proximal and distal false lumen in the FSI model showed complex flow structures caused by the expansion and contraction of the vessel wall. These flow patterns led to significantly different predictions of wall shear stress, particularly its oscillatory component, which were not captured by the rigid wall model. Through comparison with imaging data, the results of the present study indicate that the fluid-structure interaction methodology employed herein is appropriate for simulations of aortic dissection. Regions of high wall shear stress were not significantly altered by the wall motion, however, certain collocated regions of low and oscillatory wall shear stress which may be critical for disease progression were only identified in the FSI simulation. We conclude that, if patient-tailored simulations of aortic dissection are to be used as an interventional planning tool, then the additional complexity, expertise and computational expense required to model wall motion is indeed justified.

Strong Shock Propagating Over A Random Bed of Spherical Particles

NASA Astrophysics Data System (ADS)

Mehta, Yash; Salari, Kambiz; Jackson, Thomas L.; Balachandar, S.; Thakur, Siddharth

2017-11-01

The study of shock interaction with particles has been largely motivated because of its wide-ranging applications. The complex interaction between the compressible flow features, such as shock wave and expansion fan, and the dispersed phase makes this multi-phase flow very difficult to predict and control. In this talk we will be presenting results on fully resolved inviscid simulations of shock interaction with random bed of particles. One of the fascinating observations from these simulations are the flow field fluctuations due to the presence of randomly distributed particles. Rigorous averaging (Favre averaging) of the governing equations results in Reynolds stress like term, which can be classified as pseudo turbulence in this case. We have computed this ``Reynolds stress'' term along with individual fluctuations and the turbulent kinetic energy. Average pressure was also computed to characterize the strength of the transmitted and the reflected waves. This work was supported by the U.S. Department of Energy, National Nuclear Security Administration, Advanced Simulation and Computing Program, as a Cooperative Agreement under the Predictive Science Academic Alliance Program.

Facilitating Integration of Electron Beam Lithography Devices with Interactive Videodisc, Computer-Based Simulation and Job Aids.

ERIC Educational Resources Information Center

Von Der Linn, Robert Christopher

A needs assessment of the Grumman E-Beam Systems Group identified the requirement for additional skill mastery for the engineers who assemble, integrate, and maintain devices used to manufacture integrated circuits. Further analysis of the tasks involved led to the decision to develop interactive videodisc, computer-based job aids to enable…

Simulation of wave interactions with MHD

NASA Astrophysics Data System (ADS)

Batchelor, D.; Alba, C.; Bateman, G.; Bernholdt, D.; Berry, L.; Bonoli, P.; Bramley, R.; Breslau, J.; Chance, M.; Chen, J.; Choi, M.; Elwasif, W.; Fu, G.; Harvey, R.; Jaeger, E.; Jardin, S.; Jenkins, T.; Keyes, D.; Klasky, S.; Kruger, S.; Ku, L.; Lynch, V.; McCune, D.; Ramos, J.; Schissel, D.; Schnack, D.; Wright, J.

2008-07-01

The broad scientific objectives of the SWIM (Simulation 01 Wave Interaction with MHD) project are twofold: (1) improve our understanding of interactions that both radio frequency (RF) wave and particle sources have on extended-MHD phenomena, and to substantially improve our capability for predicting and optimizing the performance of burning plasmas in devices such as ITER: and (2) develop an integrated computational system for treating multiphysics phenomena with the required flexibility and extensibility to serve as a prototype for the Fusion Simulation Project. The Integrated Plasma Simulator (IPS) has been implemented. Presented here are initial physics results on RP effects on MHD instabilities in tokamaks as well as simulation results for tokamak discharge evolution using the IPS.

Fluid-structure interaction modeling of wind turbines: simulating the full machine

NASA Astrophysics Data System (ADS)

Hsu, Ming-Chen; Bazilevs, Yuri

2012-12-01

In this paper we present our aerodynamics and fluid-structure interaction (FSI) computational techniques that enable dynamic, fully coupled, 3D FSI simulation of wind turbines at full scale, and in the presence of the nacelle and tower (i.e., simulation of the "full machine"). For the interaction of wind and flexible blades we employ a nonmatching interface discretization approach, where the aerodynamics is computed using a low-order finite-element-based ALE-VMS technique, while the rotor blades are modeled as thin composite shells discretized using NURBS-based isogeometric analysis (IGA). We find that coupling FEM and IGA in this manner gives a good combination of efficiency, accuracy, and flexibility of the computational procedures for wind turbine FSI. The interaction between the rotor and tower is handled using a non-overlapping sliding-interface approach, where both moving- and stationary-domain formulations of aerodynamics are employed. At the fluid-structure and sliding interfaces, the kinematic and traction continuity is enforced weakly, which is a key ingredient of the proposed numerical methodology. We present several simulations of a three-blade 5~MW wind turbine, with and without the tower. We find that, in the case of no tower, the presence of the sliding interface has no effect on the prediction of aerodynamic loads on the rotor. From this we conclude that weak enforcement of the kinematics gives just as accurate results as the strong enforcement, and thus enables the simulation of rotor-tower interaction (as well as other applications involving mechanical components in relative motion). We also find that the blade passing the tower produces a 10-12 % drop (per blade) in the aerodynamic torque. We feel this finding may be important when it comes to the fatigue-life analysis and prediction for wind turbine blades.

KASCADE-Grande energy reconstruction based on the lateral density distribution using the QGSJet-II.04 interaction model

NASA Astrophysics Data System (ADS)

Gherghel-Lascu, A.; Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertania, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Zabierowski, J.

2017-06-01

The charged particle densities obtained from CORSIKA simulated EAS, using the QGSJet-II.04 hadronic interaction model are used for primary energy reconstruction. Simulated data are reconstructed by using Lateral Energy Correction Functions computed with a new realistic model of the Grande stations implemented in Geant4.10.

Microprocessors: Laboratory Simulation of Industrial Control Applications.

ERIC Educational Resources Information Center

Gedeon, David V.

1981-01-01

Describes a course to make technical managers more aware of computer technology and how data loggers, programmable controllers, and larger computer systems interact in a hierarchical configuration of manufacturing process control. (SK)

Integration of Ausubelian Learning Theory and Educational Computing.

ERIC Educational Resources Information Center

Heinze-Fry, Jane A.; And Others

1984-01-01

Examines possible benefits when Ausubelian learning approaches are integrated into computer-assisted instruction, presenting an example of this integration in a computer program dealing with introductory ecology concepts. The four program parts (tutorial, interactive concept mapping, simulations, and vee-mapping) are described. (JN)

Simulating the dynamic interaction of a robotic arm and the Space Shuttle remote manipulator system. M.S. Thesis - George Washington Univ., Dec. 1994

NASA Technical Reports Server (NTRS)

Garrahan, Steven L.; Tolson, Robert H.; Williams, Robert L., II

1995-01-01

Industrial robots are usually attached to a rigid base. Placing the robot on a compliant base introduces dynamic coupling between the two systems. The Vehicle Emulation System (VES) is a six DOF platform that is capable of modeling this interaction. The VES employs a force-torque sensor as the interface between robot and base. A computer simulation of the VES is presented. Each of the hardware and software components is described and Simulink is used as the programming environment. The simulation performance is compared with experimental results to validate accuracy. A second simulation which models the dynamic interaction of a robot and a flexible base acts as a comparison to the simulated motion of the VES. Results are presented that compare the simulated VES motion with the motion of the VES hardware using the same admittance model. The two computer simulations are compared to determine how well the VES is expected to emulate the desired motion. Simulation results are given for robots mounted to the end effector of the Space Shuttle Remote Manipulator System (SRMS). It is shown that for fast motions of the two robots studied, the SRMS experiences disturbances on the order of centimeters. Larger disturbances are possible if different manipulators are used.

Computationally efficient methods for modelling laser wakefield acceleration in the blowout regime

NASA Astrophysics Data System (ADS)

Cowan, B. M.; Kalmykov, S. Y.; Beck, A.; Davoine, X.; Bunkers, K.; Lifschitz, A. F.; Lefebvre, E.; Bruhwiler, D. L.; Shadwick, B. A.; Umstadter, D. P.; Umstadter

2012-08-01

Electron self-injection and acceleration until dephasing in the blowout regime is studied for a set of initial conditions typical of recent experiments with 100-terawatt-class lasers. Two different approaches to computationally efficient, fully explicit, 3D particle-in-cell modelling are examined. First, the Cartesian code vorpal (Nieter, C. and Cary, J. R. 2004 VORPAL: a versatile plasma simulation code. J. Comput. Phys. 196, 538) using a perfect-dispersion electromagnetic solver precisely describes the laser pulse and bubble dynamics, taking advantage of coarser resolution in the propagation direction, with a proportionally larger time step. Using third-order splines for macroparticles helps suppress the sampling noise while keeping the usage of computational resources modest. The second way to reduce the simulation load is using reduced-geometry codes. In our case, the quasi-cylindrical code calder-circ (Lifschitz, A. F. et al. 2009 Particle-in-cell modelling of laser-plasma interaction using Fourier decomposition. J. Comput. Phys. 228(5), 1803-1814) uses decomposition of fields and currents into a set of poloidal modes, while the macroparticles move in the Cartesian 3D space. Cylindrical symmetry of the interaction allows using just two modes, reducing the computational load to roughly that of a planar Cartesian simulation while preserving the 3D nature of the interaction. This significant economy of resources allows using fine resolution in the direction of propagation and a small time step, making numerical dispersion vanishingly small, together with a large number of particles per cell, enabling good particle statistics. Quantitative agreement of two simulations indicates that these are free of numerical artefacts. Both approaches thus retrieve the physically correct evolution of the plasma bubble, recovering the intrinsic connection of electron self-injection to the nonlinear optical evolution of the driver.

The Role of Multiphysics Simulation in Multidisciplinary Analysis

NASA Technical Reports Server (NTRS)

Rifai, Steven M.; Ferencz, Robert M.; Wang, Wen-Ping; Spyropoulos, Evangelos T.; Lawrence, Charles; Melis, Matthew E.

1998-01-01

This article describes the applications of the Spectrum(Tm) Solver in Multidisciplinary Analysis (MDA). Spectrum, a multiphysics simulation software based on the finite element method, addresses compressible and incompressible fluid flow, structural, and thermal modeling as well as the interaction between these disciplines. Multiphysics simulation is based on a single computational framework for the modeling of multiple interacting physical phenomena. Interaction constraints are enforced in a fully-coupled manner using the augmented-Lagrangian method. Within the multiphysics framework, the finite element treatment of fluids is based on Galerkin-Least-Squares (GLS) method with discontinuity capturing operators. The arbitrary-Lagrangian-Eulerian method is utilized to account for deformable fluid domains. The finite element treatment of solids and structures is based on the Hu-Washizu variational principle. The multiphysics architecture lends itself naturally to high-performance parallel computing. Aeroelastic, propulsion, thermal management and manufacturing applications are presented.

Computer simulation of electron flow in linear-beam microwave tubes

NASA Astrophysics Data System (ADS)

Kumar, Lalit

1990-12-01

The computer simulation of electron flow in linear-beam microwave tubes, such as a travelling-wave tube (TWT) and klystron, is used for designing and optimising the electron gun and collector and for analysing the large-signal beam-wave interaction phenomenon. Major aspects of simulation of electron flow in static and rf fields present in such tubes are discussed. Some advancements made in this respect and results obtained from computer programs developed by the research group at CEERI for a gridded electron gun, depressed collector, and large-signal analysis of TWT and klystron are presented.

User's instructions for the cardiovascular Walters model

NASA Technical Reports Server (NTRS)

Croston, R. C.

1973-01-01

The model is a combined, steady-state cardiovascular and thermal model. It was originally developed for interactive use, but was converted to batch mode simulation for the Sigma 3 computer. The model has the purpose to compute steady-state circulatory and thermal variables in response to exercise work loads and environmental factors. During a computer simulation run, several selected variables are printed at each time step. End conditions are also printed at the completion of the run.

COMPUTATIONAL MITRAL VALVE EVALUATION AND POTENTIAL CLINICAL APPLICATIONS

PubMed Central

Chandran, Krishnan B.; Kim, Hyunggun

2014-01-01

The mitral valve (MV) apparatus consists of the two asymmetric leaflets, the saddle-shaped annulus, the chordae tendineae, and the papillary muscles. MV function over the cardiac cycle involves complex interaction between the MV apparatus components for efficient blood circulation. Common diseases of the MV include valvular stenosis, regurgitation, and prolapse. MV repair is the most popular and most reliable surgical treatment for early MV pathology. One of the unsolved problems in MV repair is to predict the optimal repair strategy for each patient. Although experimental studies have provided valuable information to improve repair techniques, computational simulations are increasingly playing an important role in understanding the complex MV dynamics, particularly with the availability of patient-specific real-time imaging modalities. This work presents a review of computational simulation studies of MV function employing finite element (FE) structural analysis and fluid-structure interaction (FSI) approach reported in the literature to date. More recent studies towards potential applications of computational simulation approaches in the assessment of valvular repair techniques and potential pre-surgical planning of repair strategies are also discussed. It is anticipated that further advancements in computational techniques combined with the next generations of clinical imaging modalities will enable physiologically more realistic simulations. Such advancement in imaging and computation will allow for patient-specific, disease-specific, and case-specific MV evaluation and virtual prediction of MV repair. PMID:25134487

Computer Simulation of Protein-Protein and Protein-Peptide Interactions

DTIC Science & Technology

1983-12-08

a full molecular dynamic z simulation is performed, with resulting dipolar re - laxation. However, this is prohibitive when a large . number of...1993 Dr. Mike Marron Program Manager Molecular Biology Office of Naval Research 800 N. Quincy Street Arlington, VA 22217 Dear Mike, Here is the...rztnbutior is unLi--ited. , 93-30630 98 12 � 12/08/93 01/0/92-;03/31/93: Final Report, Computer Simulation of Protein-Protein and Protein-Peptide

A Machine Learning Method for the Prediction of Receptor Activation in the Simulation of Synapses

PubMed Central

Montes, Jesus; Gomez, Elena; Merchán-Pérez, Angel; DeFelipe, Javier; Peña, Jose-Maria

2013-01-01

Chemical synaptic transmission involves the release of a neurotransmitter that diffuses in the extracellular space and interacts with specific receptors located on the postsynaptic membrane. Computer simulation approaches provide fundamental tools for exploring various aspects of the synaptic transmission under different conditions. In particular, Monte Carlo methods can track the stochastic movements of neurotransmitter molecules and their interactions with other discrete molecules, the receptors. However, these methods are computationally expensive, even when used with simplified models, preventing their use in large-scale and multi-scale simulations of complex neuronal systems that may involve large numbers of synaptic connections. We have developed a machine-learning based method that can accurately predict relevant aspects of the behavior of synapses, such as the percentage of open synaptic receptors as a function of time since the release of the neurotransmitter, with considerably lower computational cost compared with the conventional Monte Carlo alternative. The method is designed to learn patterns and general principles from a corpus of previously generated Monte Carlo simulations of synapses covering a wide range of structural and functional characteristics. These patterns are later used as a predictive model of the behavior of synapses under different conditions without the need for additional computationally expensive Monte Carlo simulations. This is performed in five stages: data sampling, fold creation, machine learning, validation and curve fitting. The resulting procedure is accurate, automatic, and it is general enough to predict synapse behavior under experimental conditions that are different to the ones it has been trained on. Since our method efficiently reproduces the results that can be obtained with Monte Carlo simulations at a considerably lower computational cost, it is suitable for the simulation of high numbers of synapses and it is therefore an excellent tool for multi-scale simulations. PMID:23894367

A Guide for Developing Human-Robot Interaction Experiments in the Robotic Interactive Visualization and Experimentation Technology (RIVET) Simulation

DTIC Science & Technology

2016-05-01

research, Kunkler (2006) suggested that the similarities between computer simulation tools and robotic surgery systems (e.g., mechanized feedback...distribution is unlimited. 49 Davies B. A review of robotics in surgery . Proceedings of the Institution of Mechanical Engineers, Part H: Journal...ARL-TR-7683 ● MAY 2016 US Army Research Laboratory A Guide for Developing Human- Robot Interaction Experiments in the Robotic

Interactive visualization of Earth and Space Science computations

NASA Technical Reports Server (NTRS)

Hibbard, William L.; Paul, Brian E.; Santek, David A.; Dyer, Charles R.; Battaiola, Andre L.; Voidrot-Martinez, Marie-Francoise

1994-01-01

Computers have become essential tools for scientists simulating and observing nature. Simulations are formulated as mathematical models but are implemented as computer algorithms to simulate complex events. Observations are also analyzed and understood in terms of mathematical models, but the number of these observations usually dictates that we automate analyses with computer algorithms. In spite of their essential role, computers are also barriers to scientific understanding. Unlike hand calculations, automated computations are invisible and, because of the enormous numbers of individual operations in automated computations, the relation between an algorithm's input and output is often not intuitive. This problem is illustrated by the behavior of meteorologists responsible for forecasting weather. Even in this age of computers, many meteorologists manually plot weather observations on maps, then draw isolines of temperature, pressure, and other fields by hand (special pads of maps are printed for just this purpose). Similarly, radiologists use computers to collect medical data but are notoriously reluctant to apply image-processing algorithms to that data. To these scientists with life-and-death responsibilities, computer algorithms are black boxes that increase rather than reduce risk. The barrier between scientists and their computations can be bridged by techniques that make the internal workings of algorithms visible and that allow scientists to experiment with their computations. Here we describe two interactive systems developed at the University of Wisconsin-Madison Space Science and Engineering Center (SSEC) that provide these capabilities to Earth and space scientists.

An Educational MONTE CARLO Simulation/Animation Program for the Cosmic Rays Muons and a Prototype Computer-Driven Hardware Display.

ERIC Educational Resources Information Center

Kalkanis, G.; Sarris, M. M.

1999-01-01

Describes an educational software program for the study of and detection methods for the cosmic ray muons passing through several light transparent materials (i.e., water, air, etc.). Simulates muons and Cherenkov photons' paths and interactions and visualizes/animates them on the computer screen using Monte Carlo methods/techniques which employ…

Immersive, Interactive, Web-Enabled Computer Simulation as a Trigger for Learning: The next Generation of Problem-Based Learning in Educational Leadership

ERIC Educational Resources Information Center

Mann, Dale; Reardon, R. M.; Becker, J. D.; Shakeshaft, C.; Bacon, Nicholas

2011-01-01

This paper describes the use of advanced computer technology in an innovative educational leadership program. This program integrates full-motion video scenarios that simulate the leadership challenges typically faced by principals over the course of a full school year. These scenarios require decisions that are then coupled to consequences and…

The Effect of Interactive, Three Dimensional, High Speed Simulations on High School Science Students' Conceptions of the Molecular Structure of Water.

ERIC Educational Resources Information Center

Hakerem, Gita; And Others

The Water and Molecular Networks (WAMNet) Project uses graduate student written Reduced Instruction Set Computing (RISC) computer simulations of the molecular structure of water to assist high school students learn about the nature of water. This study examined: (1) preconceptions concerning the molecular structure of water common among high…

Tangible Landscape: Cognitively Grasping the Flow of Water

NASA Astrophysics Data System (ADS)

Harmon, B. A.; Petrasova, A.; Petras, V.; Mitasova, H.; Meentemeyer, R. K.

2016-06-01

Complex spatial forms like topography can be challenging to understand, much less intentionally shape, given the heavy cognitive load of visualizing and manipulating 3D form. Spatiotemporal processes like the flow of water over a landscape are even more challenging to understand and intentionally direct as they are dependent upon their context and require the simulation of forces like gravity and momentum. This cognitive work can be offloaded onto computers through 3D geospatial modeling, analysis, and simulation. Interacting with computers, however, can also be challenging, often requiring training and highly abstract thinking. Tangible computing - an emerging paradigm of human-computer interaction in which data is physically manifested so that users can feel it and directly manipulate it - aims to offload this added cognitive work onto the body. We have designed Tangible Landscape, a tangible interface powered by an open source geographic information system (GRASS GIS), so that users can naturally shape topography and interact with simulated processes with their hands in order to make observations, generate and test hypotheses, and make inferences about scientific phenomena in a rapid, iterative process. Conceptually Tangible Landscape couples a malleable physical model with a digital model of a landscape through a continuous cycle of 3D scanning, geospatial modeling, and projection. We ran a flow modeling experiment to test whether tangible interfaces like this can effectively enhance spatial performance by offloading cognitive processes onto computers and our bodies. We used hydrological simulations and statistics to quantitatively assess spatial performance. We found that Tangible Landscape enhanced 3D spatial performance and helped users understand water flow.

Gas-liquid coexistence in a system of dipolar soft spheres.

PubMed

Jia, Ran; Braun, Heiko; Hentschke, Reinhard

2010-12-01

The existence of gas-liquid coexistence in dipolar fluids with no other contribution to attractive interaction than dipole-dipole interaction is a basic and open question in the theory of fluids. Here we compute the gas-liquid critical point in a system of dipolar soft spheres subject to an external electric field using molecular dynamics computer simulation. Tracking the critical point as the field strength is approaching zero we find the following limiting values: T(c)=0.063 and ρ(c)=0.0033 (dipole moment μ=1). These values are confirmed by independent simulation at zero field strength.

[A new concept in digestive surgery: the computer assisted surgical procedure, from virtual reality to telemanipulation].

PubMed

Marescaux, J; Clément, J M; Nord, M; Russier, Y; Tassetti, V; Mutter, D; Cotin, S; Ayache, N

1997-11-01

Surgical simulation increasingly appears to be an essential aspect of tomorrow's surgery. The development of a hepatic surgery simulator is an advanced concept calling for a new writing system which will transform the medical world: virtual reality. Virtual reality extends the perception of our five senses by representing more than the real state of things by the means of computer sciences and robotics. It consists of three concepts: immersion, navigation and interaction. Three reasons have led us to develop this simulator: the first is to provide the surgeon with a comprehensive visualisation of the organ. The second reason is to allow for planning and surgical simulation that could be compared with the detailed flight-plan for a commercial jet pilot. The third lies in the fact that virtual reality is an integrated part of the concept of computer assisted surgical procedure. The project consists of a sophisticated simulator which has to include five requirements: visual fidelity, interactivity, physical properties, physiological properties, sensory input and output. In this report we will describe how to get a realistic 3D model of the liver from bi-dimensional 2D medical images for anatomical and surgical training. The introduction of a tumor and the consequent planning and virtual resection is also described, as are force feedback and real-time interaction.

Probabilistic lifetime strength of aerospace materials via computational simulation

NASA Technical Reports Server (NTRS)

Boyce, Lola; Keating, Jerome P.; Lovelace, Thomas B.; Bast, Callie C.

1991-01-01

The results of a second year effort of a research program are presented. The research included development of methodology that provides probabilistic lifetime strength of aerospace materials via computational simulation. A probabilistic phenomenological constitutive relationship, in the form of a randomized multifactor interaction equation, is postulated for strength degradation of structural components of aerospace propulsion systems subjected to a number of effects of primitive variables. These primitive variables often originate in the environment and may include stress from loading, temperature, chemical, or radiation attack. This multifactor interaction constitutive equation is included in the computer program, PROMISS. Also included in the research is the development of methodology to calibrate the constitutive equation using actual experimental materials data together with the multiple linear regression of that data.

Parallel Three-Dimensional Computation of Fluid Dynamics and Fluid-Structure Interactions of Ram-Air Parachutes

NASA Technical Reports Server (NTRS)

Tezduyar, Tayfun E.

1998-01-01

This is a final report as far as our work at University of Minnesota is concerned. The report describes our research progress and accomplishments in development of high performance computing methods and tools for 3D finite element computation of aerodynamic characteristics and fluid-structure interactions (FSI) arising in airdrop systems, namely ram-air parachutes and round parachutes. This class of simulations involves complex geometries, flexible structural components, deforming fluid domains, and unsteady flow patterns. The key components of our simulation toolkit are a stabilized finite element flow solver, a nonlinear structural dynamics solver, an automatic mesh moving scheme, and an interface between the fluid and structural solvers; all of these have been developed within a parallel message-passing paradigm.

An Interactive Simulation Program for Exploring Computational Models of Auto-Associative Memory.

PubMed

Fink, Christian G

2017-01-01

While neuroscience students typically learn about activity-dependent plasticity early in their education, they often struggle to conceptually connect modification at the synaptic scale with network-level neuronal dynamics, not to mention with their own everyday experience of recalling a memory. We have developed an interactive simulation program (based on the Hopfield model of auto-associative memory) that enables the user to visualize the connections generated by any pattern of neural activity, as well as to simulate the network dynamics resulting from such connectivity. An accompanying set of student exercises introduces the concepts of pattern completion, pattern separation, and sparse versus distributed neural representations. Results from a conceptual assessment administered before and after students worked through these exercises indicate that the simulation program is a useful pedagogical tool for illustrating fundamental concepts of computational models of memory.

AceCloud: Molecular Dynamics Simulations in the Cloud.

PubMed

Harvey, M J; De Fabritiis, G

2015-05-26

We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

Sharp Interface Tracking in Rotating Microflows of Solvent Extraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glimm, James; Almeida, Valmor de; Jiao, Xiangmin

2013-01-08

The objective of this project is to develop a specialized sharp interface tracking simulation capability for predicting interaction of micron-sized drops and bubbles in rotating flows relevant to optimized design of contactor devices used in solvent extraction processes of spent nuclear fuel reprocessing. The primary outcomes of this project include the capability to resolve drops and bubbles micro-hydrodynamics in solvent extraction contactors, determining from first principles continuum fluid mechanics how micro-drops and bubbles interact with each other and the surrounding shearing fluid for realistic flows. In the near term, this effort will play a central role in providing parameters andmore » insight into the flow dynamics of models that average over coarser scales, say at the millimeter unit length. In the longer term, it will prove to be the platform to conduct full-device, detailed simulations as parallel computing power reaches the exaflop level. The team will develop an accurate simulation tool for flows containing interacting droplets and bubbles with sharp interfaces under conditions that mimic those found in realistic contactor operations. The main objective is to create an off-line simulation capability to model drop and bubble interactions in a domain representative of the averaged length scale. The technical approach is to combine robust interface tracking software, subgrid modeling, validation quality experiments, powerful computational hardware, and a team with simulation modeling, physical modeling and technology integration experience. Simulations will then fully resolve the microflow of drops and bubbles at the microsecond time scale. This approach is computationally intensive but very accurate in treating important coupled physical phenomena in the vicinity of interfaces. The method makes it possible to resolve spatial scales smaller than the typical distance between bubbles and to model some non-equilibrium thermodynamic features such as finite critical tension in cavitating liquids« less

Experimental and Computational Study of Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Fletcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock-shear-layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Modeling and simulation in biomedicine.

PubMed Central

Aarts, J.; Möller, D.; van Wijk van Brievingh, R.

1991-01-01

A group of researchers and educators in The Netherlands, Germany and Czechoslovakia have developed and adapted mathematical computer models of phenomena in the field of physiology and biomedicine for use in higher education. The models are graphical and highly interactive, and are all written in TurboPascal or the mathematical simulation language PSI. An educational shell has been developed to launch the models. The shell allows students to interact with the models and teachers to edit the models, to add new models and to monitor the achievements of the students. The models and the shell have been implemented on a MS-DOS personal computer. This paper describes the features of the modeling package and presents the modeling and simulation of the heart muscle as an example. PMID:1807745

Characterization of Aerodynamic Interactions with the Mars Science Laboratory Reaction Control System Using Computation and Experiment

NASA Technical Reports Server (NTRS)

Schoenenberger, Mark; VanNorman, John; Rhode, Matthew; Paulson, John

2013-01-01

On August 5 , 2012, the Mars Science Laboratory (MSL) entry capsule successfully entered Mars' atmosphere and landed the Curiosity rover in Gale Crater. The capsule used a reaction control system (RCS) consisting of four pairs of hydrazine thrusters to fly a guided entry. The RCS provided bank control to fly along a flight path commanded by an onboard computer and also damped unwanted rates due to atmospheric disturbances and any dynamic instabilities of the capsule. A preliminary assessment of the MSL's flight data from entry showed that the capsule flew much as predicted. This paper will describe how the MSL aerodynamics team used engineering analyses, computational codes and wind tunnel testing in concert to develop the RCS system and certify it for flight. Over the course of MSL's development, the RCS configuration underwent a number of design iterations to accommodate mechanical constraints, aeroheating concerns and excessive aero/RCS interactions. A brief overview of the MSL RCS configuration design evolution is provided. Then, a brief description is presented of how the computational predictions of RCS jet interactions were validated. The primary work to certify that the RCS interactions were acceptable for flight was centered on validating computational predictions at hypersonic speeds. A comparison of computational fluid dynamics (CFD) predictions to wind tunnel force and moment data gathered in the NASA Langley 31-Inch Mach 10 Tunnel was the lynch pin to validating the CFD codes used to predict aero/RCS interactions. Using the CFD predictions and experimental data, an interaction model was developed for Monte Carlo analyses using 6-degree-of-freedom trajectory simulation. The interaction model used in the flight simulation is presented.

Simulation-Based Approach for Site-Specific Optimization of Hydrokinetic Turbine Arrays

NASA Astrophysics Data System (ADS)

Sotiropoulos, F.; Chawdhary, S.; Yang, X.; Khosronejad, A.; Angelidis, D.

2014-12-01

A simulation-based approach has been developed to enable site-specific optimization of tidal and current turbine arrays in real-life waterways. The computational code is based on the St. Anthony Falls Laboratory Virtual StreamLab (VSL3D), which is able to carry out high-fidelity simulations of turbulent flow and sediment transport processes in rivers and streams taking into account the arbitrary geometrical complexity characterizing natural waterways. The computational framework can be used either in turbine-resolving mode, to take into account all geometrical details of the turbine, or with the turbines parameterized as actuator disks or actuator lines. Locally refined grids are employed to dramatically increase the resolution of the simulation and enable efficient simulations of multi-turbine arrays. Turbine/sediment interactions are simulated using the coupled hydro-morphodynamic module of VSL3D. The predictive capabilities of the resulting computational framework will be demonstrated by applying it to simulate turbulent flow past a tri-frame configuration of hydrokinetic turbines in a rigid-bed turbulent open channel flow as well as turbines mounted on mobile bed open channels to investigate turbine/sediment interactions. The utility of the simulation-based approach for guiding the optimal development of turbine arrays in real-life waterways will also be discussed and demonstrated. This work was supported by NSF grant IIP-1318201. Simulations were carried out at the Minnesota Supercomputing Institute.

NVIDIA OptiX ray-tracing engine as a new tool for modelling medical imaging systems

NASA Astrophysics Data System (ADS)

Pietrzak, Jakub; Kacperski, Krzysztof; Cieślar, Marek

2015-03-01

The most accurate technique to model the X- and gamma radiation path through a numerically defined object is the Monte Carlo simulation which follows single photons according to their interaction probabilities. A simplified and much faster approach, which just integrates total interaction probabilities along selected paths, is known as ray tracing. Both techniques are used in medical imaging for simulating real imaging systems and as projectors required in iterative tomographic reconstruction algorithms. These approaches are ready for massive parallel implementation e.g. on Graphics Processing Units (GPU), which can greatly accelerate the computation time at a relatively low cost. In this paper we describe the application of the NVIDIA OptiX ray-tracing engine, popular in professional graphics and rendering applications, as a new powerful tool for X- and gamma ray-tracing in medical imaging. It allows the implementation of a variety of physical interactions of rays with pixel-, mesh- or nurbs-based objects, and recording any required quantities, like path integrals, interaction sites, deposited energies, and others. Using the OptiX engine we have implemented a code for rapid Monte Carlo simulations of Single Photon Emission Computed Tomography (SPECT) imaging, as well as the ray-tracing projector, which can be used in reconstruction algorithms. The engine generates efficient, scalable and optimized GPU code, ready to run on multi GPU heterogeneous systems. We have compared the results our simulations with the GATE package. With the OptiX engine the computation time of a Monte Carlo simulation can be reduced from days to minutes.

Trends in Programming Languages for Neuroscience Simulations

PubMed Central

Davison, Andrew P.; Hines, Michael L.; Muller, Eilif

2009-01-01

Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing. PMID:20198154

Trends in programming languages for neuroscience simulations.

PubMed

Davison, Andrew P; Hines, Michael L; Muller, Eilif

2009-01-01

Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing.

Simulation/Gaming and the Acquisition of Communicative Competence in Another Language.

ERIC Educational Resources Information Center

Garcia-Carbonell, Amparo; Rising, Beverly; Montero, Begona; Watts, Frances

2001-01-01

Discussion of communicative competence in second language acquisition focuses on a theoretical and practical meshing of simulation and gaming methodology with theories of foreign language acquisition, including task-based learning, interaction, and comprehensible input. Describes experiments conducted with computer-assisted simulations in…

Event-based simulation of networks with pulse delayed coupling

NASA Astrophysics Data System (ADS)

Klinshov, Vladimir; Nekorkin, Vladimir

2017-10-01

Pulse-mediated interactions are common in networks of different nature. Here we develop a general framework for simulation of networks with pulse delayed coupling. We introduce the discrete map governing the dynamics of such networks and describe the computation algorithm for its numerical simulation.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

2009-03-14

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.; Knepley, Matthew G.; Anitescu, Mihai

2009-03-01

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

On the computational modeling of the viscosity of colloidal dispersions and its relation with basic molecular interactions

NASA Astrophysics Data System (ADS)

Gama Goicochea, A.; Balderas Altamirano, M. A.; Lopez-Esparza, R.; Waldo-Mendoza, Miguel A.; Perez, E.

2015-09-01

The connection between fundamental interactions acting in molecules in a fluid and macroscopically measured properties, such as the viscosity between colloidal particles coated with polymers, is studied here. The role that hydrodynamic and Brownian forces play in colloidal dispersions is also discussed. It is argued that many-body systems in which all these interactions take place can be accurately solved using computational simulation tools. One of those modern tools is the technique known as dissipative particle dynamics, which incorporates Brownian and hydrodynamic forces, as well as basic conservative interactions. A case study is reported, as an example of the applications of this technique, which consists of the prediction of the viscosity and friction between two opposing parallel surfaces covered with polymer chains, under the influence of a steady flow. This work is intended to serve as an introduction to the subject of colloidal dispersions and computer simulations, for final-year undergraduate students and beginning graduate students who are interested in beginning research in soft matter systems. To that end, a computational code is included that students can use right away to study complex fluids in equilibrium.

Computer-aided system design

NASA Technical Reports Server (NTRS)

Walker, Carrie K.

1991-01-01

A technique has been developed for combining features of a systems architecture design and assessment tool and a software development tool. This technique reduces simulation development time and expands simulation detail. The Architecture Design and Assessment System (ADAS), developed at the Research Triangle Institute, is a set of computer-assisted engineering tools for the design and analysis of computer systems. The ADAS system is based on directed graph concepts and supports the synthesis and analysis of software algorithms mapped to candidate hardware implementations. Greater simulation detail is provided by the ADAS functional simulator. With the functional simulator, programs written in either Ada or C can be used to provide a detailed description of graph nodes. A Computer-Aided Software Engineering tool developed at the Charles Stark Draper Laboratory (CSDL CASE) automatically generates Ada or C code from engineering block diagram specifications designed with an interactive graphical interface. A technique to use the tools together has been developed, which further automates the design process.

Computer-Based Alternatives to Using Animals in Teaching Physiology.

ERIC Educational Resources Information Center

Dewhurst, David

1990-01-01

Three interactive computer-assisted learning programs are described. The use of tissues from freshly killed frogs is simulated, including the isolated sciatic nerve, the sciatic nerve-gastrocnemius muscle, and the in situ heart. (KR)

Modeling of fatigue crack induced nonlinear ultrasonics using a highly parallelized explicit local interaction simulation approach

NASA Astrophysics Data System (ADS)

Shen, Yanfeng; Cesnik, Carlos E. S.

2016-04-01

This paper presents a parallelized modeling technique for the efficient simulation of nonlinear ultrasonics introduced by the wave interaction with fatigue cracks. The elastodynamic wave equations with contact effects are formulated using an explicit Local Interaction Simulation Approach (LISA). The LISA formulation is extended to capture the contact-impact phenomena during the wave damage interaction based on the penalty method. A Coulomb friction model is integrated into the computation procedure to capture the stick-slip contact shear motion. The LISA procedure is coded using the Compute Unified Device Architecture (CUDA), which enables the highly parallelized supercomputing on powerful graphic cards. Both the explicit contact formulation and the parallel feature facilitates LISA's superb computational efficiency over the conventional finite element method (FEM). The theoretical formulations based on the penalty method is introduced and a guideline for the proper choice of the contact stiffness is given. The convergence behavior of the solution under various contact stiffness values is examined. A numerical benchmark problem is used to investigate the new LISA formulation and results are compared with a conventional contact finite element solution. Various nonlinear ultrasonic phenomena are successfully captured using this contact LISA formulation, including the generation of nonlinear higher harmonic responses. Nonlinear mode conversion of guided waves at fatigue cracks is also studied.

Computer-program documentation of an interactive-accounting model to simulate streamflow, water quality, and water-supply operations in a river basin

USGS Publications Warehouse

Burns, A.W.

1988-01-01

This report describes an interactive-accounting model used to simulate streamflow, chemical-constituent concentrations and loads, and water-supply operations in a river basin. The model uses regression equations to compute flow from incremental (internode) drainage areas. Conservative chemical constituents (typically dissolved solids) also are computed from regression equations. Both flow and water quality loads are accumulated downstream. Optionally, the model simulates the water use and the simplified groundwater systems of a basin. Water users include agricultural, municipal, industrial, and in-stream users , and reservoir operators. Water users list their potential water sources, including direct diversions, groundwater pumpage, interbasin imports, or reservoir releases, in the order in which they will be used. Direct diversions conform to basinwide water law priorities. The model is interactive, and although the input data exist in files, the user can modify them interactively. A major feature of the model is its color-graphic-output options. This report includes a description of the model, organizational charts of subroutines, and examples of the graphics. Detailed format instructions for the input data, example files of input data, definitions of program variables, and listing of the FORTRAN source code are Attachments to the report. (USGS)

Development of an Innovative Interactive Virtual Classroom System for K-12 Education Using Google App Engine

ERIC Educational Resources Information Center

Mumba, Frackson; Zhu, Mengxia

2013-01-01

This paper presents a Simulation-based interactive Virtual ClassRoom web system (SVCR: www.vclasie.com) powered by the state-of-the-art cloud computing technology from Google SVCR integrates popular free open-source math, science and engineering simulations and provides functions such as secure user access control and management of courses,…

A Comparison Study of Augmented Reality versus Interactive Simulation Technology to Support Student Learning of a Socio-Scientific Issue

ERIC Educational Resources Information Center

Chang, Hsin-Yi; Hsu, Ying-Shao; Wu, Hsin-Kai

2016-01-01

We investigated the impact of an augmented reality (AR) versus interactive simulation (IS) activity incorporated in a computer learning environment to facilitate students' learning of a socio-scientific issue (SSI) on nuclear power plants and radiation pollution. We employed a quasi-experimental research design. Two classes (a total of 45…

Cellular Particle Dynamics simulation of biomechanical relaxation processes of multi-cellular systems

NASA Astrophysics Data System (ADS)

McCune, Matthew; Kosztin, Ioan

2013-03-01

Cellular Particle Dynamics (CPD) is a theoretical-computational-experimental framework for describing and predicting the time evolution of biomechanical relaxation processes of multi-cellular systems, such as fusion, sorting and compression. In CPD, cells are modeled as an ensemble of cellular particles (CPs) that interact via short range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through numerical integration of their equations of motion. Here we present CPD simulation results for the fusion of both spherical and cylindrical multi-cellular aggregates. First, we calibrate the relevant CPD model parameters for a given cell type by comparing the CPD simulation results for the fusion of two spherical aggregates to the corresponding experimental results. Next, CPD simulations are used to predict the time evolution of the fusion of cylindrical aggregates. The latter is relevant for the formation of tubular multi-cellular structures (i.e., primitive blood vessels) created by the novel bioprinting technology. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

Teaching Microbial Growth by Simulation.

ERIC Educational Resources Information Center

Ruiz, A. Fernandez; And Others

1989-01-01

Presented is a simulation program for Apple II computer which assays the effects of a series of variables on bacterial growth and interactions between microbial populations. Results of evaluation of the program with students are summarized. (CW)

Development of Computer-Based Resources for Textile Education.

ERIC Educational Resources Information Center

Hopkins, Teresa; Thomas, Andrew; Bailey, Mike

1998-01-01

Describes the production of computer-based resources for students of textiles and engineering in the United Kingdom. Highlights include funding by the Teaching and Learning Technology Programme (TLTP), courseware author/subject expert interaction, usage test and evaluation, authoring software, graphics, computer-aided design simulation, self-test…

An interactive physics-based unmanned ground vehicle simulator leveraging open source gaming technology: progress in the development and application of the virtual autonomous navigation environment (VANE) desktop

NASA Astrophysics Data System (ADS)

Rohde, Mitchell M.; Crawford, Justin; Toschlog, Matthew; Iagnemma, Karl D.; Kewlani, Guarav; Cummins, Christopher L.; Jones, Randolph A.; Horner, David A.

2009-05-01

It is widely recognized that simulation is pivotal to vehicle development, whether manned or unmanned. There are few dedicated choices, however, for those wishing to perform realistic, end-to-end simulations of unmanned ground vehicles (UGVs). The Virtual Autonomous Navigation Environment (VANE), under development by US Army Engineer Research and Development Center (ERDC), provides such capabilities but utilizes a High Performance Computing (HPC) Computational Testbed (CTB) and is not intended for on-line, real-time performance. A product of the VANE HPC research is a real-time desktop simulation application under development by the authors that provides a portal into the HPC environment as well as interaction with wider-scope semi-automated force simulations (e.g. OneSAF). This VANE desktop application, dubbed the Autonomous Navigation Virtual Environment Laboratory (ANVEL), enables analysis and testing of autonomous vehicle dynamics and terrain/obstacle interaction in real-time with the capability to interact within the HPC constructive geo-environmental CTB for high fidelity sensor evaluations. ANVEL leverages rigorous physics-based vehicle and vehicle-terrain interaction models in conjunction with high-quality, multimedia visualization techniques to form an intuitive, accurate engineering tool. The system provides an adaptable and customizable simulation platform that allows developers a controlled, repeatable testbed for advanced simulations. ANVEL leverages several key technologies not common to traditional engineering simulators, including techniques from the commercial video-game industry. These enable ANVEL to run on inexpensive commercial, off-the-shelf (COTS) hardware. In this paper, the authors describe key aspects of ANVEL and its development, as well as several initial applications of the system.

Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits

NASA Astrophysics Data System (ADS)

Spiriti, Justin; Zuckerman, Daniel M.

2015-12-01

Traditional coarse-graining based on a reduced number of interaction sites often entails a significant sacrifice of chemical accuracy. As an alternative, we present a method for simulating large systems composed of interacting macromolecules using an energy tabulation strategy previously devised for small rigid molecules or molecular fragments [S. Lettieri and D. M. Zuckerman, J. Comput. Chem. 33, 268-275 (2012); J. Spiriti and D. M. Zuckerman, J. Chem. Theory Comput. 10, 5161-5177 (2014)]. We treat proteins as rigid and construct distance and orientation-dependent tables of the interaction energy between them. Arbitrarily detailed interactions may be incorporated into the tables, but as a proof-of-principle, we tabulate a simple α-carbon Gō-like model for interactions between dimeric subunits of the hepatitis B viral capsid. This model is significantly more structurally realistic than previous models used in capsid assembly studies. We are able to increase the speed of Monte Carlo simulations by a factor of up to 6700 compared to simulations without tables, with only minimal further loss in accuracy. To obtain further enhancement of sampling, we combine tabulation with the weighted ensemble (WE) method, in which multiple parallel simulations are occasionally replicated or pruned in order to sample targeted regions of a reaction coordinate space. In the initial study reported here, WE is able to yield pathways of the final ˜25% of the assembly process.

Physically-Based Modelling and Real-Time Simulation of Fluids.

NASA Astrophysics Data System (ADS)

Chen, Jim Xiong

1995-01-01

Simulating physically realistic complex fluid behaviors presents an extremely challenging problem for computer graphics researchers. Such behaviors include the effects of driving boats through water, blending differently colored fluids, rain falling and flowing on a terrain, fluids interacting in a Distributed Interactive Simulation (DIS), etc. Such capabilities are useful in computer art, advertising, education, entertainment, and training. We present a new method for physically-based modeling and real-time simulation of fluids in computer graphics and dynamic virtual environments. By solving the 2D Navier -Stokes equations using a CFD method, we map the surface into 3D using the corresponding pressures in the fluid flow field. This achieves realistic real-time fluid surface behaviors by employing the physical governing laws of fluids but avoiding extensive 3D fluid dynamics computations. To complement the surface behaviors, we calculate fluid volume and external boundary changes separately to achieve full 3D general fluid flow. To simulate physical activities in a DIS, we introduce a mechanism which uses a uniform time scale proportional to the clock-time and variable time-slicing to synchronize physical models such as fluids in the networked environment. Our approach can simulate many different fluid behaviors by changing the internal or external boundary conditions. It can model different kinds of fluids by varying the Reynolds number. It can simulate objects moving or floating in fluids. It can also produce synchronized general fluid flows in a DIS. Our model can serve as a testbed to simulate many other fluid phenomena which have never been successfully modeled previously.

Simulations in a Science and Society Course.

ERIC Educational Resources Information Center

Maier, Mark H.; Venanzi, Thomas

1984-01-01

Provides a course outline which includes simulation exercises designed as in-class activities related to science and society interactions. Simulations focus on the IQ debate, sociobiology, nuclear weapons and nulcear strategy, nuclear power and radiation, computer explosion, and cosmology. Indicates that learning improves when students take active…

Spatial Learning and Computer Simulations in Science

ERIC Educational Resources Information Center

Lindgren, Robb; Schwartz, Daniel L.

2009-01-01

Interactive simulations are entering mainstream science education. Their effects on cognition and learning are often framed by the legacy of information processing, which emphasized amodal problem solving and conceptual organization. In contrast, this paper reviews simulations from the vantage of research on perception and spatial learning,…

Long-range interactions and parallel scalability in molecular simulations

NASA Astrophysics Data System (ADS)

Patra, Michael; Hyvönen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko

2007-01-01

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes—we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.

Iterative load-balancing method with multigrid level relaxation for particle simulation with short-range interactions

NASA Astrophysics Data System (ADS)

Furuichi, Mikito; Nishiura, Daisuke

2017-10-01

We developed dynamic load-balancing algorithms for Particle Simulation Methods (PSM) involving short-range interactions, such as Smoothed Particle Hydrodynamics (SPH), Moving Particle Semi-implicit method (MPS), and Discrete Element method (DEM). These are needed to handle billions of particles modeled in large distributed-memory computer systems. Our method utilizes flexible orthogonal domain decomposition, allowing the sub-domain boundaries in the column to be different for each row. The imbalances in the execution time between parallel logical processes are treated as a nonlinear residual. Load-balancing is achieved by minimizing the residual within the framework of an iterative nonlinear solver, combined with a multigrid technique in the local smoother. Our iterative method is suitable for adjusting the sub-domain frequently by monitoring the performance of each computational process because it is computationally cheaper in terms of communication and memory costs than non-iterative methods. Numerical tests demonstrated the ability of our approach to handle workload imbalances arising from a non-uniform particle distribution, differences in particle types, or heterogeneous computer architecture which was difficult with previously proposed methods. We analyzed the parallel efficiency and scalability of our method using Earth simulator and K-computer supercomputer systems.

Argonne simulation framework for intelligent transportation systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ewing, T.; Doss, E.; Hanebutte, U.

1996-04-01

A simulation framework has been developed which defines a high-level architecture for a large-scale, comprehensive, scalable simulation of an Intelligent Transportation System (ITS). The simulator is designed to run on parallel computers and distributed (networked) computer systems; however, a version for a stand alone workstation is also available. The ITS simulator includes an Expert Driver Model (EDM) of instrumented ``smart`` vehicles with in-vehicle navigation units. The EDM is capable of performing optimal route planning and communicating with Traffic Management Centers (TMC). A dynamic road map data base is sued for optimum route planning, where the data is updated periodically tomore » reflect any changes in road or weather conditions. The TMC has probe vehicle tracking capabilities (display position and attributes of instrumented vehicles), and can provide 2-way interaction with traffic to provide advisories and link times. Both the in-vehicle navigation module and the TMC feature detailed graphical user interfaces that includes human-factors studies to support safety and operational research. Realistic modeling of variations of the posted driving speed are based on human factor studies that take into consideration weather, road conditions, driver`s personality and behavior and vehicle type. The simulator has been developed on a distributed system of networked UNIX computers, but is designed to run on ANL`s IBM SP-X parallel computer system for large scale problems. A novel feature of the developed simulator is that vehicles will be represented by autonomous computer processes, each with a behavior model which performs independent route selection and reacts to external traffic events much like real vehicles. Vehicle processes interact with each other and with ITS components by exchanging messages. With this approach, one will be able to take advantage of emerging massively parallel processor (MPP) systems.« less

Design and implementation of laser target simulator in hardware-in-the-loop simulation system based on LabWindows/CVI and RTX

NASA Astrophysics Data System (ADS)

Tong, Qiujie; Wang, Qianqian; Li, Xiaoyang; Shan, Bin; Cui, Xuntai; Li, Chenyu; Peng, Zhong

2016-11-01

In order to satisfy the requirements of the real-time and generality, a laser target simulator in semi-physical simulation system based on RTX+LabWindows/CVI platform is proposed in this paper. Compared with the upper-lower computers simulation platform architecture used in the most of the real-time system now, this system has better maintainability and portability. This system runs on the Windows platform, using Windows RTX real-time extension subsystem to ensure the real-time performance of the system combining with the reflective memory network to complete some real-time tasks such as calculating the simulation model, transmitting the simulation data, and keeping real-time communication. The real-time tasks of simulation system run under the RTSS process. At the same time, we use the LabWindows/CVI to compile a graphical interface, and complete some non-real-time tasks in the process of simulation such as man-machine interaction, display and storage of the simulation data, which run under the Win32 process. Through the design of RTX shared memory and task scheduling algorithm, the data interaction between the real-time tasks process of RTSS and non-real-time tasks process of Win32 is completed. The experimental results show that this system has the strongly real-time performance, highly stability, and highly simulation accuracy. At the same time, it also has the good performance of human-computer interaction.

Stochastic Convection Parameterizations

NASA Technical Reports Server (NTRS)

Teixeira, Joao; Reynolds, Carolyn; Suselj, Kay; Matheou, Georgios

2012-01-01

computational fluid dynamics, radiation, clouds, turbulence, convection, gravity waves, surface interaction, radiation interaction, cloud and aerosol microphysics, complexity (vegetation, biogeochemistry, radiation versus turbulence/convection stochastic approach, non-linearities, Monte Carlo, high resolutions, large-Eddy Simulations, cloud structure, plumes, saturation in tropics, forecasting, parameterizations, stochastic, radiation-clod interaction, hurricane forecasts

Filters for Improvement of Multiscale Data from Atomistic Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, David J.; Reynolds, Daniel R.

Multiscale computational models strive to produce accurate and efficient numerical simulations of systems involving interactions across multiple spatial and temporal scales that typically differ by several orders of magnitude. Some such models utilize a hybrid continuum-atomistic approach combining continuum approximations with first-principles-based atomistic models to capture multiscale behavior. By following the heterogeneous multiscale method framework for developing multiscale computational models, unknown continuum scale data can be computed from an atomistic model. Concurrently coupling the two models requires performing numerous atomistic simulations which can dominate the computational cost of the method. Furthermore, when the resulting continuum data is noisy due tomore » sampling error, stochasticity in the model, or randomness in the initial conditions, filtering can result in significant accuracy gains in the computed multiscale data without increasing the size or duration of the atomistic simulations. In this work, we demonstrate the effectiveness of spectral filtering for increasing the accuracy of noisy multiscale data obtained from atomistic simulations. Moreover, we present a robust and automatic method for closely approximating the optimum level of filtering in the case of additive white noise. By improving the accuracy of this filtered simulation data, it leads to a dramatic computational savings by allowing for shorter and smaller atomistic simulations to achieve the same desired multiscale simulation precision.« less

Filters for Improvement of Multiscale Data from Atomistic Simulations

DOE PAGES

Gardner, David J.; Reynolds, Daniel R.

2017-01-05

Multiscale computational models strive to produce accurate and efficient numerical simulations of systems involving interactions across multiple spatial and temporal scales that typically differ by several orders of magnitude. Some such models utilize a hybrid continuum-atomistic approach combining continuum approximations with first-principles-based atomistic models to capture multiscale behavior. By following the heterogeneous multiscale method framework for developing multiscale computational models, unknown continuum scale data can be computed from an atomistic model. Concurrently coupling the two models requires performing numerous atomistic simulations which can dominate the computational cost of the method. Furthermore, when the resulting continuum data is noisy due tomore » sampling error, stochasticity in the model, or randomness in the initial conditions, filtering can result in significant accuracy gains in the computed multiscale data without increasing the size or duration of the atomistic simulations. In this work, we demonstrate the effectiveness of spectral filtering for increasing the accuracy of noisy multiscale data obtained from atomistic simulations. Moreover, we present a robust and automatic method for closely approximating the optimum level of filtering in the case of additive white noise. By improving the accuracy of this filtered simulation data, it leads to a dramatic computational savings by allowing for shorter and smaller atomistic simulations to achieve the same desired multiscale simulation precision.« less

Augmenting Sand Simulation Environments through Subdivision and Particle Refinement

NASA Astrophysics Data System (ADS)

Clothier, M.; Bailey, M.

2012-12-01

Recent advances in computer graphics and parallel processing hardware have provided disciplines with new methods to evaluate and visualize data. These advances have proven useful for earth and planetary scientists as many researchers are using this hardware to process large amounts of data for analysis. As such, this has provided opportunities for collaboration between computer graphics and the earth sciences. Through collaboration with the Oregon Space Grant and IGERT Ecosystem Informatics programs, we are investigating techniques for simulating the behavior of sand. We are also collaborating with the Jet Propulsion Laboratory's (JPL) DARTS Lab to exchange ideas and gain feedback on our research. The DARTS Lab specializes in simulation of planetary vehicles, such as the Mars rovers. Their simulations utilize a virtual "sand box" to test how a planetary vehicle responds to different environments. Our research builds upon this idea to create a sand simulation framework so that planetary environments, such as the harsh, sandy regions on Mars, are more fully realized. More specifically, we are focusing our research on the interaction between a planetary vehicle, such as a rover, and the sand beneath it, providing further insight into its performance. Unfortunately, this can be a computationally complex problem, especially if trying to represent the enormous quantities of sand particles interacting with each other. However, through the use of high-performance computing, we have developed a technique to subdivide areas of actively participating sand regions across a large landscape. Similar to a Level of Detail (LOD) technique, we only subdivide regions of a landscape where sand particles are actively participating with another object. While the sand is within this subdivision window and moves closer to the surface of the interacting object, the sand region subdivides into smaller regions until individual sand particles are left at the surface. As an example, let's say there is a planetary rover interacting with our sand simulation environment. Sand that is actively interacting with a rover wheel will be represented as individual particles whereas sand that is further under the surface will be represented by larger regions of sand. The result of this technique allows for many particles to be represented without the computational complexity. In developing this method, we have further generalized these subdivision regions into any volumetric area suitable for use in the simulation. This is a further improvement of our method as it allows for more compact subdivision sand regions. This helps to fine tune the simulation so that more emphasis can be placed on regions of actively participating sand. We feel that through the generalization of our technique, our research can provide other opportunities within the earth and planetary sciences. Through collaboration with our academic colleagues, we continue to refine our technique and look for other opportunities to utilize our research.

Computer simulation and experimental study of the polysaccharide-polysaccharide interaction in the bacteria Azospirillum brasilense Sp245

NASA Astrophysics Data System (ADS)

Arefeva, Oksana A.; Kuznetsov, Pavel E.; Tolmachev, Sergey A.; Kupadze, Machammad S.; Khlebtsov, Boris N.; Rogacheva, Svetlana M.

2003-09-01

We have studied the conformational properties and molecular dynamics of polysaccharides by using molecular modeling methods. Theoretical and experimental results of polysaccharide-polysaccharide interactions are described.

Multispan Elevated Guideway Design for Passenger Transport Vehicles : Volume 2. Appendixes.

DOT National Transportation Integrated Search

1975-04-01

Contents: Appendix A - derivation of vehicle-guideway interaction equations; Appendix B - evaluation of pier support dynamics; Appendix C - computer simulation program of two-dimensional vehicle over a multi-span guideway; Appendix D - computer progr...

Computer Series, 13.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1981-01-01

Provides short descriptions of chemists' applications of computers in instruction: an interactive instructional program for Instrumental-Qualitative Organic Analysis; question-and-answer exercises in organic chemistry; computerized organic nomenclature drills; integration of theoretical and descriptive materials; acid-base titration simulation;…

Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Flethcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock- shear- layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Physics-based interactive volume manipulation for sharing surgical process.

PubMed

Nakao, Megumi; Minato, Kotaro

2010-05-01

This paper presents a new set of techniques by which surgeons can interactively manipulate patient-specific volumetric models for sharing surgical process. To handle physical interaction between the surgical tools and organs, we propose a simple surface-constraint-based manipulation algorithm to consistently simulate common surgical manipulations such as grasping, holding and retraction. Our computation model is capable of simulating soft-tissue deformation and incision in real time. We also present visualization techniques in order to rapidly visualize time-varying, volumetric information on the deformed image. This paper demonstrates the success of the proposed methods in enabling the simulation of surgical processes, and the ways in which this simulation facilitates preoperative planning and rehearsal.

Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

NASA Astrophysics Data System (ADS)

Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

2016-07-01

Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

Computer Games: Increase Learning in an Interactive Multidisciplinary Environment.

ERIC Educational Resources Information Center

Betz, Joseph A.

1996-01-01

Discusses the educational uses of computer games and simulations and describes a study conducted at the State University of New York College at Farmingdale that used the computer game "Sim City 2000." Highlights include whole systems learning, problem solving, student performance, nonparametric statistics, and treatment of experimental…

Modeling Mendel's Laws on Inheritance in Computational Biology and Medical Sciences

ERIC Educational Resources Information Center

Singh, Gurmukh; Siddiqui, Khalid; Singh, Mankiran; Singh, Satpal

2011-01-01

The current research article is based on a simple and practical way of employing the computational power of widely available, versatile software MS Excel 2007 to perform interactive computer simulations for undergraduate/graduate students in biology, biochemistry, biophysics, microbiology, medicine in college and university classroom setting. To…

Bio-inspired algorithms applied to molecular docking simulations.

PubMed

Heberlé, G; de Azevedo, W F

2011-01-01

Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs). These algorithms mimic biological systems to create new paradigms for computation, such as neural networks, evolutionary computing, and swarm intelligence. This review provides a description of the main concepts behind BIAs applied to molecular docking simulations. Special attention is devoted to evolutionary algorithms, guided-directed evolutionary algorithms, and Lamarckian genetic algorithms. Recent applications of these methodologies to protein targets identified in the Mycobacterium tuberculosis genome are described.

STEPS: A Simulated, Tutorable Physics Student.

ERIC Educational Resources Information Center

Ur, Sigalit; VanLehn, Kurt

1995-01-01

Describes a simulated student that learns by interacting with a human tutor. Tests suggest that simulated students, when developed past the prototype stage, could be valuable for training human tutors. Provides a computational cognitive task analysis of the skill of learning from a tutor that is useful for designing intelligent tutoring systems.…

Analyzing Interaction Patterns to Verify a Simulation/Game Model

ERIC Educational Resources Information Center

Myers, Rodney Dean

2012-01-01

In order for simulations and games to be effective for learning, instructional designers must verify that the underlying computational models being used have an appropriate degree of fidelity to the conceptual models of their real-world counterparts. A simulation/game that provides incorrect feedback is likely to promote misunderstanding and…

A Grand Canonical Monte Carlo simulation program for computing ion distributions around biomolecules in hard sphere solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

The GIBS software program is a Grand Canonical Monte Carlo (GCMC) simulation program (written in C++) that can be used for 1) computing the excess chemical potential of ions and the mean activity coefficients of salts in homogeneous electrolyte solutions; and, 2) for computing the distribution of ions around fixed macromolecules such as, nucleic acids and proteins. The solvent can be represented as neutral hard spheres or as a dielectric continuum. The ions are represented as charged hard spheres that can interact via Coulomb, hard-sphere, or Lennard-Jones potentials. In addition to hard-sphere repulsions, the ions can also be made tomore » interact with the solvent hard spheres via short-ranged attractive square-well potentials.« less

Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.

PubMed

Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David

2015-07-14

In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http://virtualchemistry.org, aimed at facilitating sharing and reuse of input files for molecular simulations.

Use of computer modeling to investigate a dynamic interaction problem in the Skylab TACS quad-valve package

NASA Technical Reports Server (NTRS)

Hesser, R. J.; Gershman, R.

1975-01-01

A valve opening-response problem encountered during development of a control valve for the Skylab thruster attitude control system (TACS) is described. The problem involved effects of dynamic interaction among valves in the quad-redundant valve package. Also described is a detailed computer simulation of the quad-valve package which was helpful in resolving the problem.

Virtual rounds: simulation-based education in procedural medicine

NASA Astrophysics Data System (ADS)

Shaffer, David W.; Meglan, Dwight A.; Ferrell, Margaret; Dawson, Steven L.

1999-07-01

Computer-based simulation is a goal for training physicians in specialties where traditional training puts patients at risk. Intuitively, interactive simulation of anatomy, pathology, and therapeutic actions should lead to shortening of the learning curve for novice or inexperienced physicians. Effective transfer of knowledge acquired in simulators must be shown for such devices to be widely accepted in the medical community. We have developed an Interventional Cardiology Training Simulator which incorporates real-time graphic interactivity coupled with haptic response, and an embedded curriculum permitting rehearsal, hypertext links, personal archiving and instructor review and testing capabilities. This linking of purely technical simulation with educational content creates a more robust educational purpose for procedural simulators.

Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

2015-03-01

Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

Parsing partial molar volumes of small molecules: a molecular dynamics study.

PubMed

Patel, Nisha; Dubins, David N; Pomès, Régis; Chalikian, Tigran V

2011-04-28

We used molecular dynamics (MD) simulations in conjunction with the Kirkwood-Buff theory to compute the partial molar volumes for a number of small solutes of various chemical natures. We repeated our computations using modified pair potentials, first, in the absence of the Coulombic term and, second, in the absence of the Coulombic and the attractive Lennard-Jones terms. Comparison of our results with experimental data and the volumetric results of Monte Carlo simulation with hard sphere potentials and scaled particle theory-based computations led us to conclude that, for small solutes, the partial molar volume computed with the Lennard-Jones potential in the absence of the Coulombic term nearly coincides with the cavity volume. On the other hand, MD simulations carried out with the pair interaction potentials containing only the repulsive Lennard-Jones term produce unrealistically large partial molar volumes of solutes that are close to their excluded volumes. Our simulation results are in good agreement with the reported schemes for parsing partial molar volume data on small solutes. In particular, our determined interaction volumes() and the thickness of the thermal volume for individual compounds are in good agreement with empirical estimates. This work is the first computational study that supports and lends credence to the practical algorithms of parsing partial molar volume data that are currently in use for molecular interpretations of volumetric data.

Learning with STEM Simulations in the Classroom: Findings and Trends from a Meta-Analysis

ERIC Educational Resources Information Center

D'Angelo, Cynthia M.; Rutstein, Daisy; Harris, Christopher J.

2016-01-01

This article presents a summary of the findings of a systematic review and meta-analysis of the literature on computer-based interactive simulations for K-12 science, technology, engineering, and mathematics (STEM) learning topics. For achievement outcomes, simulations had a moderate to strong effect on student learning. Overall, simulations have…

Interactive computer modeling of combustion chemistry and coalescence-dispersion modeling of turbulent combustion

NASA Technical Reports Server (NTRS)

Pratt, D. T.

1984-01-01

An interactive computer code for simulation of a high-intensity turbulent combustor as a single point inhomogeneous stirred reactor was developed from an existing batch processing computer code CDPSR. The interactive CDPSR code was used as a guide for interpretation and direction of DOE-sponsored companion experiments utilizing Xenon tracer with optical laser diagnostic techniques to experimentally determine the appropriate mixing frequency, and for validation of CDPSR as a mixing-chemistry model for a laboratory jet-stirred reactor. The coalescence-dispersion model for finite rate mixing was incorporated into an existing interactive code AVCO-MARK I, to enable simulation of a combustor as a modular array of stirred flow and plug flow elements, each having a prescribed finite mixing frequency, or axial distribution of mixing frequency, as appropriate. Further increase the speed and reliability of the batch kinetics integrator code CREKID was increased by rewriting in vectorized form for execution on a vector or parallel processor, and by incorporating numerical techniques which enhance execution speed by permitting specification of a very low accuracy tolerance.

An efficient solution technique for shockwave-boundary layer interactions with flow separation and slot suction effects

NASA Technical Reports Server (NTRS)

Edwards, Jack R.; Mcrae, D. Scott

1991-01-01

An efficient method for computing two-dimensional compressible Navier-Stokes flow fields is presented. The solution algorithm is a fully-implicit approximate factorization technique based on an unsymmetric line Gauss-Seidel splitting of the equation system Jacobian matrix. Convergence characteristics are improved by the addition of acceleration techniques based on Shamanskii's method for nonlinear equations and Broyden's quasi-Newton update. Characteristic-based differencing of the equations is provided by means of Van Leer's flux vector splitting. In this investigation, emphasis is placed on the fast and accurate computation of shock-wave-boundary layer interactions with and without slot suction effects. In the latter context, a set of numerical boundary conditions for simulating the transpiration flow in an open slot is devised. Both laminar and turbulent cases are considered, with turbulent closure provided by a modified Cebeci-Smith algebraic model. Comparisons with computational and experimental data sets are presented for a variety of interactions, and a fully-coupled simulation of a plenum chamber/inlet flowfield with shock interaction and suction is also shown and discussed.

An experimental and numerical investigation of shock-wave induced turbulent boundary-layer separation at hypersonic speeds

NASA Technical Reports Server (NTRS)

Marvin, J. G.; Horstman, C. C.; Rubesin, M. W.; Coakley, T. J.; Kussoy, M. I.

1975-01-01

An experiment designed to test and guide computations of the interaction of an impinging shock wave with a turbulent boundary layer is described. Detailed mean flow-field and surface data are presented for two shock strengths which resulted in attached and separated flows, respectively. Numerical computations, employing the complete time-averaged Navier-Stokes equations along with algebraic eddy-viscosity and turbulent Prandtl number models to describe shear stress and heat flux, are used to illustrate the dependence of the computations on the particulars of the turbulence models. Models appropriate for zero-pressure-gradient flows predicted the overall features of the flow fields, but were deficient in predicting many of the details of the interaction regions. Improvements to the turbulence model parameters were sought through a combination of detailed data analysis and computer simulations which tested the sensitivity of the solutions to model parameter changes. Computer simulations using these improvements are presented and discussed.

COLLABORATIVE RESEARCH AND DEVELOPMENT (CR&D) Delivery Order 0034: Aircraft Coatings Modeling and Simulation

DTIC Science & Technology

2008-03-01

bonded potentials used. The interactions between the beads were described using 6-12 Lennard - Jones (LJ) potential (Equation (1)) with a 2.5 d cutoff...in Lennard - Jones potential for the non-bonded interactions is at 1.12 d in line with the second peak. The remainder of the g(r)chain-chain has...Simulator). 40 Lennard - Jones and Coulombic interactions for pairs of organic atoms were computed using a switching function with inner and outer cutoffs of

Flexible Inhibitor Fluid-Structure Interaction Simulation in RSRM.

NASA Astrophysics Data System (ADS)

Wasistho, Bono

2005-11-01

We employ our tightly coupled fluid/structure/combustion simulation code 'Rocstar-3' for solid propellant rocket motors to study 3D flows past rigid and flexible inhibitors in the Reusable Solid Rocket Motor (RSRM). We perform high resolution simulations of a section of the rocket near the center joint slot at 100 seconds after ignition, using inflow conditions based on less detailed 3D simulations of the full RSRM. Our simulations include both inviscid and turbulent flows (using LES dynamic subgrid-scale model), and explore the interaction between the inhibitor and the resulting fluid flow. The response of the solid components is computed by an implicit finite element solver. The internal mesh motion scheme in our block-structured fluid solver enables our code to handle significant changes in geometry. We compute turbulent statistics and determine the compound instabilities originated from the natural hydrodynamic instabilities and the inhibitor motion. The ultimate goal is to studdy the effect of inhibitor flexing on the turbulent field.

Investigation on the forced response of a radial turbine under aerodynamic excitations

NASA Astrophysics Data System (ADS)

Ma, Chaochen; Huang, Zhi; Qi, Mingxu

2016-04-01

Rotor blades in a radial turbine with nozzle guide vanes typically experience harmonic aerodynamic excitations due to the rotor stator interaction. Dynamic stresses induced by the harmonic excitations can result in high cycle fatigue (HCF) of the blades. A reliable prediction method for forced response issue is essential to avoid the HCF problem. In this work, the forced response mechanisms were investigated based on a fluid structure interaction (FSI) method. Aerodynamic excitations were obtained by three-dimensional unsteady computational fluid dynamics (CFD) simulation with phase shifted periodic boundary conditions. The first two harmonic pressures were determined as the primary components of the excitation and applied to finite element (FE) model to conduct the computational structural dynamics (CSD) simulation. The computed results from the harmonic forced response analysis show good agreement with the predictions of Singh's advanced frequency evaluation (SAFE) diagram. Moreover, the mode superposition method used in FE simulation offers an efficient way to provide quantitative assessments of mode response levels and resonant strength.

Detecting Unsteady Blade Row Interaction in a Francis Turbine using a Phase-Lag Boundary Condition

NASA Astrophysics Data System (ADS)

Wouden, Alex; Cimbala, John; Lewis, Bryan

2013-11-01

For CFD simulations in turbomachinery, methods are typically used to reduce the computational cost. For example, the standard periodic assumption reduces the underlying mesh to a single blade passage in axisymmetric applications. If the simulation includes only a single array of blades with an uniform inlet condition, this assumption is adequate. However, to compute the interaction between successive blade rows of differing periodicity in an unsteady simulation, the periodic assumption breaks down and may produce inaccurate results. As a viable alternative the phase-lag boundary condition assumes that the periodicity includes a temporal component which, if considered, allows for a single passage to be modeled per blade row irrespective of differing periodicity. Prominently used in compressible CFD codes for the analysis of gas turbines/compressors, the phase-lag boundary condition is adapted to analyze the interaction between the guide vanes and rotor blades in an incompressible simulation of the 1989 GAMM Workshop Francis turbine using OpenFOAM. The implementation is based on the ``direct-storage'' method proposed in 1977 by Erdos and Alzner. The phase-lag simulation is compared with available data from the GAMM workshop as well as a full-wheel simulation. Funding provided by DOE Award number: DE-EE0002667.

Exploring biological interaction networks with tailored weighted quasi-bicliques

PubMed Central

2012-01-01

Background Biological networks provide fundamental insights into the functional characterization of genes and their products, the characterization of DNA-protein interactions, the identification of regulatory mechanisms, and other biological tasks. Due to the experimental and biological complexity, their computational exploitation faces many algorithmic challenges. Results We introduce novel weighted quasi-biclique problems to identify functional modules in biological networks when represented by bipartite graphs. In difference to previous quasi-biclique problems, we include biological interaction levels by using edge-weighted quasi-bicliques. While we prove that our problems are NP-hard, we also describe IP formulations to compute exact solutions for moderately sized networks. Conclusions We verify the effectiveness of our IP solutions using both simulation and empirical data. The simulation shows high quasi-biclique recall rates, and the empirical data corroborate the abilities of our weighted quasi-bicliques in extracting features and recovering missing interactions from biological networks. PMID:22759421

Interactive Display of Surfaces Using Subdivision Surfaces and Wavelets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duchaineau, M A; Bertram, M; Porumbescu, S

2001-10-03

Complex surfaces and solids are produced by large-scale modeling and simulation activities in a variety of disciplines. Productive interaction with these simulations requires that these surfaces or solids be viewable at interactive rates--yet many of these surfaced solids can contain hundreds of millions of polygondpolyhedra. Interactive display of these objects requires compression techniques to minimize storage, and fast view-dependent triangulation techniques to drive the graphics hardware. In this paper, we review recent advances in subdivision-surface wavelet compression and optimization that can be used to provide a framework for both compression and triangulation. These techniques can be used to produce suitablemore » approximations of complex surfaces of arbitrary topology, and can be used to determine suitable triangulations for display. The techniques can be used in a variety of applications in computer graphics, computer animation and visualization.« less

Complex molecular assemblies at hand via interactive simulations.

PubMed

Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

2009-11-30

Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. Copyright 2009 Wiley Periodicals, Inc.

Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics.

PubMed

Sevink, G J A; Schmid, F; Kawakatsu, T; Milano, G

2017-02-22

We have extended an existing hybrid MD-SCF simulation technique that employs a coarsening step to enhance the computational efficiency of evaluating non-bonded particle interactions. This technique is conceptually equivalent to the single chain in mean-field (SCMF) method in polymer physics, in the sense that non-bonded interactions are derived from the non-ideal chemical potential in self-consistent field (SCF) theory, after a particle-to-field projection. In contrast to SCMF, however, MD-SCF evolves particle coordinates by the usual Newton's equation of motion. Since collisions are seriously affected by the softening of non-bonded interactions that originates from their evaluation at the coarser continuum level, we have devised a way to reinsert the effect of collisions on the structural evolution. Merging MD-SCF with multi-particle collision dynamics (MPCD), we mimic particle collisions at the level of computational cells and at the same time properly account for the momentum transfer that is important for a realistic system evolution. The resulting hybrid MD-SCF/MPCD method was validated for a particular coarse-grained model of phospholipids in aqueous solution, against reference full-particle simulations and the original MD-SCF model. We additionally implemented and tested an alternative and more isotropic finite difference gradient. Our results show that efficiency is improved by merging MD-SCF with MPCD, as properly accounting for hydrodynamic interactions considerably speeds up the phase separation dynamics, with negligible additional computational costs compared to efficient MD-SCF. This new method enables realistic simulations of large-scale systems that are needed to investigate the applications of self-assembled structures of lipids in nanotechnologies.

Microcomputer Simulation of Real Gases--Part 1.

ERIC Educational Resources Information Center

Sperandeo-Mineo, R. M.; Tripi, G.

1987-01-01

Describes some simple computer programs designed to simulate the molecular dynamics of two-dimensional systems with a Lennard-Jones interaction potential. Discusses the use of the software in introductory physics courses at the high school and college level. (TW)

Metrics for comparing dynamic earthquake rupture simulations

USGS Publications Warehouse

Barall, Michael; Harris, Ruth A.

2014-01-01

Earthquakes are complex events that involve a myriad of interactions among multiple geologic features and processes. One of the tools that is available to assist with their study is computer simulation, particularly dynamic rupture simulation. A dynamic rupture simulation is a numerical model of the physical processes that occur during an earthquake. Starting with the fault geometry, friction constitutive law, initial stress conditions, and assumptions about the condition and response of the near‐fault rocks, a dynamic earthquake rupture simulation calculates the evolution of fault slip and stress over time as part of the elastodynamic numerical solution (Ⓔ see the simulation description in the electronic supplement to this article). The complexity of the computations in a dynamic rupture simulation make it challenging to verify that the computer code is operating as intended, because there are no exact analytic solutions against which these codes’ results can be directly compared. One approach for checking if dynamic rupture computer codes are working satisfactorily is to compare each code’s results with the results of other dynamic rupture codes running the same earthquake simulation benchmark. To perform such a comparison consistently, it is necessary to have quantitative metrics. In this paper, we present a new method for quantitatively comparing the results of dynamic earthquake rupture computer simulation codes.

An Object-Oriented Graphical User Interface for a Reusable Rocket Engine Intelligent Control System

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Musgrave, Jeffrey L.; Guo, Ten-Huei; Paxson, Daniel E.; Wong, Edmond; Saus, Joseph R.; Merrill, Walter C.

1994-01-01

An intelligent control system for reusable rocket engines under development at NASA Lewis Research Center requires a graphical user interface to allow observation of the closed-loop system in operation. The simulation testbed consists of a real-time engine simulation computer, a controls computer, and several auxiliary computers for diagnostics and coordination. The system is set up so that the simulation computer could be replaced by the real engine and the change would be transparent to the control system. Because of the hard real-time requirement of the control computer, putting a graphical user interface on it was not an option. Thus, a separate computer used strictly for the graphical user interface was warranted. An object-oriented LISP-based graphical user interface has been developed on a Texas Instruments Explorer 2+ to indicate the condition of the engine to the observer through plots, animation, interactive graphics, and text.

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

PubMed

Chavent, Matthieu; Duncan, Anna L; Sansom, Mark Sp

2016-10-01

Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Technology transfer of operator-in-the-loop simulation

NASA Technical Reports Server (NTRS)

Yae, K. H.; Lin, H. C.; Lin, T. C.; Frisch, H. P.

1994-01-01

The technology developed for operator-in-the-loop simulation in space teleoperation has been applied to Caterpillar's backhoe, wheel loader, and off-highway truck. On an SGI workstation, the simulation integrates computer modeling of kinematics and dynamics, real-time computational and visualization, and an interface with the operator through the operator's console. The console is interfaced with the workstation through an IBM-PC in which the operator's commands were digitized and sent through an RS-232 serial port. The simulation gave visual feedback adequate for the operator in the loop, with the camera's field of vision projected on a large screen in multiple view windows. The view control can emulate either stationary or moving cameras. This simulator created an innovative engineering design environment by integrating computer software and hardware with the human operator's interactions. The backhoe simulation has been adopted by Caterpillar in building a virtual reality tool for backhoe design.

Exploiting Motion Capture to Enhance Avoidance Behaviour in Games

NASA Astrophysics Data System (ADS)

van Basten, Ben J. H.; Jansen, Sander E. M.; Karamouzas, Ioannis

Realistic simulation of interacting virtual characters is essential in computer games, training and simulation applications. The problem is very challenging since people are accustomed to real-world situations and thus, they can easily detect inconsistencies and artifacts in the simulations. Over the past twenty years several models have been proposed for simulating individuals, groups and crowds of characters. However, little effort has been made to actually understand how humans solve interactions and avoid inter-collisions in real-life. In this paper, we exploit motion capture data to gain more insights into human-human interactions. We propose four measures to describe the collision-avoidance behavior. Based on these measures, we extract simple rules that can be applied on top of existing agent and force based approaches, increasing the realism of the resulting simulations.

Protein-membrane electrostatic interactions: Application of the Lekner summation technique

NASA Astrophysics Data System (ADS)

Juffer, André H.; Shepherd, Craig M.; Vogel, Hans J.

2001-01-01

A model has been developed to calculate the electrostatic interaction between biomolecules and lipid bilayers. The effect of ionic strength is included by means of explicit ions, while water is described as a background continuum. The bilayer is considered at the atomic level. The Lekner summation technique is employed to calculate the long-range electrostatic interactions. The new method is employed to estimate the electrostatic contribution to the free energy of binding of sandostatin, a cyclic eight-residue analogue of the peptide hormone somatostatin, to lipid bilayers with thermodynamic integration. Monte Carlo simulation techniques were employed to determine ion distributions and peptide orientations. Both neutral as well as negatively charged lipid bilayers were used. An error analysis to judge the quality of the computation is also presented. The applicability of the Lekner summation technique to combine it with computer simulation models that simulate the adsorption of peptides (and proteins) into the interfacial region of lipid bilayers is discussed.

Multi-disciplinary coupling for integrated design of propulsion systems

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Singhal, S. N.

1993-01-01

Effective computational simulation procedures are described for modeling the inherent multi-disciplinary interactions for determining the true response of propulsion systems. Results are presented for propulsion system responses including multi-discipline coupling effects via (1) coupled multi-discipline tailoring, (2) an integrated system of multidisciplinary simulators, (3) coupled material-behavior/fabrication-process tailoring, (4) sensitivities using a probabilistic simulator, and (5) coupled materials/structures/fracture/probabilistic behavior simulator. The results show that the best designs can be determined if the analysis/tailoring methods account for the multi-disciplinary coupling effects. The coupling across disciplines can be used to develop an integrated interactive multi-discipline numerical propulsion system simulator.

Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

PubMed

Hafner, Jürgen

2010-09-29

During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

A TREETOPS simulation of the Hubble Space Telescope-High Gain Antenna interaction

NASA Technical Reports Server (NTRS)

Sharkey, John P.

1987-01-01

Virtually any project dealing with the control of a Large Space Structure (LSS) will involve some level of verification by digital computer simulation. While the Hubble Space Telescope might not normally be included in a discussion of LSS, it is presented to highlight a recently developed simulation and analysis program named TREETOPS. TREETOPS provides digital simulation, linearization, and control system interaction of flexible, multibody spacecraft which admit to a point-connected tree topology. The HST application of TREETOPS is intended to familiarize the LSS community with TREETOPS by presenting a user perspective of its key features.

Compute-to-Learn: Authentic Learning via Development of Interactive Computer Demonstrations within a Peer-Led Studio Environment

ERIC Educational Resources Information Center

Jafari, Mina; Welden, Alicia Rae; Williams, Kyle L.; Winograd, Blair; Mulvihill, Ellen; Hendrickson, Heidi P.; Lenard, Michael; Gottfried, Amy; Geva, Eitan

2017-01-01

In this paper, we report on the implementation of a novel compute-to-learn pedagogy, which is based upon the theories of situated cognition and meaningful learning. The "compute-to-learn" pedagogy is designed to simulate an authentic research experience as part of the undergraduate curriculum, including project development, teamwork,…

A Comparative Study of Simulated and Measured Gear-Flap Flow Interaction

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Mineck, Raymond E.; Yao, Chungsheng; Jenkins, Luther N.; Fares, Ehab

2015-01-01

The ability of two CFD solvers to accurately characterize the transient, complex, interacting flowfield asso-ciated with a realistic gear-flap configuration is assessed via comparison of simulated flow with experimental measurements. The simulated results, obtained with NASA's FUN3D and Exa's PowerFLOW® for a high-fidelity, 18% scale semi-span model of a Gulfstream aircraft in landing configuration (39 deg flap deflection, main landing gear on and off) are compared to two-dimensional and stereo particle image velocimetry measurements taken within the gear-flap flow interaction region during wind tunnel tests of the model. As part of the bench-marking process, direct comparisons of the mean and fluctuating velocity fields are presented in the form of planar contour plots and extracted line profiles at measurement planes in various orientations stationed in the main gear wake. The measurement planes in the vicinity of the flap side edge and downstream of the flap trailing edge are used to highlight the effects of gear presence on tip vortex development and the ability of the computational tools to accurately capture such effects. The present study indicates that both computed datasets contain enough detail to construct a relatively accurate depiction of gear-flap flow interaction. Such a finding increases confidence in using the simulated volumetric flow solutions to examine the behavior of pertinent aer-odynamic mechanisms within the gear-flap interaction zone.

Connectionist Interaction Information Retrieval.

ERIC Educational Resources Information Center

Dominich, Sandor

2003-01-01

Discussion of connectionist views for adaptive clustering in information retrieval focuses on a connectionist clustering technique and activation spreading-based information retrieval model using the interaction information retrieval method. Presents theoretical as well as simulation results as regards computational complexity and includes…

Proposed standards for peer-reviewed publication of computer code

USDA-ARS?s Scientific Manuscript database

Computer simulation models are mathematical abstractions of physical systems. In the area of natural resources and agriculture, these physical systems encompass selected interacting processes in plants, soils, animals, or watersheds. These models are scientific products and have become important i...

Computer-automated opponent for manned air-to-air combat simulations

NASA Technical Reports Server (NTRS)

Hankins, W. W., III

1979-01-01

Two versions of a real-time digital-computer program that operates a fighter airplane interactively against a human pilot in simulated air combat were evaluated. They function by replacing one of two pilots in the Langley differential maneuvering simulator. Both versions make maneuvering decisions from identical information and logic; they differ essentially in the aerodynamic models that they control. One is very complete, but the other is much simpler, primarily characterizing the airplane's performance (lift, drag, and thrust). Both models competed extremely well against highly trained U.S. fighter pilots.

JETSPIN: A specific-purpose open-source software for simulations of nanofiber electrospinning

NASA Astrophysics Data System (ADS)

Lauricella, Marco; Pontrelli, Giuseppe; Coluzza, Ivan; Pisignano, Dario; Succi, Sauro

2015-12-01

We present the open-source computer program JETSPIN, specifically designed to simulate the electrospinning process of nanofibers. Its capabilities are shown with proper reference to the underlying model, as well as a description of the relevant input variables and associated test-case simulations. The various interactions included in the electrospinning model implemented in JETSPIN are discussed in detail. The code is designed to exploit different computational architectures, from single to parallel processor workstations. This paper provides an overview of JETSPIN, focusing primarily on its structure, parallel implementations, functionality, performance, and availability.

Using spatial principles to optimize distributed computing for enabling the physical science discoveries

PubMed Central

Yang, Chaowei; Wu, Huayi; Huang, Qunying; Li, Zhenlong; Li, Jing

2011-01-01

Contemporary physical science studies rely on the effective analyses of geographically dispersed spatial data and simulations of physical phenomena. Single computers and generic high-end computing are not sufficient to process the data for complex physical science analysis and simulations, which can be successfully supported only through distributed computing, best optimized through the application of spatial principles. Spatial computing, the computing aspect of a spatial cyberinfrastructure, refers to a computing paradigm that utilizes spatial principles to optimize distributed computers to catalyze advancements in the physical sciences. Spatial principles govern the interactions between scientific parameters across space and time by providing the spatial connections and constraints to drive the progression of the phenomena. Therefore, spatial computing studies could better position us to leverage spatial principles in simulating physical phenomena and, by extension, advance the physical sciences. Using geospatial science as an example, this paper illustrates through three research examples how spatial computing could (i) enable data intensive science with efficient data/services search, access, and utilization, (ii) facilitate physical science studies with enabling high-performance computing capabilities, and (iii) empower scientists with multidimensional visualization tools to understand observations and simulations. The research examples demonstrate that spatial computing is of critical importance to design computing methods to catalyze physical science studies with better data access, phenomena simulation, and analytical visualization. We envision that spatial computing will become a core technology that drives fundamental physical science advancements in the 21st century. PMID:21444779

Using spatial principles to optimize distributed computing for enabling the physical science discoveries.

PubMed

Yang, Chaowei; Wu, Huayi; Huang, Qunying; Li, Zhenlong; Li, Jing

2011-04-05

Contemporary physical science studies rely on the effective analyses of geographically dispersed spatial data and simulations of physical phenomena. Single computers and generic high-end computing are not sufficient to process the data for complex physical science analysis and simulations, which can be successfully supported only through distributed computing, best optimized through the application of spatial principles. Spatial computing, the computing aspect of a spatial cyberinfrastructure, refers to a computing paradigm that utilizes spatial principles to optimize distributed computers to catalyze advancements in the physical sciences. Spatial principles govern the interactions between scientific parameters across space and time by providing the spatial connections and constraints to drive the progression of the phenomena. Therefore, spatial computing studies could better position us to leverage spatial principles in simulating physical phenomena and, by extension, advance the physical sciences. Using geospatial science as an example, this paper illustrates through three research examples how spatial computing could (i) enable data intensive science with efficient data/services search, access, and utilization, (ii) facilitate physical science studies with enabling high-performance computing capabilities, and (iii) empower scientists with multidimensional visualization tools to understand observations and simulations. The research examples demonstrate that spatial computing is of critical importance to design computing methods to catalyze physical science studies with better data access, phenomena simulation, and analytical visualization. We envision that spatial computing will become a core technology that drives fundamental physical science advancements in the 21st century.

Computer simulations of equilibrium magnetization and microstructure in magnetic fluids

NASA Astrophysics Data System (ADS)

Rosa, A. P.; Abade, G. C.; Cunha, F. R.

2017-09-01

In this work, Monte Carlo and Brownian Dynamics simulations are developed to compute the equilibrium magnetization of a magnetic fluid under action of a homogeneous applied magnetic field. The particles are free of inertia and modeled as hard spheres with the same diameters. Two different periodic boundary conditions are implemented: the minimum image method and Ewald summation technique by replicating a finite number of particles throughout the suspension volume. A comparison of the equilibrium magnetization resulting from the minimum image approach and Ewald sums is performed by using Monte Carlo simulations. The Monte Carlo simulations with minimum image and lattice sums are used to investigate suspension microstructure by computing the important radial pair-distribution function go(r), which measures the probability density of finding a second particle at a distance r from a reference particle. This function provides relevant information on structure formation and its anisotropy through the suspension. The numerical results of go(r) are compared with theoretical predictions based on quite a different approach in the absence of the field and dipole-dipole interactions. A very good quantitative agreement is found for a particle volume fraction of 0.15, providing a validation of the present simulations. In general, the investigated suspensions are dominated by structures like dimmer and trimmer chains with trimmers having probability to form an order of magnitude lower than dimmers. Using Monte Carlo with lattice sums, the density distribution function g2(r) is also examined. Whenever this function is different from zero, it indicates structure-anisotropy in the suspension. The dependence of the equilibrium magnetization on the applied field, the magnetic particle volume fraction, and the magnitude of the dipole-dipole magnetic interactions for both boundary conditions are explored in this work. Results show that at dilute regimes and with moderate dipole-dipole interactions, the standard method of minimum image is both accurate and computationally efficient. Otherwise, lattice sums of magnetic particle interactions are required to accelerate convergence of the equilibrium magnetization. The accuracy of the numerical code is also quantitatively verified by comparing the magnetization obtained from numerical results with asymptotic predictions of high order in the particle volume fraction, in the presence of dipole-dipole interactions. In addition, Brownian Dynamics simulations are used in order to examine magnetization relaxation of a ferrofluid and to calculate the magnetic relaxation time as a function of the magnetic particle interaction strength for a given particle volume fraction and a non-dimensional applied field. The simulations of magnetization relaxation have shown the existence of a critical value of the dipole-dipole interaction parameter. For strength of the interactions below the critical value at a given particle volume fraction, the magnetic relaxation time is close to the Brownian relaxation time and the suspension has no appreciable memory. On the other hand, for strength of dipole interactions beyond its critical value, the relaxation time increases exponentially with the strength of dipole-dipole interaction. Although we have considered equilibrium conditions, the obtained results have far-reaching implications for the analysis of magnetic suspensions under external flow.

Department of Defense High Performance Computing Modernization Program. 2007 Annual Report

DTIC Science & Technology

2008-03-01

Directorate, Kirtland AFB, NM Applications of Time-Accurate CFD in Order to Account for Blade -Row Interactions and Distortion Transfer in the Design of...Patterson AFB, OH Direct Numerical Simulations of Active Control for Low- Pressure Turbine Blades Herman Fasel, University of Arizona, Tucson, AZ (Air Force...interactions with the rotor wake . These HI-ARMS computations compare favorably with available wind tunnel test measurements of surface and flowfield

Nucleic acids: theory and computer simulation, Y2K.

PubMed

Beveridge, D L; McConnell, K J

2000-04-01

Molecular dynamics simulations on DNA and RNA that include solvent are now being performed under realistic environmental conditions of water activity and salt. Improvements to force-fields and treatments of long-range interactions have significantly increased the reliability of simulations. New studies of sequence effects, axis bending, solvation and conformational transitions have appeared.

Measuring excess free energies of self-assembled membrane structures.

PubMed

Norizoe, Yuki; Daoulas, Kostas Ch; Müller, Marcus

2010-01-01

Using computer simulation of a solvent-free, coarse-grained model for amphiphilic membranes, we study the excess free energy of hourglass-shaped connections (i.e., stalks) between two apposed bilayer membranes. In order to calculate the free energy by simulation in the canonical ensemble, we reversibly transfer two apposed bilayers into a configuration with a stalk in three steps. First, we gradually replace the intermolecular interactions by an external, ordering field. The latter is chosen such that the structure of the non-interacting system in this field closely resembles the structure of the original, interacting system in the absence of the external field. The absence of structural changes along this path suggests that it is reversible; a fact which is confirmed by expanded-ensemble simulations. Second, the external, ordering field is changed as to transform the non-interacting system from the apposed bilayer structure to two-bilayers connected by a stalk. The final external field is chosen such that the structure of the non-interacting system resembles the structure of the stalk in the interacting system without a field. On the third branch of the transformation path, we reversibly replace the external, ordering field by non-bonded interactions. Using expanded-ensemble techniques, the free energy change along this reversible path can be obtained with an accuracy of 10(-3)k(B)T per molecule in the n VT-ensemble. Calculating the chemical potential, we obtain the free energy of a stalk in the grandcanonical ensemble, and employing semi-grandcanonical techniques, we calculate the change of the excess free energy upon altering the molecular architecture. This computational strategy can be applied to compute the free energy of self-assembled phases in lipid and copolymer systems, and the excess free energy of defects or interfaces.

Look and Feel: Haptic Interaction for Biomedicine

DTIC Science & Technology

1995-10-01

algorithm that is evaluated within the topology of the model. During each time step, forces are summed for each mobile atom based on external forces...volumetric properties; (b) conserving computation power by rendering media local to the interaction point; and (c) evaluating the simulation within...alteration of the model topology. Simulation of the DSM state is accomplished by a multi-step algorithm that is evaluated within the topology of the

Modeling and simulation of protein-surface interactions: achievements and challenges.

PubMed

Ozboyaci, Musa; Kokh, Daria B; Corni, Stefano; Wade, Rebecca C

2016-01-01

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

Computer simulation of ledge formation and ledge interaction for the silicon (111) free surface

NASA Technical Reports Server (NTRS)

Balamane, H.; Halicioglu, T.; Tiller, W. A.

1987-01-01

Both strip and triangular clusters, composed of 2 -1 -1 line ledges, have been simulated on the Si (111) surface. The long-range ledge-ledge interaction and the surface stress tensor distribution have been evaluated for these two pill-box geometries using a semiempirical potential-energy function that incorporates both two-body and three-body contributions. The consequences of the ledge-ledge interaction on two-dimensional nucleation for Si (111) has been evaluated as a function of Si adatom supersaturation and shown to differ significantly from conventional theory, where such interaction is neglected.

Towards an interactive electromechanical model of the heart

PubMed Central

Talbot, Hugo; Marchesseau, Stéphanie; Duriez, Christian; Sermesant, Maxime; Cotin, Stéphane; Delingette, Hervé

2013-01-01

In this work, we develop an interactive framework for rehearsal of and training in cardiac catheter ablation, and for planning cardiac resynchronization therapy. To this end, an interactive and real-time electrophysiology model of the heart is developed to fit patient-specific data. The proposed interactive framework relies on two main contributions. First, an efficient implementation of cardiac electrophysiology is proposed, using the latest graphics processing unit computing techniques. Second, a mechanical simulation is then coupled to the electrophysiological signals to produce realistic motion of the heart. We demonstrate that pathological mechanical and electrophysiological behaviour can be simulated. PMID:24427533

Computational Simulation of the Formation and Material Behavior of Ice

NASA Technical Reports Server (NTRS)

Tong, Michael T.; Singhal, Surendra N.; Chamis, Christos C.

1994-01-01

Computational methods are described for simulating the formation and the material behavior of ice in prevailing transient environments. The methodology developed at the NASA Lewis Research Center was adopted. A three dimensional finite-element heat transfer analyzer was used to predict the thickness of ice formed under prevailing environmental conditions. A multi-factor interaction model for simulating the material behavior of time-variant ice layers is presented. The model, used in conjunction with laminated composite mechanics, updates the material properties of an ice block as its thickness increases with time. A sample case of ice formation in a body of water was used to demonstrate the methodology. The results showed that the formation and the material behavior of ice can be computationally simulated using the available composites technology.

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

NASA Astrophysics Data System (ADS)

Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

2014-01-01

Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

Human-Centered Design of Human-Computer-Human Dialogs in Aerospace Systems

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.

1998-01-01

A series of ongoing research programs at Georgia Tech established a need for a simulation support tool for aircraft computer-based aids. This led to the design and development of the Georgia Tech Electronic Flight Instrument Research Tool (GT-EFIRT). GT-EFIRT is a part-task flight simulator specifically designed to study aircraft display design and single pilot interaction. ne simulator, using commercially available graphics and Unix workstations, replicates to a high level of fidelity the Electronic Flight Instrument Systems (EFIS), Flight Management Computer (FMC) and Auto Flight Director System (AFDS) of the Boeing 757/767 aircraft. The simulator can be configured to present information using conventional looking B757n67 displays or next generation Primary Flight Displays (PFD) such as found on the Beech Starship and MD-11.

Simulating the interaction of the heliosphere with the local interstellar medium: MHD results from a finite volume approach, first bidimensional results

NASA Technical Reports Server (NTRS)

Chanteur, G.; Khanfir, R.

1995-01-01

We have designed a full compressible MHD code working on unstructured meshes in order to be able to compute accurately sharp structures embedded in large scale simulations. The code is based on a finite volume method making use of a kinetic flux splitting. A bidimensional version of the code has been used to simulate the interaction of a moving interstellar medium, magnetized or unmagnetized with a rotating and magnetized heliopspheric plasma source. Being aware that these computations are not realistic due to the restriction to two dimensions, we present it to demonstrate the ability of this new code to handle this problem. An axisymetric version, now under development, will be operational in a few months. Ultimately we plan to run a full 3d version.

Mechatronics Interface for Computer Assisted Prostate Surgery Training

NASA Astrophysics Data System (ADS)

Altamirano del Monte, Felipe; Padilla Castañeda, Miguel A.; Arámbula Cosío, Fernando

2006-09-01

In this work is presented the development of a mechatronics device to simulate the interaction of the surgeon with the surgical instrument (resectoscope) used during a Transurethral Resection of the Prostate (TURP). Our mechatronics interface is part of a computer assisted system for training in TURP, which is based on a 3D graphics model of the prostate which can be deformed and resected interactively by the user. The mechatronics interface, is the device that the urology residents will manipulate to simulate the movements performed during surgery. Our current prototype has five degrees of freedom, which are enough to have a realistic simulation of the surgery movements. Two of these degrees of freedom are linear, to determinate the linear displacement of the resecting loop and the other three are rotational to determinate three directions and amounts of rotation.

Modeling of electron-specimen interaction in scanning electron microscope for e-beam metrology and inspection: challenges and perspectives

NASA Astrophysics Data System (ADS)

Suzuki, Makoto; Kameda, Toshimasa; Doi, Ayumi; Borisov, Sergey; Babin, Sergey

2018-03-01

The interpretation of scanning electron microscopy (SEM) images of the latest semiconductor devices is not intuitive and requires comparison with computed images based on theoretical modeling and simulations. For quantitative image prediction and geometrical reconstruction of the specimen structure, the accuracy of the physical model is essential. In this paper, we review the current models of electron-solid interaction and discuss their accuracy. We perform the comparison of the simulated results with our experiments of SEM overlay of under-layer, grain imaging of copper interconnect, and hole bottom visualization by angular selective detectors, and show that our model well reproduces the experimental results. Remaining issues for quantitative simulation are also discussed, including the accuracy of the charge dynamics, treatment of beam skirt, and explosive increase in computing time.

Real-time simulation of a spiking neural network model of the basal ganglia circuitry using general purpose computing on graphics processing units.

PubMed

Igarashi, Jun; Shouno, Osamu; Fukai, Tomoki; Tsujino, Hiroshi

2011-11-01

Real-time simulation of a biologically realistic spiking neural network is necessary for evaluation of its capacity to interact with real environments. However, the real-time simulation of such a neural network is difficult due to its high computational costs that arise from two factors: (1) vast network size and (2) the complicated dynamics of biologically realistic neurons. In order to address these problems, mainly the latter, we chose to use general purpose computing on graphics processing units (GPGPUs) for simulation of such a neural network, taking advantage of the powerful computational capability of a graphics processing unit (GPU). As a target for real-time simulation, we used a model of the basal ganglia that has been developed according to electrophysiological and anatomical knowledge. The model consists of heterogeneous populations of 370 spiking model neurons, including computationally heavy conductance-based models, connected by 11,002 synapses. Simulation of the model has not yet been performed in real-time using a general computing server. By parallelization of the model on the NVIDIA Geforce GTX 280 GPU in data-parallel and task-parallel fashion, faster-than-real-time simulation was robustly realized with only one-third of the GPU's total computational resources. Furthermore, we used the GPU's full computational resources to perform faster-than-real-time simulation of three instances of the basal ganglia model; these instances consisted of 1100 neurons and 33,006 synapses and were synchronized at each calculation step. Finally, we developed software for simultaneous visualization of faster-than-real-time simulation output. These results suggest the potential power of GPGPU techniques in real-time simulation of realistic neural networks. Copyright © 2011 Elsevier Ltd. All rights reserved.

Determination of partial molar volumes from free energy perturbation theory†

PubMed Central

Vilseck, Jonah Z.; Tirado-Rives, Julian

2016-01-01

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood–Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm3 mol−1. The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute–solvent interactions. PMID:25589343

Determination of partial molar volumes from free energy perturbation theory.

PubMed

Vilseck, Jonah Z; Tirado-Rives, Julian; Jorgensen, William L

2015-04-07

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.

Improved Interactive Medical-Imaging System

NASA Technical Reports Server (NTRS)

Ross, Muriel D.; Twombly, Ian A.; Senger, Steven

2003-01-01

An improved computational-simulation system for interactive medical imaging has been invented. The system displays high-resolution, three-dimensional-appearing images of anatomical objects based on data acquired by such techniques as computed tomography (CT) and magnetic-resonance imaging (MRI). The system enables users to manipulate the data to obtain a variety of views for example, to display cross sections in specified planes or to rotate images about specified axes. Relative to prior such systems, this system offers enhanced capabilities for synthesizing images of surgical cuts and for collaboration by users at multiple, remote computing sites.

Fast Multipole Methods for Three-Dimensional N-body Problems

NASA Technical Reports Server (NTRS)

Koumoutsakos, P.

1995-01-01

We are developing computational tools for the simulations of three-dimensional flows past bodies undergoing arbitrary motions. High resolution viscous vortex methods have been developed that allow for extended simulations of two-dimensional configurations such as vortex generators. Our objective is to extend this methodology to three dimensions and develop a robust computational scheme for the simulation of such flows. A fundamental issue in the use of vortex methods is the ability of employing efficiently large numbers of computational elements to resolve the large range of scales that exist in complex flows. The traditional cost of the method scales as Omicron (N(sup 2)) as the N computational elements/particles induce velocities at each other, making the method unacceptable for simulations involving more than a few tens of thousands of particles. In the last decade fast methods have been developed that have operation counts of Omicron (N log N) or Omicron (N) (referred to as BH and GR respectively) depending on the details of the algorithm. These methods are based on the observation that the effect of a cluster of particles at a certain distance may be approximated by a finite series expansion. In order to exploit this observation we need to decompose the element population spatially into clusters of particles and build a hierarchy of clusters (a tree data structure) - smaller neighboring clusters combine to form a cluster of the next size up in the hierarchy and so on. This hierarchy of clusters allows one to determine efficiently when the approximation is valid. This algorithm is an N-body solver that appears in many fields of engineering and science. Some examples of its diverse use are in astrophysics, molecular dynamics, micro-magnetics, boundary element simulations of electromagnetic problems, and computer animation. More recently these N-body solvers have been implemented and applied in simulations involving vortex methods. Koumoutsakos and Leonard (1995) implemented the GR scheme in two dimensions for vector computer architectures allowing for simulations of bluff body flows using millions of particles. Winckelmans presented three-dimensional, viscous simulations of interacting vortex rings, using vortons and an implementation of a BH scheme for parallel computer architectures. Bhatt presented a vortex filament method to perform inviscid vortex ring interactions, with an alternative implementation of a BH scheme for a Connection Machine parallel computer architecture.

A brief introduction to computer-intensive methods, with a view towards applications in spatial statistics and stereology.

PubMed

Mattfeldt, Torsten

2011-04-01

Computer-intensive methods may be defined as data analytical procedures involving a huge number of highly repetitive computations. We mention resampling methods with replacement (bootstrap methods), resampling methods without replacement (randomization tests) and simulation methods. The resampling methods are based on simple and robust principles and are largely free from distributional assumptions. Bootstrap methods may be used to compute confidence intervals for a scalar model parameter and for summary statistics from replicated planar point patterns, and for significance tests. For some simple models of planar point processes, point patterns can be simulated by elementary Monte Carlo methods. The simulation of models with more complex interaction properties usually requires more advanced computing methods. In this context, we mention simulation of Gibbs processes with Markov chain Monte Carlo methods using the Metropolis-Hastings algorithm. An alternative to simulations on the basis of a parametric model consists of stochastic reconstruction methods. The basic ideas behind the methods are briefly reviewed and illustrated by simple worked examples in order to encourage novices in the field to use computer-intensive methods. © 2010 The Authors Journal of Microscopy © 2010 Royal Microscopical Society.

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Benchmarking of Heavy Ion Transport Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in designing and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Simulating electric field interactions with polar molecules using spectroscopic databases

NASA Astrophysics Data System (ADS)

Owens, Alec; Zak, Emil J.; Chubb, Katy L.; Yurchenko, Sergei N.; Tennyson, Jonathan; Yachmenev, Andrey

2017-03-01

Ro-vibrational Stark-associated phenomena of small polyatomic molecules are modelled using extensive spectroscopic data generated as part of the ExoMol project. The external field Hamiltonian is built from the computed ro-vibrational line list of the molecule in question. The Hamiltonian we propose is general and suitable for any polar molecule in the presence of an electric field. By exploiting precomputed data, the often prohibitively expensive computations associated with high accuracy simulations of molecule-field interactions are avoided. Applications to strong terahertz field-induced ro-vibrational dynamics of PH3 and NH3, and spontaneous emission data for optoelectrical Sisyphus cooling of H2CO and CH3Cl are discussed.

Computer simulations of rapid granular flows of spheres interacting with a flat, frictional boundary

DOE Office of Scientific and Technical Information (OSTI.GOV)

Louge, M.Y.

This paper employs computer simulations to test the theory of Jenkins [J. Applied Mech. [bold 59], 120 (1992)] for the interaction between a rapid granular flow of spheres and a flat, frictional wall. This paper examines the boundary conditions that relate the shear stress and energy flux at the wall to the normal stress, slip velocity, and fluctuation energy, and to the parameters that characterize a collision. It is found that while the theory captures the trends of the boundary conditions at low friction, it does not anticipate their behavior at large friction. A critical evaluation of Jenkins' assumptions suggestsmore » where his theory may be improved.« less

Chemical Computer Man: Chemical Agent Response Simulation (CARS). Technical report, January 1983-September 1985

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, E.G.; Mioduszewski, R.J.

The Chemical Computer Man: Chemical Agent Response Simulation (CARS) is a computer model and simulation program for estimating the dynamic changes in human physiological dysfunction resulting from exposures to chemical-threat nerve agents. The newly developed CARS methodology simulates agent exposure effects on the following five indices of human physiological function: mental, vision, cardio-respiratory, visceral, and limbs. Mathematical models and the application of basic pharmacokinetic principles were incorporated into the simulation so that for each chemical exposure, the relationship between exposure dosage, absorbed dosage (agent blood plasma concentration), and level of physiological response are computed as a function of time. CARS,more » as a simulation tool, is designed for the users with little or no computer-related experience. The model combines maximum flexibility with a comprehensive user-friendly interactive menu-driven system. Users define an exposure problem and obtain immediate results displayed in tabular, graphical, and image formats. CARS has broad scientific and engineering applications, not only in technology for the soldier in the area of Chemical Defense, but also in minimizing animal testing in biomedical and toxicological research and the development of a modeling system for human exposure to hazardous-waste chemicals.« less

Development of a computer-simulation model for a plant-nematode system.

PubMed

Ferris, H

1976-07-01

A computer-simulation model (MELSIM) of a Meloidogyne-grapevine system is developed. The objective is to attempt a holistic approach to the study of nematode population dynamics by using experimental data from controlled environmental conditions. A simulator with predictive ability would be useful in considering pest management alternatives and in teaching. Rates of flow and interaction between the components of the system are governed by environmental conditions. Equations for these rates are determined by fitting curves to data from controlled environment studies. Development of the model and trial simulations have revealed deficiencies in understanding of the system and identified areas where further research is necessary.

Computer simulation in mechanical spectroscopy

NASA Astrophysics Data System (ADS)

Blanter, M. S.

2012-09-01

Several examples are given for use of computer simulation in mechanical spectroscopy. On one hand simulation makes it possible to study relaxation mechanisms, and on the other hand to use the colossal accumulation of experimental material to study metals and alloys. The following examples are considered: the effect of Al atom ordering on the Snoek carbon peak in alloys of the system Fe - Al - C; the effect of plastic strain on Finkel'shtein - Rozin relaxation in Fe - Ni - C austenitic steel; checking the adequacy of energy interactions of interstitial atoms, calculated on the basis of a first-principle model by simulation of the concentration dependence of Snoek relaxation parameters in Nb - O.

Computer simulation of multigrid body dynamics and control

NASA Technical Reports Server (NTRS)

Swaminadham, M.; Moon, Young I.; Venkayya, V. B.

1990-01-01

The objective is to set up and analyze benchmark problems on multibody dynamics and to verify the predictions of two multibody computer simulation codes. TREETOPS and DISCOS have been used to run three example problems - one degree-of-freedom spring mass dashpot system, an inverted pendulum system, and a triple pendulum. To study the dynamics and control interaction, an inverted planar pendulum with an external body force and a torsional control spring was modeled as a hinge connected two-rigid body system. TREETOPS and DISCOS affected the time history simulation of this problem. System state space variables and their time derivatives from two simulation codes were compared.

RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Guan, W.; Cheng, X.; Huang, J.; Huber, G.; Li, W.; McCammon, J. A.; Zhang, B.

2018-06-01

RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) (Greengard and Rokhlin, 1997) where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library (DeBuhr et al., 2016, 2018). Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12,288 cores, while achieving approximately 54% strong-scaling efficiency.

Using a computer simulation for teaching communication skills: A blinded multisite mixed methods randomized controlled trial.

PubMed

Kron, Frederick W; Fetters, Michael D; Scerbo, Mark W; White, Casey B; Lypson, Monica L; Padilla, Miguel A; Gliva-McConvey, Gayle A; Belfore, Lee A; West, Temple; Wallace, Amelia M; Guetterman, Timothy C; Schleicher, Lauren S; Kennedy, Rebecca A; Mangrulkar, Rajesh S; Cleary, James F; Marsella, Stacy C; Becker, Daniel M

2017-04-01

To assess advanced communication skills among second-year medical students exposed either to a computer simulation (MPathic-VR) featuring virtual humans, or to a multimedia computer-based learning module, and to understand each group's experiences and learning preferences. A single-blinded, mixed methods, randomized, multisite trial compared MPathic-VR (N=210) to computer-based learning (N=211). Primary outcomes: communication scores during repeat interactions with MPathic-VR's intercultural and interprofessional communication scenarios and scores on a subsequent advanced communication skills objective structured clinical examination (OSCE). Multivariate analysis of variance was used to compare outcomes. student attitude surveys and qualitative assessments of their experiences with MPathic-VR or computer-based learning. MPathic-VR-trained students improved their intercultural and interprofessional communication performance between their first and second interactions with each scenario. They also achieved significantly higher composite scores on the OSCE than computer-based learning-trained students. Attitudes and experiences were more positive among students trained with MPathic-VR, who valued its providing immediate feedback, teaching nonverbal communication skills, and preparing them for emotion-charged patient encounters. MPathic-VR was effective in training advanced communication skills and in enabling knowledge transfer into a more realistic clinical situation. MPathic-VR's virtual human simulation offers an effective and engaging means of advanced communication training. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Using a computer simulation for teaching communication skills: A blinded multisite mixed methods randomized controlled trial

PubMed Central

Kron, Frederick W.; Fetters, Michael D.; Scerbo, Mark W.; White, Casey B.; Lypson, Monica L.; Padilla, Miguel A.; Gliva-McConvey, Gayle A.; Belfore, Lee A.; West, Temple; Wallace, Amelia M.; Guetterman, Timothy C.; Schleicher, Lauren S.; Kennedy, Rebecca A.; Mangrulkar, Rajesh S.; Cleary, James F.; Marsella, Stacy C.; Becker, Daniel M.

2016-01-01

Objectives To assess advanced communication skills among second-year medical students exposed either to a computer simulation (MPathic-VR) featuring virtual humans, or to a multimedia computer-based learning module, and to understand each group’s experiences and learning preferences. Methods A single-blinded, mixed methods, randomized, multisite trial compared MPathic-VR (N=210) to computer-based learning (N=211). Primary outcomes: communication scores during repeat interactions with MPathic-VR’s intercultural and interprofessional communication scenarios and scores on a subsequent advanced communication skills objective structured clinical examination (OSCE). Multivariate analysis of variance was used to compare outcomes. Secondary outcomes: student attitude surveys and qualitative assessments of their experiences with MPathic-VR or computer-based learning. Results MPathic-VR-trained students improved their intercultural and interprofessional communication performance between their first and second interactions with each scenario. They also achieved significantly higher composite scores on the OSCE than computer-based learning-trained students. Attitudes and experiences were more positive among students trained with MPathic-VR, who valued its providing immediate feedback, teaching nonverbal communication skills, and preparing them for emotion-charged patient encounters. Conclusions MPathic-VR was effective in training advanced communication skills and in enabling knowledge transfer into a more realistic clinical situation. Practice Implications MPathic-VR’s virtual human simulation offers an effective and engaging means of advanced communication training. PMID:27939846

Deformation of Soft Tissue and Force Feedback Using the Smoothed Particle Hydrodynamics

PubMed Central

Liu, Xuemei; Wang, Ruiyi; Li, Yunhua; Song, Dongdong

2015-01-01

We study the deformation and haptic feedback of soft tissue in virtual surgery based on a liver model by using a force feedback device named PHANTOM OMNI developed by SensAble Company in USA. Although a significant amount of research efforts have been dedicated to simulating the behaviors of soft tissue and implementing force feedback, it is still a challenging problem. This paper introduces a kind of meshfree method for deformation simulation of soft tissue and force computation based on viscoelastic mechanical model and smoothed particle hydrodynamics (SPH). Firstly, viscoelastic model can present the mechanical characteristics of soft tissue which greatly promotes the realism. Secondly, SPH has features of meshless technique and self-adaption, which supply higher precision than methods based on meshes for force feedback computation. Finally, a SPH method based on dynamic interaction area is proposed to improve the real time performance of simulation. The results reveal that SPH methodology is suitable for simulating soft tissue deformation and force feedback calculation, and SPH based on dynamic local interaction area has a higher computational efficiency significantly compared with usual SPH. Our algorithm has a bright prospect in the area of virtual surgery. PMID:26417380

Integrating interactive computational modeling in biology curricula.

PubMed

Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

2015-03-01

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Fluid–Structure Interaction Analysis of Papillary Muscle Forces Using a Comprehensive Mitral Valve Model with 3D Chordal Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toma, Milan; Jensen, Morten Ø.; Einstein, Daniel R.

2015-07-17

Numerical models of native heart valves are being used to study valve biomechanics to aid design and development of repair procedures and replacement devices. These models have evolved from simple two-dimensional approximations to complex three-dimensional, fully coupled fluid-structure interaction (FSI) systems. Such simulations are useful for predicting the mechanical and hemodynamic loading on implanted valve devices. A current challenge for improving the accuracy of these predictions is choosing and implementing modeling boundary conditions. In order to address this challenge, we are utilizing an advanced in-vitro system to validate FSI conditions for the mitral valve system. Explanted ovine mitral valves weremore » mounted in an in vitro setup, and structural data for the mitral valve was acquired with *CT. Experimental data from the in-vitro ovine mitral valve system were used to validate the computational model. As the valve closes, the hemodynamic data, high speed lea et dynamics, and force vectors from the in-vitro system were compared to the results of the FSI simulation computational model. The total force of 2.6 N per papillary muscle is matched by the computational model. In vitro and in vivo force measurements are important in validating and adjusting material parameters in computational models. The simulations can then be used to answer questions that are otherwise not possible to investigate experimentally. This work is important to maximize the validity of computational models of not just the mitral valve, but any biomechanical aspect using computational simulation in designing medical devices.« less

Fluid-Structure Interaction Analysis of Papillary Muscle Forces Using a Comprehensive Mitral Valve Model with 3D Chordal Structure.

PubMed

Toma, Milan; Jensen, Morten Ø; Einstein, Daniel R; Yoganathan, Ajit P; Cochran, Richard P; Kunzelman, Karyn S

2016-04-01

Numerical models of native heart valves are being used to study valve biomechanics to aid design and development of repair procedures and replacement devices. These models have evolved from simple two-dimensional approximations to complex three-dimensional, fully coupled fluid-structure interaction (FSI) systems. Such simulations are useful for predicting the mechanical and hemodynamic loading on implanted valve devices. A current challenge for improving the accuracy of these predictions is choosing and implementing modeling boundary conditions. In order to address this challenge, we are utilizing an advanced in vitro system to validate FSI conditions for the mitral valve system. Explanted ovine mitral valves were mounted in an in vitro setup, and structural data for the mitral valve was acquired with [Formula: see text]CT. Experimental data from the in vitro ovine mitral valve system were used to validate the computational model. As the valve closes, the hemodynamic data, high speed leaflet dynamics, and force vectors from the in vitro system were compared to the results of the FSI simulation computational model. The total force of 2.6 N per papillary muscle is matched by the computational model. In vitro and in vivo force measurements enable validating and adjusting material parameters to improve the accuracy of computational models. The simulations can then be used to answer questions that are otherwise not possible to investigate experimentally. This work is important to maximize the validity of computational models of not just the mitral valve, but any biomechanical aspect using computational simulation in designing medical devices.

Community as client: environmental issues in the real world. A SimCity computer simulation.

PubMed

Bareford, C G

2001-01-01

The ability to think critically has become a crucial part of professional practice and education. SimCity, a popular computer simulation game, provides an opportunity to practice community assessment and interventions using a systems approach. SimCity is an interactive computer simulation game in which the player takes an active part in community planning. SimCity is supported on either a Windows 95/98 or a Macintosh platform and is available on CD-ROM at retail stores or at www.simcity.com. Students complete a tutorial and then apply a selected scenario in SimCity. Scenarios consist of hypothetical communities that have varying types and degrees of environmental problems, e.g., traffic, crime, nuclear meltdown, flooding, fire, and earthquakes. In problem solving with the simulated scenarios, students (a) identify systems and subsystems within the community that are critical factors impacting the environmental health of the community, (b) create changes in the systems and subsystems in an effort to solve the environmental health problem, and (c) evaluate the effectiveness of interventions based on the game score, demographic and fiscal data, and amount of community support. Because the consequences of planned intervention are part of the simulation, nursing students are able to develop critical-thinking skills. The simulation provides essential content in community planning in an interesting and interactive format.

Stochastic optimization of GeantV code by use of genetic algorithms

DOE PAGES

Amadio, G.; Apostolakis, J.; Bandieramonte, M.; ...

2017-10-01

GeantV is a complex system based on the interaction of different modules needed for detector simulation, which include transport of particles in fields, physics models simulating their interactions with matter and a geometrical modeler library for describing the detector and locating the particles and computing the path length to the current volume boundary. The GeantV project is recasting the classical simulation approach to get maximum benefit from SIMD/MIMD computational architectures and highly massive parallel systems. This involves finding the appropriate balance between several aspects influencing computational performance (floating-point performance, usage of off-chip memory bandwidth, specification of cache hierarchy, etc.) andmore » handling a large number of program parameters that have to be optimized to achieve the best simulation throughput. This optimization task can be treated as a black-box optimization problem, which requires searching the optimum set of parameters using only point-wise function evaluations. Here, the goal of this study is to provide a mechanism for optimizing complex systems (high energy physics particle transport simulations) with the help of genetic algorithms and evolution strategies as tuning procedures for massive parallel simulations. One of the described approaches is based on introducing a specific multivariate analysis operator that could be used in case of resource expensive or time consuming evaluations of fitness functions, in order to speed-up the convergence of the black-box optimization problem.« less

Stochastic optimization of GeantV code by use of genetic algorithms

NASA Astrophysics Data System (ADS)

Amadio, G.; Apostolakis, J.; Bandieramonte, M.; Behera, S. P.; Brun, R.; Canal, P.; Carminati, F.; Cosmo, G.; Duhem, L.; Elvira, D.; Folger, G.; Gheata, A.; Gheata, M.; Goulas, I.; Hariri, F.; Jun, S. Y.; Konstantinov, D.; Kumawat, H.; Ivantchenko, V.; Lima, G.; Nikitina, T.; Novak, M.; Pokorski, W.; Ribon, A.; Seghal, R.; Shadura, O.; Vallecorsa, S.; Wenzel, S.

2017-10-01

GeantV is a complex system based on the interaction of different modules needed for detector simulation, which include transport of particles in fields, physics models simulating their interactions with matter and a geometrical modeler library for describing the detector and locating the particles and computing the path length to the current volume boundary. The GeantV project is recasting the classical simulation approach to get maximum benefit from SIMD/MIMD computational architectures and highly massive parallel systems. This involves finding the appropriate balance between several aspects influencing computational performance (floating-point performance, usage of off-chip memory bandwidth, specification of cache hierarchy, etc.) and handling a large number of program parameters that have to be optimized to achieve the best simulation throughput. This optimization task can be treated as a black-box optimization problem, which requires searching the optimum set of parameters using only point-wise function evaluations. The goal of this study is to provide a mechanism for optimizing complex systems (high energy physics particle transport simulations) with the help of genetic algorithms and evolution strategies as tuning procedures for massive parallel simulations. One of the described approaches is based on introducing a specific multivariate analysis operator that could be used in case of resource expensive or time consuming evaluations of fitness functions, in order to speed-up the convergence of the black-box optimization problem.

Stochastic optimization of GeantV code by use of genetic algorithms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amadio, G.; Apostolakis, J.; Bandieramonte, M.

GeantV is a complex system based on the interaction of different modules needed for detector simulation, which include transport of particles in fields, physics models simulating their interactions with matter and a geometrical modeler library for describing the detector and locating the particles and computing the path length to the current volume boundary. The GeantV project is recasting the classical simulation approach to get maximum benefit from SIMD/MIMD computational architectures and highly massive parallel systems. This involves finding the appropriate balance between several aspects influencing computational performance (floating-point performance, usage of off-chip memory bandwidth, specification of cache hierarchy, etc.) andmore » handling a large number of program parameters that have to be optimized to achieve the best simulation throughput. This optimization task can be treated as a black-box optimization problem, which requires searching the optimum set of parameters using only point-wise function evaluations. Here, the goal of this study is to provide a mechanism for optimizing complex systems (high energy physics particle transport simulations) with the help of genetic algorithms and evolution strategies as tuning procedures for massive parallel simulations. One of the described approaches is based on introducing a specific multivariate analysis operator that could be used in case of resource expensive or time consuming evaluations of fitness functions, in order to speed-up the convergence of the black-box optimization problem.« less

Man-in-the-control-loop simulation of manipulators

NASA Technical Reports Server (NTRS)

Chang, J. L.; Lin, Tsung-Chieh; Yae, K. Harold

1989-01-01

A method to achieve man-in-the-control-loop simulation is presented. Emerging real-time dynamics simulation suggests a potential for creating an interactive design workstation with a human operator in the control loop. The recursive formulation for multibody dynamics simulation is studied to determine requirements for man-in-the-control-loop simulation. High speed computer graphics techniques provides realistic visual cues for the simulator. Backhoe and robot arm simulations are implemented to demonstrate the capability of man-in-the-control-loop simulation.

Videodisc/Microcomputer Technology in Wildland Fire Behavior Training

Treesearch

M. J. Jenkins; K.Y. Matsumoto-Grah

1987-01-01

Interactive video is a powerful medium, bringing together the emotional impact of video and film and the interactive capabilities of the computer. Interactive videodisc instruction can be used as a tutorial, for drill and practice and in simulations, as well as for information storage. Videodisc technology is being used in industrial, military and medical applications...

Polynomial-time quantum algorithm for the simulation of chemical dynamics

PubMed Central

Kassal, Ivan; Jordan, Stephen P.; Love, Peter J.; Mohseni, Masoud; Aspuru-Guzik, Alán

2008-01-01

The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can be applied only to small systems. By contrast, we demonstrate that quantum computers could exactly simulate chemical reactions in polynomial time. Our algorithm uses the split-operator approach and explicitly simulates all electron-nuclear and interelectronic interactions in quadratic time. Surprisingly, this treatment is not only more accurate than the Born–Oppenheimer approximation but faster and more efficient as well, for all reactions with more than about four atoms. This is the case even though the entire electronic wave function is propagated on a grid with appropriately short time steps. Although the preparation and measurement of arbitrary states on a quantum computer is inefficient, here we demonstrate how to prepare states of chemical interest efficiently. We also show how to efficiently obtain chemically relevant observables, such as state-to-state transition probabilities and thermal reaction rates. Quantum computers using these techniques could outperform current classical computers with 100 qubits. PMID:19033207

Computer simulations of the interaction of human immunodeficiency virus (HIV) aspartic protease with spherical gold nanoparticles: implications in acquired immunodeficiency syndrome (AIDS)

NASA Astrophysics Data System (ADS)

Whiteley, Chris G.; Lee, Duu-Jong

2016-09-01

The interaction of gold nanoparticles (AuNP) with human immune-deficiency virus aspartic protease (HIVPR) is modelled using a regime of molecular dynamics simulations. The simulations of the ‘docking’, first as a rigid-body complex, and eventually through flexible-fit analysis, creates 36 different complexes from four initial orientations of the nanoparticle strategically positioned around the surface of the enzyme. The structural deviations of the enzymes from the initial x-ray crystal structure during each docking simulation are assessed by comparative analysis of secondary structural elements, root mean square deviations, B-factors, interactive bonding energies, dihedral angles, radius of gyration (R g), circular dichroism (CD), volume occupied by C α , electrostatic potentials, solvation energies and hydrophobicities. Normalisation of the data narrows the selection from the initial 36 to one ‘final’ probable structure. It is concluded that, after computer simulations on each of the 36 initial complexes incorporating the 12 different biophysical techniques, the top five complexes are the same no matter which technique is explored. The significance of the present work is an expansion of an earlier study on the molecular dynamic simulation for the interaction of HIVPR with silver nanoparticles. This work is supported by experimental evidence since the initial ‘orientation’ of the AgNP with the enzyme is the same as the ‘final’ AuNP-HIVPR complex generated in the present study. The findings will provide insight into the forces of the binding of the HIVPR to AuNP. It is anticipated that the protocol developed in this study will act as a standard process for the interaction of any nanoparticle with any biomedical target.

Computer simulations of the interaction of human immunodeficiency virus (HIV) aspartic protease with spherical gold nanoparticles: implications in acquired immunodeficiency syndrome (AIDS).

PubMed

Whiteley, Chris G; Lee, Duu-Jong

2016-09-09

The interaction of gold nanoparticles (AuNP) with human immune-deficiency virus aspartic protease (HIVPR) is modelled using a regime of molecular dynamics simulations. The simulations of the 'docking', first as a rigid-body complex, and eventually through flexible-fit analysis, creates 36 different complexes from four initial orientations of the nanoparticle strategically positioned around the surface of the enzyme. The structural deviations of the enzymes from the initial x-ray crystal structure during each docking simulation are assessed by comparative analysis of secondary structural elements, root mean square deviations, B-factors, interactive bonding energies, dihedral angles, radius of gyration (R g), circular dichroism (CD), volume occupied by C α , electrostatic potentials, solvation energies and hydrophobicities. Normalisation of the data narrows the selection from the initial 36 to one 'final' probable structure. It is concluded that, after computer simulations on each of the 36 initial complexes incorporating the 12 different biophysical techniques, the top five complexes are the same no matter which technique is explored. The significance of the present work is an expansion of an earlier study on the molecular dynamic simulation for the interaction of HIVPR with silver nanoparticles. This work is supported by experimental evidence since the initial 'orientation' of the AgNP with the enzyme is the same as the 'final' AuNP-HIVPR complex generated in the present study. The findings will provide insight into the forces of the binding of the HIVPR to AuNP. It is anticipated that the protocol developed in this study will act as a standard process for the interaction of any nanoparticle with any biomedical target.

Advanced Techniques for Simulating the Behavior of Sand

NASA Astrophysics Data System (ADS)

Clothier, M.; Bailey, M.

2009-12-01

Computer graphics and visualization techniques continue to provide untapped research opportunities, particularly when working with earth science disciplines. Through collaboration with the Oregon Space Grant and IGERT Ecosystem Informatics programs we are developing new techniques for simulating sand. In addition, through collaboration with the Oregon Space Grant, we’ve been communicating with the Jet Propulsion Laboratory (JPL) to exchange ideas and gain feedback on our work. More specifically, JPL’s DARTS Laboratory specializes in planetary vehicle simulation, such as the Mars rovers. This simulation utilizes a virtual "sand box" to test how planetary rovers respond to different terrains while traversing them. Unfortunately, this simulation is unable to fully mimic the harsh, sandy environments of those found on Mars. Ideally, these simulations should allow a rover to interact with the sand beneath it, particularly for different sand granularities and densities. In particular, there may be situations where a rover may become stuck in sand due to lack of friction between the sand and wheels. In fact, in May 2009, the Spirit rover became stuck in the Martian sand and has provided additional motivation for this research. In order to develop a new sand simulation model, high performance computing will play a very important role in this work. More specifically, graphics processing units (GPUs) are useful due to their ability to run general purpose algorithms and ability to perform massively parallel computations. In prior research, simulating vast quantities of sand has been difficult to compute in real-time due to the computational complexity of many colliding particles. With the use of GPUs however, each particle collision will be parallelized, allowing for a dramatic performance increase. In addition, spatial partitioning will also provide a speed boost as this will help limit the number of particle collision calculations. However, since the goal of this research is to simulate the look and behavior of sand, this work will go beyond simple particle collision. In particular, we can continue to use our parallel algorithms not only on single particles but on particle “clumps” that consist of multiple combined particles. Since sand is typically not spherical in nature, these particle “clumps” help to simulate the coarse nature of sand. In a simulation environment, multiple combined particles could be used to simulate the polygonal and granular nature of sand grains. Thus, a diversity of sand particles can be generated. The interaction between these particles can then be parallelized using GPU hardware. As such, this research will investigate different graphics and physics techniques and determine the tradeoffs in performance and visual quality for sand simulation. An enhanced sand model through the use of high performance computing and GPUs has great potential to impact research for both earth and space scientists. Interaction with JPL has provided an opportunity for us to refine our simulation techniques that can ultimately be used for their vehicle simulator. As an added benefit of this work, advancements in simulating sand can also benefit scientists here on earth, especially in regard to understanding landslides and debris flows.

DSMC simulations of shock interactions about sharp double cones

NASA Astrophysics Data System (ADS)

Moss, James N.

2001-08-01

This paper presents the results of a numerical study of shock interactions resulting from Mach 10 flow about sharp double cones. Computations are made by using the direct simulation Monte Carlo (DSMC) method of Bird. The sensitivity and characteristics of the interactions are examined by varying flow conditions, model size, and configuration. The range of conditions investigated includes those for which experiments have been or will be performed in the ONERA R5Ch low-density wind tunnel and the Calspan-University of Buffalo Research Center (CUBRC) Large Energy National Shock (LENS) tunnel.

DSMC Simulations of Shock Interactions About Sharp Double Cones

NASA Technical Reports Server (NTRS)

Moss, James N.

2000-01-01

This paper presents the results of a numerical study of shock interactions resulting from Mach 10 flow about sharp double cones. Computations are made by using the direct simulation Monte Carlo (DSMC) method of Bird. The sensitivity and characteristics of the interactions are examined by varying flow conditions, model size, and configuration. The range of conditions investigated includes those for which experiments have been or will be performed in the ONERA R5Ch low-density wind tunnel and the Calspan-University of Buffalo Research Center (CUBRC) Large Energy National Shock (LENS) tunnel.

Hydrodynamic interactions in active colloidal crystal microrheology.

PubMed

Weeber, R; Harting, J

2012-11-01

In dense colloids it is commonly assumed that hydrodynamic interactions do not play a role. However, a found theoretical quantification is often missing. We present computer simulations that are motivated by experiments where a large colloidal particle is dragged through a colloidal crystal. To qualify the influence of long-ranged hydrodynamics, we model the setup by conventional Langevin dynamics simulations and by an improved scheme with limited hydrodynamic interactions. This scheme significantly improves our results and allows to show that hydrodynamics strongly impacts the development of defects, the crystal regeneration, as well as the jamming behavior.

Predictive wind turbine simulation with an adaptive lattice Boltzmann method for moving boundaries

NASA Astrophysics Data System (ADS)

Deiterding, Ralf; Wood, Stephen L.

2016-09-01

Operating horizontal axis wind turbines create large-scale turbulent wake structures that affect the power output of downwind turbines considerably. The computational prediction of this phenomenon is challenging as efficient low dissipation schemes are necessary that represent the vorticity production by the moving structures accurately and that are able to transport wakes without significant artificial decay over distances of several rotor diameters. We have developed a parallel adaptive lattice Boltzmann method for large eddy simulation of turbulent weakly compressible flows with embedded moving structures that considers these requirements rather naturally and enables first principle simulations of wake-turbine interaction phenomena at reasonable computational costs. The paper describes the employed computational techniques and presents validation simulations for the Mexnext benchmark experiments as well as simulations of the wake propagation in the Scaled Wind Farm Technology (SWIFT) array consisting of three Vestas V27 turbines in triangular arrangement.

The visible ear simulator: a public PC application for GPU-accelerated haptic 3D simulation of ear surgery based on the visible ear data.

PubMed

Sorensen, Mads Solvsten; Mosegaard, Jesper; Trier, Peter

2009-06-01

Existing virtual simulators for middle ear surgery are based on 3-dimensional (3D) models from computed tomographic or magnetic resonance imaging data in which image quality is limited by the lack of detail (maximum, approximately 50 voxels/mm3), natural color, and texture of the source material.Virtual training often requires the purchase of a program, a customized computer, and expensive peripherals dedicated exclusively to this purpose. The Visible Ear freeware library of digital images from a fresh-frozen human temporal bone was segmented, and real-time volume rendered as a 3D model of high-fidelity, true color, and great anatomic detail and realism of the surgically relevant structures. A haptic drilling model was developed for surgical interaction with the 3D model. Realistic visualization in high-fidelity (approximately 125 voxels/mm3) and true color, 2D, or optional anaglyph stereoscopic 3D was achieved on a standard Core 2 Duo personal computer with a GeForce 8,800 GTX graphics card, and surgical interaction was provided through a relatively inexpensive (approximately $2,500) Phantom Omni haptic 3D pointing device. This prototype is published for download (approximately 120 MB) as freeware at http://www.alexandra.dk/ves/index.htm.With increasing personal computer performance, future versions may include enhanced resolution (up to 8,000 voxels/mm3) and realistic interaction with deformable soft tissue components such as skin, tympanic membrane, dura, and cholesteatomas-features some of which are not possible with computed tomographic-/magnetic resonance imaging-based systems.

Terascale Visualization: Multi-resolution Aspirin for Big-Data Headaches

NASA Astrophysics Data System (ADS)

Duchaineau, Mark

2001-06-01

Recent experience on the Accelerated Strategic Computing Initiative (ASCI) computers shows that computational physicists are successfully producing a prodigious collection of numbers on several thousand processors. But with this wealth of numbers comes an unprecedented difficulty in processing and moving them to provide useful insight and analysis. In this talk, a few simulations are highlighted where recent advancements in multiple-resolution mathematical representations and algorithms have provided some hope of seeing most of the physics of interest while keeping within the practical limits of the post-simulation storage and interactive data-exploration resources. A whole host of visualization research activities was spawned by the 1999 Gordon Bell Prize-winning computation of a shock-tube experiment showing Richtmyer-Meshkov turbulent instabilities. This includes efforts for the entire data pipeline from running simulation to interactive display: wavelet compression of field data, multi-resolution volume rendering and slice planes, out-of-core extraction and simplification of mixing-interface surfaces, shrink-wrapping to semi-regularize the surfaces, semi-structured surface wavelet compression, and view-dependent display-mesh optimization. More recently on the 12 TeraOps ASCI platform, initial results from a 5120-processor, billion-atom molecular dynamics simulation showed that 30-to-1 reductions in storage size can be achieved with no human-observable errors for the analysis required in simulations of supersonic crack propagation. This made it possible to store the 25 trillion bytes worth of simulation numbers in the available storage, which was under 1 trillion bytes. While multi-resolution methods and related systems are still in their infancy, for the largest-scale simulations there is often no other choice should the science require detailed exploration of the results.

Simulating regolith ejecta due to gas impingement

NASA Astrophysics Data System (ADS)

Chambers, Wesley Allen; Metzger, Philip; Dove, Adrienne; Britt, Daniel

2016-10-01

Space missions operating at or near the surface of a planet or small body must consider possible gas-regolith interactions, as they can cause hazardous effects or, conversely, be employed to accomplish mission goals. They are also directly related to a body's surface properties; thus understanding these interactions could provide an additional tool to analyze mission data. The Python Regolith Interaction Calculator (PyRIC), built upon a computational technique developed in the Apollo era, was used to assess interactions between rocket exhaust and an asteroid's surface. It focused specifically on threshold conditions for causing regolith ejecta. To improve this model, and learn more about the underlying physics, we have begun ground-based experiments studying the interaction between gas impingement and regolith simulant. Compressed air, initially standing in for rocket exhaust, is directed through a rocket nozzle at a bed of simulant. We assess the qualitative behavior of various simulants when subjected to a known maximum surface pressure, both in atmosphere and in a chamber initially at vacuum. These behaviors are compared to prior computational results, and possible flow patterns are inferred. Our future work will continue these experiments in microgravity through the use of a drop tower. These will use several simulant types and various pressure levels to observe the effects gas flow can have on target surfaces. Combining this with a characterization of the surface pressure distribution, tighter bounds can be set on the cohesive threshold necessary to maintain regolith integrity. This will aid the characterization of actual regolith distributions, as well as informing the surface operation phase of mission design.

Application of control theory to dynamic systems simulation

NASA Technical Reports Server (NTRS)

Auslander, D. M.; Spear, R. C.; Young, G. E.

1982-01-01

The application of control theory is applied to dynamic systems simulation. Theory and methodology applicable to controlled ecological life support systems are considered. Spatial effects on system stability, design of control systems with uncertain parameters, and an interactive computing language (PARASOL-II) designed for dynamic system simulation, report quality graphics, data acquisition, and simple real time control are discussed.

Games, Simulations, and Visual Metaphors in Education: Antagonism between Enjoyment and Learning

ERIC Educational Resources Information Center

Rieber, Lloyd P.; Noah, David

2008-01-01

The purpose of this study was to investigate the influence of game-like activities on adult learning during a computer-based simulation. This research also studied the use of visual metaphors as graphic organizers to help make the underlying science principles explicit without interfering with the interactive nature of the simulation. A total of…

Micro-Ramp Flow Control for Oblique Shock Interactions: Comparisons of Computational and Experimental Data

NASA Technical Reports Server (NTRS)

Hirt, Stefanie M.; Reich, David B.; O'Connor, Michael B.

2010-01-01

Computational fluid dynamics was used to study the effectiveness of micro-ramp vortex generators to control oblique shock boundary layer interactions. Simulations were based on experiments previously conducted in the 15 x 15 cm supersonic wind tunnel at NASA Glenn Research Center. Four micro-ramp geometries were tested at Mach 2.0 varying the height, chord length, and spanwise spacing between micro-ramps. The overall flow field was examined. Additionally, key parameters such as boundary-layer displacement thickness, momentum thickness and incompressible shape factor were also examined. The computational results predicted the effects of the micro-ramps well, including the trends for the impact that the devices had on the shock boundary layer interaction. However, computing the shock boundary layer interaction itself proved to be problematic since the calculations predicted more pronounced adverse effects on the boundary layer due to the shock than were seen in the experiment.

Micro-Ramp Flow Control for Oblique Shock Interactions: Comparisons of Computational and Experimental Data

NASA Technical Reports Server (NTRS)

Hirt, Stephanie M.; Reich, David B.; O'Connor, Michael B.

2012-01-01

Computational fluid dynamics was used to study the effectiveness of micro-ramp vortex generators to control oblique shock boundary layer interactions. Simulations were based on experiments previously conducted in the 15- by 15-cm supersonic wind tunnel at the NASA Glenn Research Center. Four micro-ramp geometries were tested at Mach 2.0 varying the height, chord length, and spanwise spacing between micro-ramps. The overall flow field was examined. Additionally, key parameters such as boundary-layer displacement thickness, momentum thickness and incompressible shape factor were also examined. The computational results predicted the effects of the microramps well, including the trends for the impact that the devices had on the shock boundary layer interaction. However, computing the shock boundary layer interaction itself proved to be problematic since the calculations predicted more pronounced adverse effects on the boundary layer due to the shock than were seen in the experiment.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

PubMed Central

Chen, Yang; Zhang, Michael Q.

2018-01-01

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. PMID:29440282

A molecular dynamics approach for predicting the glass transition temperature and plasticization effect in amorphous pharmaceuticals.

PubMed

Gupta, Jasmine; Nunes, Cletus; Jonnalagadda, Sriramakamal

2013-11-04

The objectives of this study were as follows: (i) To develop an in silico technique, based on molecular dynamics (MD) simulations, to predict glass transition temperatures (Tg) of amorphous pharmaceuticals. (ii) To computationally study the effect of plasticizer on Tg. (iii) To investigate the intermolecular interactions using radial distribution function (RDF). Amorphous sucrose and water were selected as the model compound and plasticizer, respectively. MD simulations were performed using COMPASS force field and isothermal-isobaric ensembles. The specific volumes of amorphous cells were computed in the temperature range of 440-265 K. The characteristic "kink" observed in volume-temperature curves, in conjunction with regression analysis, defined the Tg. The MD computed Tg values were 367 K, 352 K and 343 K for amorphous sucrose containing 0%, 3% and 5% w/w water, respectively. The MD technique thus effectively simulated the plasticization effect of water; and the corresponding Tg values were in reasonable agreement with theoretical models and literature reports. The RDF measurements revealed strong hydrogen bond interactions between sucrose hydroxyl oxygens and water oxygen. Steric effects led to weak interactions between sucrose acetal oxygens and water oxygen. MD is thus a powerful predictive tool for probing temperature and water effects on the stability of amorphous systems during drug development.

GRAPE-4: A special-purpose computer for gravitational N-body problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makino, Junichiro; Taiji, Makoto; Ebisuzaki, Toshikazu

1995-12-01

We describe GRAPE-4, a special-purpose computer for gravitational N-body simulations. In gravitational N-body simulations, almost all computing time is spent for the calculation of interaction between particles. GRAPE-4 is a specialized hardware to calculate the interaction between particles. It is used with a general-purpose host computer that performs all calculations other than the force calculation. With this architecture, it is relatively easy to realize a massively parallel system. In 1991, we developed the GRAPE-3 system with the peak speed equivalent to 14.4 Gflops. It consists of 48 custom pipelined processors. In 1992 we started the development of GRAPE-4. The GRAPE-4more » system will consist of 1920 custom pipeline chips. Each chip has the speed of 600 Mflops, when operated on 30 MHz clock. A prototype system with two custom LSIs has been completed July 1994, and the full system is now under manufacturing.« less

OpenSees

Science.gov Websites

, through soil-structure interaction, to structural response. New computer simulation tools are necessary to of structures and soils to investigate challenging problems in soil-structure-foundation interaction including foundations and soils is used to study the effects of soil liquefaction and permanent

Challenges in reducing the computational time of QSTS simulations for distribution system analysis.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deboever, Jeremiah; Zhang, Xiaochen; Reno, Matthew J.

The rapid increase in penetration of distributed energy resources on the electric power distribution system has created a need for more comprehensive interconnection modelling and impact analysis. Unlike conventional scenario - based studies , quasi - static time - series (QSTS) simulation s can realistically model time - dependent voltage controllers and the diversity of potential impacts that can occur at different times of year . However, to accurately model a distribution system with all its controllable devices, a yearlong simulation at 1 - second resolution is often required , which could take conventional computers a computational time of 10more » to 120 hours when an actual unbalanced distribution feeder is modeled . This computational burden is a clear l imitation to the adoption of QSTS simulation s in interconnection studies and for determining optimal control solutions for utility operations . Our ongoing research to improve the speed of QSTS simulation has revealed many unique aspects of distribution system modelling and sequential power flow analysis that make fast QSTS a very difficult problem to solve. In this report , the most relevant challenges in reducing the computational time of QSTS simulations are presented: number of power flows to solve, circuit complexity, time dependence between time steps, multiple valid power flow solutions, controllable element interactions, and extensive accurate simulation analysis.« less

Local free energies for the coarse-graining of adsorption phenomena: The interacting pair approximation

NASA Astrophysics Data System (ADS)

Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco

2018-05-01

We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.

The Technologies of EXPER SIM.

ERIC Educational Resources Information Center

Hedberg, John G.

EXPER SIM has been translated into two basic software systems: the Michigan Experimental Simulation Supervisor (MESS) and Louisville Experiment Simulation Supervisor (LESS). MESS and LESS have been programed to facilitate student interaction with the computer for research purposes. The programs contain models for several statistical analyses, and…

Characterizing Representational Learning: A Combined Simulation and Tutorial on Perturbation Theory

ERIC Educational Resources Information Center

Kohnle, Antje; Passante, Gina

2017-01-01

Analyzing, constructing, and translating between graphical, pictorial, and mathematical representations of physics ideas and reasoning flexibly through them ("representational competence") is a key characteristic of expertise in physics but is a challenge for learners to develop. Interactive computer simulations and University of…

Computer simulation of surface and film processes

NASA Technical Reports Server (NTRS)

Tiller, W. A.; Halicioglu, M. T.

1984-01-01

All the investigations which were performed employed in one way or another a computer simulation technique based on atomistic level considerations. In general, three types of simulation methods were used for modeling systems with discrete particles that interact via well defined potential functions: molecular dynamics (a general method for solving the classical equations of motion of a model system); Monte Carlo (the use of Markov chain ensemble averaging technique to model equilibrium properties of a system); and molecular statics (provides properties of a system at T = 0 K). The effects of three-body forces on the vibrational frequencies of triatomic cluster were investigated. The multilayer relaxation phenomena for low index planes of an fcc crystal was analyzed also as a function of the three-body interactions. Various surface properties for Si and SiC system were calculated. Results obtained from static simulation calculations for slip formation were presented. The more elaborate molecular dynamics calculations on the propagation of cracks in two-dimensional systems were outlined.

Regularization method for large eddy simulations of shock-turbulence interactions

NASA Astrophysics Data System (ADS)

Braun, N. O.; Pullin, D. I.; Meiron, D. I.

2018-05-01

The rapid change in scales over a shock has the potential to introduce unique difficulties in Large Eddy Simulations (LES) of compressible shock-turbulence flows if the governing model does not sufficiently capture the spectral distribution of energy in the upstream turbulence. A method for the regularization of LES of shock-turbulence interactions is presented which is constructed to enforce that the energy content in the highest resolved wavenumbers decays as k - 5 / 3, and is computed locally in physical-space at low computational cost. The application of the regularization to an existing subgrid scale model is shown to remove high wavenumber errors while maintaining agreement with Direct Numerical Simulations (DNS) of forced and decaying isotropic turbulence. Linear interaction analysis is implemented to model the interaction of a shock with isotropic turbulence from LES. Comparisons to analytical models suggest that the regularization significantly improves the ability of the LES to predict amplifications in subgrid terms over the modeled shockwave. LES and DNS of decaying, modeled post shock turbulence are also considered, and inclusion of the regularization in shock-turbulence LES is shown to improve agreement with lower Reynolds number DNS.

A model-based approach to monitor complex road-vehicle interactions through first principles

NASA Astrophysics Data System (ADS)

Chakravarty, T.; Srinivasarengan, K.; Roy, S.; Bilal, S.; Balamuralidhar, P.

2013-02-01

The increasing availability of portable computing devices and their interaction with physical systems ask for designing compact models and simulations to understand and characterize such interactions. For instance, monitoring a road's grade using accelerometer stationed inside a moving ground vehicle is an emerging trend in city administration. Typically the focus has largely been to develop algorithms to articulate meaning from that. But, the experimentation cannot provide with an exhaustive analysis of all scenarios and the characteristics of them. We propose an approach of modeling these interactions of physical systems with gadgets through first principles, in a compact manner to focus on limited number of interactions. We derive an approach to model the vehicle interaction with a pothole on a road, a specific case, but allowing for selectable car parameters like natural damped frequency, tire size etc, thus generalizing it. Different road profiles are also created to represent rough road with sharp irregularities. These act as excitation to the moving vehicle and the interaction is computed to determine the vertical/ lateral vibration of the system i.e vehicle with sensors using joint time-frequency signal analysis methods. The simulation is compared with experimental data for validation. We show some directions as to how simulation of such models can reveal different characteristics of the interaction through analysis of their frequency spectrum. It is envisioned that the proposed models will get enriched further as and when large data set of real life data is captured and appropriate sensitivity analysis is done.

Comparison of three large-eddy simulations of shock-induced turbulent separation bubbles

NASA Astrophysics Data System (ADS)

Touber, Emile; Sandham, Neil D.

2009-12-01

Three different large-eddy simulation investigations of the interaction between an impinging oblique shock and a supersonic turbulent boundary layer are presented. All simulations made use of the same inflow technique, specifically aimed at avoiding possible low-frequency interferences with the shock/boundary-layer interaction system. All simulations were run on relatively wide computational domains and integrated over times greater than twenty five times the period of the most commonly reported low-frequency shock-oscillation, making comparisons at both time-averaged and low-frequency-dynamic levels possible. The results confirm previous experimental results which suggested a simple linear relation between the interaction length and the oblique-shock strength if scaled using the boundary-layer thickness and wall-shear stress. All the tested cases show evidences of significant low-frequency shock motions. At the wall, energetic low-frequency pressure fluctuations are observed, mainly in the initial part of interaction.

Pairwise Interaction Extended Point-Particle (PIEP) model for multiphase jets and sedimenting particles

NASA Astrophysics Data System (ADS)

Liu, Kai; Balachandar, S.

2017-11-01

We perform a series of Euler-Lagrange direct numerical simulations (DNS) for multiphase jets and sedimenting particles. The forces the flow exerts on the particles in these two-way coupled simulations are computed using the Basset-Bousinesq-Oseen (BBO) equations. These forces do not explicitly account for particle-particle interactions, even though such pairwise interactions induced by the perturbations from neighboring particles may be important especially when the particle volume fraction is high. Such effects have been largely unaddressed in the literature. Here, we implement the Pairwise Interaction Extended Point-Particle (PIEP) model to simulate the effect of neighboring particle pairs. A simple collision model is also applied to avoid unphysical overlapping of solid spherical particles. The simulation results indicate that the PIEP model provides a more elaborative and complicated movement of the dispersed phase (droplets and particles). Office of Naval Research (ONR) Multidisciplinary University Research Initiative (MURI) project N00014-16-1-2617.

Navier-Stokes Simulation of UH-60A Rotor/Wake Interaction Using Adaptive Mesh Refinement

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

2017-01-01

Time-dependent Navier-Stokes simulations have been carried out for a flexible UH-60A rotor in forward flight, where the rotor wake interacts with the rotor blades. These flow conditions involved blade vortex interaction and dynamic stall, two common conditions that occur as modern helicopter designs strive to achieve greater flight speeds and payload capacity. These numerical simulations utilized high-order spatial accuracy and delayed detached eddy simulation. Emphasis was placed on understanding how improved rotor wake resolution affects the prediction of the normal force, pitching moment, and chord force of the rotor. Adaptive mesh refinement was used to highly resolve the turbulent rotor wake in a computationally efficient manner. Moreover, blade vortex interaction was found to trigger dynamic stall. Time-dependent flow visualization was utilized to provide an improved understanding of the numerical and physical mechanisms involved with three-dimensional dynamic stall.

The effectiveness of interactive computer simulations on college engineering student conceptual understanding and problem-solving ability related to circular motion

NASA Astrophysics Data System (ADS)

Chien, Cheng-Chih

In the past thirty years, the effectiveness of computer assisted learning was found varied by individual studies. Today, with drastic technical improvement, computers have been widely spread in schools and used in a variety of ways. In this study, a design model involving educational technology, pedagogy, and content domain is proposed for effective use of computers in learning. Computer simulation, constructivist and Vygotskian perspectives, and circular motion are the three elements of the specific Chain Model for instructional design. The goal of the physics course is to help students remove the ideas which are not consistent with the physics community and rebuild new knowledge. To achieve the learning goal, the strategies of using conceptual conflicts and using language to internalize specific tasks into mental functions were included. Computer simulations and accompanying worksheets were used to help students explore their own ideas and to generate questions for discussions. Using animated images to describe the dynamic processes involved in the circular motion may reduce the complexity and possible miscommunications resulting from verbal explanations. The effectiveness of the instructional material on student learning is evaluated. The results of problem solving activities show that students using computer simulations had significantly higher scores than students not using computer simulations. For conceptual understanding, on the pretest students in the non-simulation group had significantly higher score than students in the simulation group. There was no significant difference observed between the two groups in the posttest. The relations of gender, prior physics experience, and frequency of computer uses outside the course to student achievement were also studied. There were fewer female students than male students and fewer students using computer simulations than students not using computer simulations. These characteristics affect the statistical power for detecting differences. For the future research, more intervention of simulations may be introduced to explore the potential of computer simulation in helping students learning. A test for conceptual understanding with more problems and appropriate difficulty level may be needed.

Radio Emmision during the interaction of two Interplanetary Coronal Mass Ejections

NASA Astrophysics Data System (ADS)

Lara, Alejandro; Niembro, Tatiana; González, Ricardo

2016-07-01

We show that some sporadic radio emission observed by the WIND/WAVES experiment in the decametric/kilometric bands are due to the interaction of two interplanetary Coronal Mass Ejections. We have performed hydrodynamic simulations of the evolution of two consecutive Coronal Mass ejections in the interplanetary medium. With these simulations it is possible to follow the density evolution of the merged structure, and therefore, compute the frequency limits of the possible plasma emission. We study four well documented ICME interaction events, and found radio emission at the time and frequencies predicted by the simulations. This emission may help to anticipate the complexity of the merged region before it reaches one AU.

Coulomb interactions in charged fluids.

PubMed

Vernizzi, Graziano; Guerrero-García, Guillermo Iván; de la Cruz, Monica Olvera

2011-07-01

The use of Ewald summation schemes for calculating long-range Coulomb interactions, originally applied to ionic crystalline solids, is a very common practice in molecular simulations of charged fluids at present. Such a choice imposes an artificial periodicity which is generally absent in the liquid state. In this paper we propose a simple analytical O(N(2)) method which is based on Gauss's law for computing exactly the Coulomb interaction between charged particles in a simulation box, when it is averaged over all possible orientations of a surrounding infinite lattice. This method mitigates the periodicity typical of crystalline systems and it is suitable for numerical studies of ionic liquids, charged molecular fluids, and colloidal systems with Monte Carlo and molecular dynamics simulations.

Simulation training tools for nonlethal weapons using gaming environments

NASA Astrophysics Data System (ADS)

Donne, Alexsana; Eagan, Justin; Tse, Gabriel; Vanderslice, Tom; Woods, Jerry

2006-05-01

Modern simulation techniques have a growing role for evaluating new technologies and for developing cost-effective training programs. A mission simulator facilitates the productive exchange of ideas by demonstration of concepts through compellingly realistic computer simulation. Revolutionary advances in 3D simulation technology have made it possible for desktop computers to process strikingly realistic and complex interactions with results depicted in real-time. Computer games now allow for multiple real human players and "artificially intelligent" (AI) simulated robots to play together. Advances in computer processing power have compensated for the inherent intensive calculations required for complex simulation scenarios. The main components of the leading game-engines have been released for user modifications, enabling game enthusiasts and amateur programmers to advance the state-of-the-art in AI and computer simulation technologies. It is now possible to simulate sophisticated and realistic conflict situations in order to evaluate the impact of non-lethal devices as well as conflict resolution procedures using such devices. Simulations can reduce training costs as end users: learn what a device does and doesn't do prior to use, understand responses to the device prior to deployment, determine if the device is appropriate for their situational responses, and train with new devices and techniques before purchasing hardware. This paper will present the status of SARA's mission simulation development activities, based on the Half-Life gameengine, for the purpose of evaluating the latest non-lethal weapon devices, and for developing training tools for such devices.

Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations

PubMed Central

2015-01-01

Many commonly used coarse-grained models for proteins are based on simplified interaction sites and consequently may suffer from significant limitations, such as the inability to properly model protein secondary structure without the addition of restraints. Recent work on a benzene fluid (LettieriS.; ZuckermanD. M.J. Comput. Chem.2012, 33, 268−27522120971) suggested an alternative strategy of tabulating and smoothing fully atomistic orientation-dependent interactions among rigid molecules or fragments. Here we report our initial efforts to apply this approach to the polar and covalent interactions intrinsic to polypeptides. We divide proteins into nearly rigid fragments, construct distance and orientation-dependent tables of the atomistic interaction energies between those fragments, and apply potential energy smoothing techniques to those tables. The amount of smoothing can be adjusted to give coarse-grained models that range from the underlying atomistic force field all the way to a bead-like coarse-grained model. For a moderate amount of smoothing, the method is able to preserve about 70–90% of the α-helical structure while providing a factor of 3–10 improvement in sampling per unit computation time (depending on how sampling is measured). For a greater amount of smoothing, multiple folding–unfolding transitions of the peptide were observed, along with a factor of 10–100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations. For a β hairpin, secondary structure is also preserved, albeit for a narrower range of the smoothing parameter and, consequently, for a more modest improvement in sampling. We have also applied the new method in a “resolution exchange” setting, in which each replica runs a Monte Carlo simulation with a different degree of smoothing. We obtain exchange rates that compare favorably to our previous efforts at resolution exchange (LymanE.; ZuckermanD. M.J. Chem. Theory Comput.2006, 2, 656−666). PMID:25400525

Algebraic Turbulence-Chemistry Interaction Model

NASA Technical Reports Server (NTRS)

Norris, Andrew T.

2012-01-01

The results of a series of Perfectly Stirred Reactor (PSR) and Partially Stirred Reactor (PaSR) simulations are compared to each other over a wide range of operating conditions. It is found that the PaSR results can be simulated by a PSR solution with just an adjusted chemical reaction rate. A simple expression has been developed that gives the required change in reaction rate for a PSR solution to simulate the PaSR results. This expression is the basis of a simple turbulence-chemistry interaction model. The interaction model that has been developed is intended for use with simple one-step global reaction mechanisms and for steady-state flow simulations. Due to the simplicity of the model there is very little additional computational cost in adding it to existing CFD codes.

Analysis of Inlet-Compressor Acoustic Interactions Using Coupled CFD Codes

NASA Technical Reports Server (NTRS)

Suresh, A.; Townsend, S. E.; Cole, G. L.; Slater, J. W.; Chima, R.

1998-01-01

A problem that arises in the numerical simulation of supersonic inlets is the lack of a suitable boundary condition at the engine face. In this paper, a coupled approach, in which the inlet computation is coupled dynamically to a turbomachinery computation, is proposed as a means to overcome this problem. The specific application chosen for validation of this approach is the collapsing bump experiment performed at the University of Cincinnati. The computed results are found to be in reasonable agreement with experimental results. The coupled simulation results could also be used to aid development of a simplified boundary condition.

Validation of a 3D computational fluid-structure interaction model simulating flow through an elastic aperture.

PubMed

Quaini, A; Canic, S; Glowinski, R; Igo, S; Hartley, C J; Zoghbi, W; Little, S

2012-01-10

This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. Copyright © 2011 Elsevier Ltd. All rights reserved.

Tackling some of the most intricate geophysical challenges via high-performance computing

NASA Astrophysics Data System (ADS)

Khosronejad, A.

2016-12-01

Recently, world has been witnessing significant enhancements in computing power of supercomputers. Computer clusters in conjunction with the advanced mathematical algorithms has set the stage for developing and applying powerful numerical tools to tackle some of the most intricate geophysical challenges that today`s engineers face. One such challenge is to understand how turbulent flows, in real-world settings, interact with (a) rigid and/or mobile complex bed bathymetry of waterways and sea-beds in the coastal areas; (b) objects with complex geometry that are fully or partially immersed; and (c) free-surface of waterways and water surface waves in the coastal area. This understanding is especially important because the turbulent flows in real-world environments are often bounded by geometrically complex boundaries, which dynamically deform and give rise to multi-scale and multi-physics transport phenomena, and characterized by multi-lateral interactions among various phases (e.g. air/water/sediment phases). Herein, I present some of the multi-scale and multi-physics geophysical fluid mechanics processes that I have attempted to study using an in-house high-performance computational model, the so-called VFS-Geophysics. More specifically, I will present the simulation results of turbulence/sediment/solute/turbine interactions in real-world settings. Parts of the simulations I present are performed to gain scientific insights into the processes such as sand wave formation (A. Khosronejad, and F. Sotiropoulos, (2014), Numerical simulation of sand waves in a turbulent open channel flow, Journal of Fluid Mechanics, 753:150-216), while others are carried out to predict the effects of climate change and large flood events on societal infrastructures ( A. Khosronejad, et al., (2016), Large eddy simulation of turbulence and solute transport in a forested headwater stream, Journal of Geophysical Research:, doi: 10.1002/2014JF003423).

Biocellion: accelerating computer simulation of multicellular biological system models

PubMed Central

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-01-01

Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. Contact: seunghwa.kang@pnnl.gov PMID:25064572

Robot, computer problem solving system

NASA Technical Reports Server (NTRS)

Becker, J. D.

1972-01-01

The development of a computer problem solving system is reported that considers physical problems faced by an artificial robot moving around in a complex environment. Fundamental interaction constraints with a real environment are simulated for the robot by visual scan and creation of an internal environmental model. The programming system used in constructing the problem solving system for the simulated robot and its simulated world environment is outlined together with the task that the system is capable of performing. A very general framework for understanding the relationship between an observed behavior and an adequate description of that behavior is included.

Quantum phases with differing computational power.

PubMed

Cui, Jian; Gu, Mile; Kwek, Leong Chuan; Santos, Marcelo França; Fan, Heng; Vedral, Vlatko

2012-05-01

The observation that concepts from quantum information has generated many alternative indicators of quantum phase transitions hints that quantum phase transitions possess operational significance with respect to the processing of quantum information. Yet, studies on whether such transitions lead to quantum phases that differ in their capacity to process information remain limited. Here we show that there exist quantum phase transitions that cause a distinct qualitative change in our ability to simulate certain quantum systems under perturbation of an external field by local operations and classical communication. In particular, we show that in certain quantum phases of the XY model, adiabatic perturbations of the external magnetic field can be simulated by local spin operations, whereas the resulting effect within other phases results in coherent non-local interactions. We discuss the potential implications to adiabatic quantum computation, where a computational advantage exists only when adiabatic perturbation results in coherent multi-body interactions.

Simulation of glioblastoma multiforme (GBM) tumor cells using ising model on the Creutz Cellular Automaton

NASA Astrophysics Data System (ADS)

Züleyha, Artuç; Ziya, Merdan; Selçuk, Yeşiltaş; Kemal, Öztürk M.; Mesut, Tez

2017-11-01

Computational models for tumors have difficulties due to complexity of tumor nature and capacities of computational tools, however, these models provide visions to understand interactions between tumor and its micro environment. Moreover computational models have potential to develop strategies for individualized treatments for cancer. To observe a solid brain tumor, glioblastoma multiforme (GBM), we present a two dimensional Ising Model applied on Creutz cellular automaton (CCA). The aim of this study is to analyze avascular spherical solid tumor growth, considering transitions between non tumor cells and cancer cells are like phase transitions in physical system. Ising model on CCA algorithm provides a deterministic approach with discrete time steps and local interactions in position space to view tumor growth as a function of time. Our simulation results are given for fixed tumor radius and they are compatible with theoretical and clinic data.

The use of computer simulations in whole-class versus small-group settings

NASA Astrophysics Data System (ADS)

Smetana, Lara Kathleen

This study explored the use of computer simulations in a whole-class as compared to small-group setting. Specific consideration was given to the nature and impact of classroom conversations and interactions when computer simulations were incorporated into a high school chemistry course. This investigation fills a need for qualitative research that focuses on the social dimensions of actual classrooms. Participants included a novice chemistry teacher experienced in the use of educational technologies and two honors chemistry classes. The study was conducted in a rural school in the south-Atlantic United States at the end of the fall 2007 semester. The study took place during one instructional unit on atomic structure. Data collection allowed for triangulation of evidence from a variety of sources approximately 24 hours of video- and audio-taped classroom observations, supplemented with the researcher's field notes and analytic journal; miscellaneous classroom artifacts such as class notes, worksheets, and assignments; open-ended pre- and post-assessments; student exit interviews; teacher entrance, exit and informal interviews. Four web-based simulations were used, three of which were from the ExploreLearning collection. Assessments were analyzed using descriptive statistics and classroom observations, artifacts and interviews were analyzed using Erickson's (1986) guidelines for analytic induction. Conversational analysis was guided by methods outlined by Erickson (1982). Findings indicated (a) the teacher effectively incorporated simulations in both settings (b) students in both groups significantly improved their understanding of the chemistry concepts (c) there was no statistically significant difference between groups' achievement (d) there was more frequent exploratory talk in the whole-class group (e) there were more frequent and meaningful teacher-student interactions in the whole-class group (f) additional learning experiences not measured on the assessment resulted from conversations and interactions in the whole-class setting (g) the potential benefits of exploratory talk in the whole-class setting were not fully realized. These findings suggest that both whole-class and small-group settings are appropriate for using computer simulations in science. The effective incorporation of simulations into whole-class instruction may provide a solution to the dilemma of technology penetration versus integration in today's classrooms.

The effect of individual variation on the structure and function of interaction networks in harvester ants

PubMed Central

Pinter-Wollman, Noa; Wollman, Roy; Guetz, Adam; Holmes, Susan; Gordon, Deborah M.

2011-01-01

Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant's interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow. PMID:21490001

A potential-energy scaling model to simulate the initial stages of thin-film growth

NASA Technical Reports Server (NTRS)

Heinbockel, J. H.; Outlaw, R. A.; Walker, G. H.

1983-01-01

A solid on solid (SOS) Monte Carlo computer simulation employing a potential energy scaling technique was used to model the initial stages of thin film growth. The model monitors variations in the vertical interaction potential that occur due to the arrival or departure of selected adatoms or impurities at all sites in the 400 sq. ft. array. Boltzmann ordered statistics are used to simulate fluctuations in vibrational energy at each site in the array, and the resulting site energy is compared with threshold levels of possible atomic events. In addition to adsorption, desorption, and surface migration, adatom incorporation and diffusion of a substrate atom to the surface are also included. The lateral interaction of nearest, second nearest, and third nearest neighbors is also considered. A series of computer experiments are conducted to illustrate the behavior of the model.

Multi-scale modeling in cell biology

PubMed Central

Meier-Schellersheim, Martin; Fraser, Iain D. C.; Klauschen, Frederick

2009-01-01

Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multi-scale systems quantitatively with the help of simulations have to incorporate several different simulation techniques due to the different time and space scales involved. Here, we provide a non-technical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multi-scale models without having to become involved with the underlying technical details of computational modeling. PMID:20448808

A study of application of remote sensing to river forecasting. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1975-01-01

A project is described whose goal was to define, implement and evaluate a pilot demonstration test to show the practicability of applying remotely sensed data to operational river forecasting in gaged or previously ungaged watersheds. A secondary objective was to provide NASA with documentation describing the computer programs that comprise the streamflow forecasting simulation model used. A computer-based simulation model was adapted to a streamflow forecasting application and implemented in an IBM System/360 Model 44 computer, operating in a dedicated mode, with operator interactive control through a Model 2250 keyboard/graphic CRT terminal. The test site whose hydrologic behavior was simulated is a small basin (365 square kilometers) designated Town Creek near Geraldine, Alabama.

Particle physics and polyedra proximity calculation for hazard simulations in large-scale industrial plants

NASA Astrophysics Data System (ADS)

Plebe, Alice; Grasso, Giorgio

2016-12-01

This paper describes a system developed for the simulation of flames inside an open-source 3D computer graphic software, Blender, with the aim of analyzing in virtual reality scenarios of hazards in large-scale industrial plants. The advantages of Blender are of rendering at high resolution the very complex structure of large industrial plants, and of embedding a physical engine based on smoothed particle hydrodynamics. This particle system is used to evolve a simulated fire. The interaction of this fire with the components of the plant is computed using polyhedron separation distance, adopting a Voronoi-based strategy that optimizes the number of feature distance computations. Results on a real oil and gas refining industry are presented.

CFD: A Castle in the Sand?

NASA Technical Reports Server (NTRS)

Kleb, William L.; Wood, William A.

2004-01-01

The computational simulation community is not routinely publishing independently verifiable tests to accompany new models or algorithms. A survey reveals that only 22% of new models published are accompanied by tests suitable for independently verifying the new model. As the community develops larger codes with increased functionality, and hence increased complexity in terms of the number of building block components and their interactions, it becomes prohibitively expensive for each development group to derive the appropriate tests for each component. Therefore, the computational simulation community is building its collective castle on a very shaky foundation of components with unpublished and unrepeatable verification tests. The computational simulation community needs to begin publishing component level verification tests before the tide of complexity undermines its foundation.

Computer Series, 60: Bits and Pieces, 23.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1985-01-01

Describes: (1) an interactive computer simulation for a science fair display of chromatography inks; (2) analytical chemistry programs; (3) microcomputer-assisted drills in organic synthesis; (4) programs for conformation analysis of ethane and butane; (5) MOLPIX--a program for generating and displaying molecular structures; and (6) chemical…

Computer Series, 89.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1988-01-01

Describes five computer software packages; four for MS-DOS Systems and one for Apple II. Included are SPEC20, an interactive simulation of a Bausch and Lomb Spectronic-20; a database for laboratory chemicals and programs for visualizing Boltzmann-like distributions, orbital plot for the hydrogen atom and molecular orbital theory. (CW)

Causal Reasoning in Medicine: Analysis of a Protocol.

ERIC Educational Resources Information Center

Kuipers, Benjamin; Kassirer, Jerome P.

1984-01-01

Describes the construction of a knowledge representation from the identification of the problem (nephrotic syndrome) to a running computer simulation of causal reasoning to provide a vertical slice of the construction of a cognitive model. Interactions between textbook knowledge, observations of human experts, and computational requirements are…

Interaction between IGFBP7 and insulin: a theoretical and experimental study

NASA Astrophysics Data System (ADS)

Ruan, Wenjing; Kang, Zhengzhong; Li, Youzhao; Sun, Tianyang; Wang, Lipei; Liang, Lijun; Lai, Maode; Wu, Tao

2016-04-01

Insulin-like growth factor binding protein 7 (IGFBP7) can bind to insulin with high affinity which inhibits the early steps of insulin action. Lack of recognition mechanism impairs our understanding of insulin regulation before it binds to insulin receptor. Here we combine computational simulations with experimental methods to investigate the interaction between IGFBP7 and insulin. Molecular dynamics simulations indicated that His200 and Arg198 in IGFBP7 were key residues. Verified by experimental data, the interaction remained strong in single mutation systems R198E and H200F but became weak in double mutation system R198E-H200F relative to that in wild-type IGFBP7. The results and methods in present study could be adopted in future research of discovery of drugs by disrupting protein-protein interactions in insulin signaling. Nevertheless, the accuracy, reproducibility, and costs of free-energy calculation are still problems that need to be addressed before computational methods can become standard binding prediction tools in discovery pipelines.

Fast estimation of first-order scattering in a medical x-ray computed tomography scanner using a ray-tracing technique.

PubMed

Liu, Xin

2014-01-01

This study describes a deterministic method for simulating the first-order scattering in a medical computed tomography scanner. The method was developed based on a physics model of x-ray photon interactions with matter and a ray tracing technique. The results from simulated scattering were compared to the ones from an actual scattering measurement. Two phantoms with homogeneous and heterogeneous material distributions were used in the scattering simulation and measurement. It was found that the simulated scatter profile was in agreement with the measurement result, with an average difference of 25% or less. Finally, tomographic images with artifacts caused by scatter were corrected based on the simulated scatter profiles. The image quality improved significantly.

Computational Growth and Remodeling of Abdominal Aortic Aneurysms Constrained by the Spine.

PubMed

Farsad, Mehdi; Zeinali-Davarani, Shahrokh; Choi, Jongeun; Baek, Seungik

2015-09-01

Abdominal aortic aneurysms (AAAs) evolve over time, and the vertebral column, which acts as an external barrier, affects their biomechanical properties. Mechanical interaction between AAAs and the spine is believed to alter the geometry, wall stress distribution, and blood flow, although the degree of this interaction may depend on AAAs specific configurations. In this study, we use a growth and remodeling (G&R) model, which is able to trace alterations of the geometry, thus allowing us to computationally investigate the effect of the spine for progression of the AAA. Medical image-based geometry of an aorta is constructed along with the spine surface, which is incorporated into the computational model as a cloud of points. The G&R simulation is initiated by local elastin degradation with different spatial distributions. The AAA-spine interaction is accounted for using a penalty method when the AAA surface meets the spine surface. The simulation results show that, while the radial growth of the AAA wall is prevented on the posterior side due to the spine acting as a constraint, the AAA expands faster on the anterior side, leading to higher curvature and asymmetry in the AAA configuration compared to the simulation excluding the spine. Accordingly, the AAA wall stress increases on the lateral, posterolateral, and the shoulder regions of the anterior side due to the AAA-spine contact. In addition, more collagen is deposited on the regions with a maximum diameter. We show that an image-based computational G&R model not only enhances the prediction of the geometry, wall stress, and strength distributions of AAAs but also provides a framework to account for the interactions between an enlarging AAA and the spine for a better rupture potential assessment and management of AAA patients.

Computational Growth and Remodeling of Abdominal Aortic Aneurysms Constrained by the Spine

PubMed Central

Farsad, Mehdi; Zeinali-Davarani, Shahrokh; Choi, Jongeun; Baek, Seungik

2015-01-01

Abdominal aortic aneurysms (AAAs) evolve over time, and the vertebral column, which acts as an external barrier, affects their biomechanical properties. Mechanical interaction between AAAs and the spine is believed to alter the geometry, wall stress distribution, and blood flow, although the degree of this interaction may depend on AAAs specific configurations. In this study, we use a growth and remodeling (G&R) model, which is able to trace alterations of the geometry, thus allowing us to computationally investigate the effect of the spine for progression of the AAA. Medical image-based geometry of an aorta is constructed along with the spine surface, which is incorporated into the computational model as a cloud of points. The G&R simulation is initiated by local elastin degradation with different spatial distributions. The AAA–spine interaction is accounted for using a penalty method when the AAA surface meets the spine surface. The simulation results show that, while the radial growth of the AAA wall is prevented on the posterior side due to the spine acting as a constraint, the AAA expands faster on the anterior side, leading to higher curvature and asymmetry in the AAA configuration compared to the simulation excluding the spine. Accordingly, the AAA wall stress increases on the lateral, posterolateral, and the shoulder regions of the anterior side due to the AAA–spine contact. In addition, more collagen is deposited on the regions with a maximum diameter. We show that an image-based computational G&R model not only enhances the prediction of the geometry, wall stress, and strength distributions of AAAs but also provides a framework to account for the interactions between an enlarging AAA and the spine for a better rupture potential assessment and management of AAA patients. PMID:26158885

Exploring GPCR-Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward.

PubMed

Sengupta, Durba; Prasanna, Xavier; Mohole, Madhura; Chattopadhyay, Amitabha

2018-06-07

Gprotein-coupled receptors (GPCRs) are seven transmembrane receptors that mediate a large number of cellular responses and are important drug targets. One of the current challenges in GPCR biology is to analyze the molecular signatures of receptor-lipid interactions and their subsequent effects on GPCR structure, organization, and function. Molecular dynamics simulation studies have been successful in predicting molecular determinants of receptor-lipid interactions. In particular, predicted cholesterol interaction sites appear to correspond well with experimentally determined binding sites and estimated time scales of association. In spite of several success stories, the methodologies in molecular dynamics simulations are still emerging. In this Feature Article, we provide a comprehensive overview of coarse-grain and atomistic molecular dynamics simulations of GPCR-lipid interaction in the context of experimental observations. In addition, we discuss the effect of secondary and tertiary structural constraints in coarse-grain simulations in the context of functional dynamics and structural plasticity of GPCRs. We envision that this comprehensive overview will help resolve differences in computational studies and provide a way forward.

Theoretical Chemistry Comes Alive: Full Partner with Experiment.

ERIC Educational Resources Information Center

Goddard, William A., III

1985-01-01

The expected thrust for theoretical chemistry in the next decade will be to combine knowledge of fundamental chemical steps/interactions with advances in chemical dynamics, irreversible statistical mechanics, and computer technology to produce simulations of chemical systems with reaction site competition. A sample simulation (using the enzyme…

Studies of protein-protein and protein-water interactions by small angle x-ray scattering, terahertz spectroscopy, ASMOS, and computer simulation

NASA Astrophysics Data System (ADS)

Kim, Seung Joong

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 microm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

DOE PAGES

Xu, Shuozhi; Xiong, Liming; Chen, Youping; ...

2017-04-26

Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Shuozhi; Xiong, Liming; Chen, Youping

Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

An experimental-computational platform for investigating microbial interactions and dynamics in communities with two codependent species

NASA Astrophysics Data System (ADS)

Fuentes-Cabrera, Miguel; Anderson, John D.; Wilmoth, Jared; Ginovart, Marta; Prats, Clara; Portell-Canal, Xavier; Retterer, Scott

Microbial interactions are critical for governing community behavior and structure in natural environments. Examination of microbial interactions in the lab involves growth under ideal conditions in batch culture; conditions that occur in nature are, however, characterized by disequilibrium. Of particular interest is the role that system variables play in shaping cell-to-cell interactions and organization at ultrafine spatial scales. We seek to use experiments and agent-based modeling to help discover mechanisms relevant to microbial dynamics and interactions in the environment. Currently, we are using an agent-based model to simulate microbial growth, dynamics and interactions that occur on a microwell-array device developed in our lab. Bacterial cells growing in the microwells of this platform can be studied with high-throughput and high-content image analyses using brightfield and fluorescence microscopy. The agent-based model is written in the language Netlogo, which in turn is ''plugged into'' a computational framework that allows submitting many calculations in parallel for different initial parameters; visualizing the outcomes in an interactive phase-like diagram; and searching, with a genetic algorithm, for the parameters that lead to the most optimal simulation outcome.

Consider a non-spherical elephant: computational fluid dynamics simulations of heat transfer coefficients and drag verified using wind tunnel experiments.

PubMed

Dudley, Peter N; Bonazza, Riccardo; Porter, Warren P

2013-07-01

Animal momentum and heat transfer analysis has historically used direct animal measurements or approximations to calculate drag and heat transfer coefficients. Research can now use modern 3D rendering and computational fluid dynamics software to simulate animal-fluid interactions. Key questions are the level of agreement between simulations and experiments and how superior they are to classical approximations. In this paper we compared experimental and simulated heat transfer and drag calculations on a scale model solid aluminum African elephant casting. We found good agreement between experimental and simulated data and large differences from classical approximations. We used the simulation results to calculate coefficients for heat transfer and drag of the elephant geometry. Copyright © 2013 Wiley Periodicals, Inc.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

PubMed

Duan, Lili; Liu, Xiao; Zhang, John Z H

2016-05-04

Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

Simulation of Quantum Many-Body Dynamics for Generic Strongly-Interacting Systems

NASA Astrophysics Data System (ADS)

Meyer, Gregory; Machado, Francisco; Yao, Norman

2017-04-01

Recent experimental advances have enabled the bottom-up assembly of complex, strongly interacting quantum many-body systems from individual atoms, ions, molecules and photons. These advances open the door to studying dynamics in isolated quantum systems as well as the possibility of realizing novel out-of-equilibrium phases of matter. Numerical studies provide insight into these systems; however, computational time and memory usage limit common numerical methods such as exact diagonalization to relatively small Hilbert spaces of dimension 215 . Here we present progress toward a new software package for dynamical time evolution of large generic quantum systems on massively parallel computing architectures. By projecting large sparse Hamiltonians into a much smaller Krylov subspace, we are able to compute the evolution of strongly interacting systems with Hilbert space dimension nearing 230. We discuss and benchmark different design implementations, such as matrix-free methods and GPU based calculations, using both pre-thermal time crystals and the Sachdev-Ye-Kitaev model as examples. We also include a simple symbolic language to describe generic Hamiltonians, allowing simulation of diverse quantum systems without any modification of the underlying C and Fortran code.

Interactive Computation for Undergraduates: The Next Generation

NASA Astrophysics Data System (ADS)

Kolan, Amy J.

2017-05-01

A generation ago (29 years ago), Leo Kadanoff and Michael Vinson created the Computers, Chaos, and Physics course. A major pedagogical thrust of this course was to help students form and test hypotheses via computer simulation of small problems in physics. Recently, this aspect of the 1987 course has been revived for use with first year physics undergraduate students at St. Olaf College.

Modeling and computational simulation and the potential of virtual and augmented reality associated to the teaching of nanoscience and nanotechnology

NASA Astrophysics Data System (ADS)

Ribeiro, Allan; Santos, Helen

With the advent of new information and communication technologies (ICTs), the communicative interaction changes the way of being and acting of people, at the same time that changes the way of work activities related to education. In this range of possibilities provided by the advancement of computational resources include virtual reality (VR) and augmented reality (AR), are highlighted as new forms of information visualization in computer applications. While the RV allows user interaction with a virtual environment totally computer generated; in RA the virtual images are inserted in real environment, but both create new opportunities to support teaching and learning in formal and informal contexts. Such technologies are able to express representations of reality or of the imagination, as systems in nanoscale and low dimensionality, being imperative to explore, in the most diverse areas of knowledge, the potential offered by ICT and emerging technologies. In this sense, this work presents computer applications of virtual and augmented reality developed with the use of modeling and simulation in computational approaches to topics related to nanoscience and nanotechnology, and articulated with innovative pedagogical practices.

Human agency beliefs influence behaviour during virtual social interactions.

PubMed

Caruana, Nathan; Spirou, Dean; Brock, Jon

2017-01-01

In recent years, with the emergence of relatively inexpensive and accessible virtual reality technologies, it is now possible to deliver compelling and realistic simulations of human-to-human interaction. Neuroimaging studies have shown that, when participants believe they are interacting via a virtual interface with another human agent, they show different patterns of brain activity compared to when they know that their virtual partner is computer-controlled. The suggestion is that users adopt an "intentional stance" by attributing mental states to their virtual partner. However, it remains unclear how beliefs in the agency of a virtual partner influence participants' behaviour and subjective experience of the interaction. We investigated this issue in the context of a cooperative "joint attention" game in which participants interacted via an eye tracker with a virtual onscreen partner, directing each other's eye gaze to different screen locations. Half of the participants were correctly informed that their partner was controlled by a computer algorithm ("Computer" condition). The other half were misled into believing that the virtual character was controlled by a second participant in another room ("Human" condition). Those in the "Human" condition were slower to make eye contact with their partner and more likely to try and guide their partner before they had established mutual eye contact than participants in the "Computer" condition. They also responded more rapidly when their partner was guiding them, although the same effect was also found for a control condition in which they responded to an arrow cue. Results confirm the influence of human agency beliefs on behaviour in this virtual social interaction context. They further suggest that researchers and developers attempting to simulate social interactions should consider the impact of agency beliefs on user experience in other social contexts, and their effect on the achievement of the application's goals.

Numerical Simulation of the Interaction of a Vortex with Stationary Airfoil in Transonic Flow,

DTIC Science & Technology

1984-01-12

Goorjian, P. M., "Implicit Vortex Wakes ," AIAA Journal, Vol. 15, No. 4, April Finite- Difference Computations of Unsteady Transonic 1977, pp. 581-590... Difference Simulations of Three- tion of Wing- Vortex Interaction in Transonic Flow Dimensional Flow," AIAA Journal, Vol. 18, No. 2, Using Implicit...assumptions are made in p = density modeling the nonlinear vortex wake structure. Numerical algorithms based on the Euler equations p_ = free stream density

Numerical approach of the injection molding process of fiber-reinforced composite with considering fiber orientation

NASA Astrophysics Data System (ADS)

Nguyen Thi, T. B.; Yokoyama, A.; Ota, K.; Kodama, K.; Yamashita, K.; Isogai, Y.; Furuichi, K.; Nonomura, C.

2014-05-01

One of the most important challenges in the injection molding process of the short-glass fiber/thermoplastic composite parts is being able to predict the fiber orientation, since it controls the mechanical and the physical properties of the final parts. Folgar and Tucker included into the Jeffery equation a diffusive type of term, which introduces a phenomenological coefficient for modeling the randomizing effect of the mechanical interactions between the fibers, to predict the fiber orientation in concentrated suspensions. Their experiments indicated that this coefficient depends on the fiber volume fraction and aspect ratio. However, a definition of the fiber interaction coefficient, which is very necessary in the fiber orientation simulations, hasn't still been proven yet. Consequently, this study proposed a developed fiber interaction model that has been introduced a fiber dynamics simulation in order to obtain a global fiber interaction coefficient. This supposed that the coefficient is a sum function of the fiber concentration, aspect ratio, and angular velocity. The proposed model was incorporated into a computer aided engineering simulation package C-Mold. Short-glass fiber/polyamide-6 composites were produced in the injection molding with the fiber weight concentration of 30 wt.%, 50 wt.%, and 70 wt.%. The physical properties of these composites were examined, and their fiber orientation distributions were measured by micro-computed-tomography equipment μ-CT. The simulation results showed a good agreement with experiment results.

Study-simulation of space station dynamics

NASA Technical Reports Server (NTRS)

Gaitens, M. J.

1971-01-01

Matrix algebra translator and executor /MATE/ takes equations describing structural control system environmental interaction problem for flexible spacecraft components and loads them into self programming computer.

Molecular simulations of the pairwise interaction of monoclonal antibodies.

PubMed

Lapelosa, Mauro; Patapoff, Thomas W; Zarraga, Isidro E

2014-11-20

Molecular simulations are employed to compute the free energy of pairwise monoclonal antibodies (mAbs) association using a conformational sampling algorithm with a scoring function. The work reported here is aimed at investigating the mAb-mAb association driven by weak interactions with a computational method capable of predicting experimental observations of low binding affinity. The simulations are able to explore the free energy landscape. A steric interaction component, electrostatic interactions, and a nonpolar component of the free energy form the energy scoring function. Electrostatic interactions are calculated by solving the Poisson-Boltzmann equation. The nonpolar component is derived from the van der Waals interactions upon close contact of the protein surfaces. Two mAbs with similar IgG1 framework but with small sequence differences, mAb1 and mAb2, are considered for their different viscosity and propensity to form a weak interacting dimer. mAb1 presents favorable free energy of association at pH 6 with 15 mM of ion concentration reproducing experimental trends of high viscosity and dimer formation at high concentration. Free energy landscape and minimum free energy configurations of the dimer, as well as the second virial coefficient (B22) values are calculated. The energy distributions for mAb1 are obtained, and the most probable configurations are seen to be consistent with experimental measurements. In contrast, mAb2 shows an unfavorable average free energy at the same buffer conditions due to poor electrostatic complementarity, and reversible dimer configurations with favorable free energy are found to be unlikely. Finally, the simulations of the mAb association dynamics provide insights on the self-association responsible for bulk solution behavior and aggregation, which are important to the processing and the quality of biopharmaceuticals.

Benchmarking of neutron production of heavy-ion transport codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

An efficient approach to the analysis of rail surface irregularities accounting for dynamic train-track interaction and inelastic deformations

NASA Astrophysics Data System (ADS)

Andersson, Robin; Torstensson, Peter T.; Kabo, Elena; Larsson, Fredrik

2015-11-01

A two-dimensional computational model for assessment of rolling contact fatigue induced by discrete rail surface irregularities, especially in the context of so-called squats, is presented. Dynamic excitation in a wide frequency range is considered in computationally efficient time-domain simulations of high-frequency dynamic vehicle-track interaction accounting for transient non-Hertzian wheel-rail contact. Results from dynamic simulations are mapped onto a finite element model to resolve the cyclic, elastoplastic stress response in the rail. Ratcheting under multiple wheel passages is quantified. In addition, low cycle fatigue impact is quantified using the Jiang-Sehitoglu fatigue parameter. The functionality of the model is demonstrated by numerical examples.

Guided waves in anisotropic and quasi-isotropic aerospace composites: three-dimensional simulation and experiment.

PubMed

Leckey, Cara A C; Rogge, Matthew D; Raymond Parker, F

2014-01-01

Three-dimensional (3D) elastic wave simulations can be used to investigate and optimize nondestructive evaluation (NDE) and structural health monitoring (SHM) ultrasonic damage detection techniques for aerospace materials. 3D anisotropic elastodynamic finite integration technique (EFIT) has been implemented for ultrasonic waves in carbon fiber reinforced polymer (CFRP) composite laminates. This paper describes 3D EFIT simulations of guided wave propagation in undamaged and damaged anisotropic and quasi-isotropic composite plates. Comparisons are made between simulations of guided waves in undamaged anisotropic composite plates and both experimental laser Doppler vibrometer (LDV) wavefield data and dispersion curves. Time domain and wavenumber domain comparisons are described. Wave interaction with complex geometry delamination damage is then simulated to investigate how simulation tools incorporating realistic damage geometries can aid in the understanding of wave interaction with CFRP damage. In order to move beyond simplistic assumptions of damage geometry, volumetric delamination data acquired via X-ray microfocus computed tomography is directly incorporated into the simulation. Simulated guided wave interaction with the complex geometry delamination is compared to experimental LDV time domain data and 3D wave interaction with the volumetric damage is discussed. Published by Elsevier B.V.

Middle Rio Grande Cooperative Water Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tidwell, Vince; Passell, Howard

2005-11-01

This is computer simulation model built in a commercial modeling product Called Studio Expert, developed by Powersim, Inc. The simulation model is built in a system dynamics environment, allowing the simulation of the interaction among multiple systems that are all changing over time. The model focuses on hydrology, ecology, demography, and economy of the Middle Rio Grande, with Water as the unifying feature.

Real-time simulation of contact and cutting of heterogeneous soft-tissues.

PubMed

Courtecuisse, Hadrien; Allard, Jérémie; Kerfriden, Pierre; Bordas, Stéphane P A; Cotin, Stéphane; Duriez, Christian

2014-02-01

This paper presents a numerical method for interactive (real-time) simulations, which considerably improves the accuracy of the response of heterogeneous soft-tissue models undergoing contact, cutting and other topological changes. We provide an integrated methodology able to deal both with the ill-conditioning issues associated with material heterogeneities, contact boundary conditions which are one of the main sources of inaccuracies, and cutting which is one of the most challenging issues in interactive simulations. Our approach is based on an implicit time integration of a non-linear finite element model. To enable real-time computations, we propose a new preconditioning technique, based on an asynchronous update at low frequency. The preconditioner is not only used to improve the computation of the deformation of the tissues, but also to simulate the contact response of homogeneous and heterogeneous bodies with the same accuracy. We also address the problem of cutting the heterogeneous structures and propose a method to update the preconditioner according to the topological modifications. Finally, we apply our approach to three challenging demonstrators: (i) a simulation of cataract surgery (ii) a simulation of laparoscopic hepatectomy (iii) a brain tumor surgery. Copyright © 2013 Elsevier B.V. All rights reserved.

Accelerating sino-atrium computer simulations with graphic processing units.

PubMed

Zhang, Hong; Xiao, Zheng; Lin, Shien-fong

2015-01-01

Sino-atrial node cells (SANCs) play a significant role in rhythmic firing. To investigate their role in arrhythmia and interactions with the atrium, computer simulations based on cellular dynamic mathematical models are generally used. However, the large-scale computation usually makes research difficult, given the limited computational power of Central Processing Units (CPUs). In this paper, an accelerating approach with Graphic Processing Units (GPUs) is proposed in a simulation consisting of the SAN tissue and the adjoining atrium. By using the operator splitting method, the computational task was made parallel. Three parallelization strategies were then put forward. The strategy with the shortest running time was further optimized by considering block size, data transfer and partition. The results showed that for a simulation with 500 SANCs and 30 atrial cells, the execution time taken by the non-optimized program decreased 62% with respect to a serial program running on CPU. The execution time decreased by 80% after the program was optimized. The larger the tissue was, the more significant the acceleration became. The results demonstrated the effectiveness of the proposed GPU-accelerating methods and their promising applications in more complicated biological simulations.

Progress in Computational Simulation of Earthquakes

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay; Lyzenga, Gregory; Judd, Michele; Li, P. Peggy; Norton, Charles; Tisdale, Edwin; Granat, Robert

2006-01-01

GeoFEST(P) is a computer program written for use in the QuakeSim project, which is devoted to development and improvement of means of computational simulation of earthquakes. GeoFEST(P) models interacting earthquake fault systems from the fault-nucleation to the tectonic scale. The development of GeoFEST( P) has involved coupling of two programs: GeoFEST and the Pyramid Adaptive Mesh Refinement Library. GeoFEST is a message-passing-interface-parallel code that utilizes a finite-element technique to simulate evolution of stress, fault slip, and plastic/elastic deformation in realistic materials like those of faulted regions of the crust of the Earth. The products of such simulations are synthetic observable time-dependent surface deformations on time scales from days to decades. Pyramid Adaptive Mesh Refinement Library is a software library that facilitates the generation of computational meshes for solving physical problems. In an application of GeoFEST(P), a computational grid can be dynamically adapted as stress grows on a fault. Simulations on workstations using a few tens of thousands of stress and displacement finite elements can now be expanded to multiple millions of elements with greater than 98-percent scaled efficiency on over many hundreds of parallel processors (see figure).

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

PubMed

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

2012-06-22

Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development. In this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

Documentation of a computer program to simulate stream-aquifer relations using a modular, finite-difference, ground-water flow model

USGS Publications Warehouse

Prudic, David E.

1989-01-01

Computer models are widely used to simulate groundwater flow for evaluating and managing the groundwater resource of many aquifers, but few are designed to also account for surface flow in streams. A computer program was written for use in the US Geological Survey modular finite difference groundwater flow model to account for the amount of flow in streams and to simulate the interaction between surface streams and groundwater. The new program is called the Streamflow-Routing Package. The Streamflow-Routing Package is not a true surface water flow model, but rather is an accounting program that tracks the flow in one or more streams which interact with groundwater. The program limits the amount of groundwater recharge to the available streamflow. It permits two or more streams to merge into one with flow in the merged stream equal to the sum of the tributary flows. The program also permits diversions from streams. The groundwater flow model with the Streamflow-Routing Package has an advantage over the analytical solution in simulating the interaction between aquifer and stream because it can be used to simulate complex systems that cannot be readily solved analytically. The Streamflow-Routing Package does not include a time function for streamflow but rather streamflow entering the modeled area is assumed to be instantly available to downstream reaches during each time period. This assumption is generally reasonable because of the relatively slow rate of groundwater flow. Another assumption is that leakage between streams and aquifers is instantaneous. This assumption may not be reasonable if the streams and aquifers are separated by a thick unsaturated zone. Documentation of the Streamflow-Routing Package includes data input instructions; flow charts, narratives, and listings of the computer program for each of four modules; and input data sets and printed results for two test problems, and one example problem. (Lantz-PTT)

Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example.

PubMed

Ren, Li-Hong; Ding, Yong-Sheng; Shen, Yi-Zhen; Zhang, Xiang-Feng

2008-10-01

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein-protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

Recent advances in computational methodology for simulation of mechanical circulatory assist devices

PubMed Central

Marsden, Alison L.; Bazilevs, Yuri; Long, Christopher C.; Behr, Marek

2014-01-01

Ventricular assist devices (VADs) provide mechanical circulatory support to offload the work of one or both ventricles during heart failure. They are used in the clinical setting as destination therapy, as bridge to transplant, or more recently as bridge to recovery to allow for myocardial remodeling. Recent developments in computational simulation allow for detailed assessment of VAD hemodynamics for device design and optimization for both children and adults. Here, we provide a focused review of the recent literature on finite element methods and optimization for VAD simulations. As VAD designs typically fall into two categories, pulsatile and continuous flow devices, we separately address computational challenges of both types of designs, and the interaction with the circulatory system with three representative case studies. In particular, we focus on recent advancements in finite element methodology that has increased the fidelity of VAD simulations. We outline key challenges, which extend to the incorporation of biological response such as thrombosis and hemolysis, as well as shape optimization methods and challenges in computational methodology. PMID:24449607

Palpation simulator with stable haptic feedback.

PubMed

Kim, Sang-Youn; Ryu, Jee-Hwan; Lee, WooJeong

2015-01-01

The main difficulty in constructing palpation simulators is to compute and to generate stable and realistic haptic feedback without vibration. When a user haptically interacts with highly non-homogeneous soft tissues through a palpation simulator, a sudden change of stiffness in target tissues causes unstable interaction with the object. We propose a model consisting of a virtual adjustable damper and an energy measuring element. The energy measuring element gauges energy which is stored in a palpation simulator and the virtual adjustable damper dissipates the energy to achieve stable haptic interaction. To investigate the haptic behavior of the proposed method, impulse and continuous inputs are provided to target tissues. If a haptic interface point meets with the hardest portion in the target tissues modeled with a conventional method, we observe unstable motion and feedback force. However, when the target tissues are modeled with the proposed method, a palpation simulator provides stable interaction without vibration. The proposed method overcomes a problem in conventional haptic palpation simulators where unstable force or vibration can be generated if there is a big discrepancy in material property between an element and its neighboring elements in target tissues.

ShinyGPAS: interactive genomic prediction accuracy simulator based on deterministic formulas.

PubMed

Morota, Gota

2017-12-20

Deterministic formulas for the accuracy of genomic predictions highlight the relationships among prediction accuracy and potential factors influencing prediction accuracy prior to performing computationally intensive cross-validation. Visualizing such deterministic formulas in an interactive manner may lead to a better understanding of how genetic factors control prediction accuracy. The software to simulate deterministic formulas for genomic prediction accuracy was implemented in R and encapsulated as a web-based Shiny application. Shiny genomic prediction accuracy simulator (ShinyGPAS) simulates various deterministic formulas and delivers dynamic scatter plots of prediction accuracy versus genetic factors impacting prediction accuracy, while requiring only mouse navigation in a web browser. ShinyGPAS is available at: https://chikudaisei.shinyapps.io/shinygpas/ . ShinyGPAS is a shiny-based interactive genomic prediction accuracy simulator using deterministic formulas. It can be used for interactively exploring potential factors that influence prediction accuracy in genome-enabled prediction, simulating achievable prediction accuracy prior to genotyping individuals, or supporting in-class teaching. ShinyGPAS is open source software and it is hosted online as a freely available web-based resource with an intuitive graphical user interface.

Development of a systems theoretical procedure for evaluation of the work organization of the cockpit crew of a civil transport airplane

NASA Technical Reports Server (NTRS)

Fricke, M.; Vees, C.

1983-01-01

To achieve optimum design for the man machine interface with aircraft, a description of the interaction and work organization of the cockpit crew is needed. The development of system procedure to evaluate the work organization of pilots while structuring the work process is examined. Statistical data are needed to simulate sequences of pilot actions on the computer. Investigations of computer simulation and applicability for evaluation of crew concepts are discussed.

Point-Process Models of Social Network Interactions: Parameter Estimation and Missing Data Recovery

DTIC Science & Technology

2014-08-01

treating them as zero will have a de minimis impact on the results, but avoiding computing them (and computing with them) saves tremendous time. Set a... test the methods on simulated time series on artificial social networks, including some toy networks and some meant to resemble IkeNet. We conclude...the section by discussing the results in detail. In each of our tests we begin with a complete data set, whether it is real (IkeNet) or simulated. Then

Variance-based interaction index measuring heteroscedasticity

NASA Astrophysics Data System (ADS)

Ito, Keiichi; Couckuyt, Ivo; Poles, Silvia; Dhaene, Tom

2016-06-01

This work is motivated by the need to deal with models with high-dimensional input spaces of real variables. One way to tackle high-dimensional problems is to identify interaction or non-interaction among input parameters. We propose a new variance-based sensitivity interaction index that can detect and quantify interactions among the input variables of mathematical functions and computer simulations. The computation is very similar to first-order sensitivity indices by Sobol'. The proposed interaction index can quantify the relative importance of input variables in interaction. Furthermore, detection of non-interaction for screening can be done with as low as 4 n + 2 function evaluations, where n is the number of input variables. Using the interaction indices based on heteroscedasticity, the original function may be decomposed into a set of lower dimensional functions which may then be analyzed separately.

A Pipeline for Constructing a Catalog of Multi-method Models of Interacting Galaxies

NASA Astrophysics Data System (ADS)

Holincheck, Anthony

Galaxies represent a fundamental unit of matter for describing the large-scale structure of the universe. One of the major processes affecting the formation and evolution of galaxies are mutual interactions. These interactions can including gravitational tidal distortion, mass transfer, and even mergers. In any hierarchical model, mergers are the key mechanism in galaxy formation and evolution. Computer simulations of interacting galaxies have evolved in the last four decades from simple restricted three-body algorithms to full n-body gravity models. These codes often included sophisticated physical mechanisms such as gas dynamics, supernova feedback, and central blackholes. As the level of complexity, and perhaps realism, increases so does the amount of computational resources needed. These advanced simulations are often used in parameter studies of interactions. They are usually only employed in an ad hoc fashion to recreate the dynamical history of specific sets of interacting galaxies. These specific models are often created with only a few dozen or at most few hundred sets of simulation parameters being attempted. This dissertation presents a prototype pipeline for modeling specific pairs of interacting galaxies in bulk. The process begins with a simple image of the current disturbed morphology and an estimate of distance to the system and mass of the galaxies. With the use of an updated restricted three-body simulation code and the help of Citizen Scientists, the pipeline is able to sample hundreds of thousands of points in parameter space for each system. Through the use of a convenient interface and innovative scoring algorithm, the pipeline aids researchers in identifying the best set of simulation parameters. This dissertation demonstrates a successful recreation of the disturbed morphologies of 62 pairs of interacting galaxies. The pipeline also provides for examining the level of convergence and uniqueness of the dynamical properties of each system. By creating a population of models for actual systems, the current research is able to compare simulation-based and observational values on a larger scale than previous efforts. Several potential relationships between star formation rate and dynamical time since closest approach are presented.

Interaction entropy for protein-protein binding

NASA Astrophysics Data System (ADS)

Sun, Zhaoxi; Yan, Yu N.; Yang, Maoyou; Zhang, John Z. H.

2017-03-01

Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interaction entropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interaction entropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

Reaction-mediated entropic effect on phase separation in a binary polymer system

NASA Astrophysics Data System (ADS)

Sun, Shujun; Guo, Miaocai; Yi, Xiaosu; Zhang, Zuoguang

2017-10-01

We present a computer simulation to study the phase separation behavior induced by polymerization in a binary system comprising polymer chains and reactive monomers. We examined the influence of interaction parameter between components and monomer concentration on the reaction-induced phase separation. The simulation results demonstrate that increasing interaction parameter (enthalpic effect) would accelerate phase separation, while entropic effect plays a key role in the process of phase separation. Furthermore, scanning electron microscopy observations illustrate identical morphologies as found in theoretical simulation. This study may enrich our comprehension of phase separation in polymer mixture.

Computer-Based Physics: An Anthology.

ERIC Educational Resources Information Center

Blum, Ronald, Ed.

Designed to serve as a guide for integrating interactive problem-solving or simulating computers into a college-level physics course, this anthology contains nine articles each of which includes an introduction, a student manual, and a teacher's guide. Among areas covered in the articles are the computerized reduction of data to a Gaussian…

Teaching Pulmonary Gas Exchange Physiology Using Computer Modeling

ERIC Educational Resources Information Center

Kapitan, Kent S.

2008-01-01

Students often have difficulty understanding the relationship of O[subscript 2] consumption, CO[subscript 2] production, cardiac output, and distribution of ventilation-perfusion ratios in the lung to the final arterial blood gas composition. To overcome this difficulty, I have developed an interactive computer simulation of pulmonary gas exchange…

Web-Compatible Graphics Visualization Framework for Online Instruction and Assessment of Hardware Concepts

ERIC Educational Resources Information Center

Chandramouli, Magesh; Chittamuru, Siva-Teja

2016-01-01

This paper explains the design of a graphics-based virtual environment for instructing computer hardware concepts to students, especially those at the beginner level. Photorealistic visualizations and simulations are designed and programmed with interactive features allowing students to practice, explore, and test themselves on computer hardware…

Plume-Free Stream Interaction Heating Effects During Orion Crew Module Reentry

NASA Technical Reports Server (NTRS)

Marichalar, J.; Lumpkin, F.; Boyles, K.

2012-01-01

During reentry of the Orion Crew Module (CM), vehicle attitude control will be performed by firing reaction control system (RCS) thrusters. Simulation of RCS plumes and their interaction with the oncoming flow has been difficult for the analysis community due to the large scarf angles of the RCS thrusters and the unsteady nature of the Orion capsule backshell environments. The model for the aerothermal database has thus relied on wind tunnel test data to capture the heating effects of thruster plume interactions with the freestream. These data are only valid for the continuum flow regime of the reentry trajectory. A Direct Simulation Monte Carlo (DSMC) analysis was performed to study the vehicle heating effects that result from the RCS thruster plume interaction with the oncoming freestream flow at high altitudes during Orion CM reentry. The study was performed with the DSMC Analysis Code (DAC). The inflow boundary conditions for the jets were obtained from Data Parallel Line Relaxation (DPLR) computational fluid dynamics (CFD) solutions. Simulations were performed for the roll, yaw, pitch-up and pitch-down jets at altitudes of 105 km, 125 km and 160 km as well as vacuum conditions. For comparison purposes (see Figure 1), the freestream conditions were based on previous DAC simulations performed without active RCS to populate the aerodynamic database for the Orion CM. Other inputs to the analysis included a constant Orbital reentry velocity of 7.5 km/s and angle of attack of 160 degrees. The results of the study showed that the interaction effects decrease quickly with increasing altitude. Also, jets with highly scarfed nozzles cause more severe heating compared to the nozzles with lower scarf angles. The difficulty of performing these simulations was based on the maximum number density and the ratio of number densities between the freestream and the plume for each simulation. The lowest altitude solutions required a substantial amount of computational resources (up to 1800 processors) to simulate approximately 2 billion molecules for the refined (adapted) solutions.

Reading Aloud: Discrete Stage(s) Redux

PubMed Central

Robidoux, Serje; Besner, Derek

2017-01-01

Interactive activation accounts of processing have had a broad and deep influence on cognitive psychology, particularly so in the context of computational accounts of reading aloud at the single word level. Here we address the issue of whether such a framework can simulate the joint effects of stimulus quality and word frequency (which have been shown to produce both additive and interactive effects depending on the context). We extend previous work on this question by considering an alternative implementation of a stimulus quality manipulation, and the role of interactive activation. Simulations with a version of the Dual Route Cascaded model (a model with interactive activation dynamics along the lexical route) demonstrate that the model is unable to simulate the entire pattern seen in human performance. We discuss how a hybrid interactive activation model that includes some context dependent staged processing could accommodate these data. PMID:28289395

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

PubMed

Djekidel, Mohamed Nadhir; Chen, Yang; Zhang, Michael Q

2018-02-12

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. © 2018 Djekidel et al.; Published by Cold Spring Harbor Laboratory Press.

Simulated and Virtual Science Laboratory Experiments: Improving Critical Thinking and Higher-Order Learning Skills

ERIC Educational Resources Information Center

Simon, Nicole A.

2013-01-01

Virtual laboratory experiments using interactive computer simulations are not being employed as viable alternatives to laboratory science curriculum at extensive enough rates within higher education. Rote traditional lab experiments are currently the norm and are not addressing inquiry, Critical Thinking, and cognition throughout the laboratory…

Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks.

PubMed

Spirov, Alexander; Holloway, David

2013-07-15

This paper surveys modeling approaches for studying the evolution of gene regulatory networks (GRNs). Modeling of the design or 'wiring' of GRNs has become increasingly common in developmental and medical biology, as a means of quantifying gene-gene interactions, the response to perturbations, and the overall dynamic motifs of networks. Drawing from developments in GRN 'design' modeling, a number of groups are now using simulations to study how GRNs evolve, both for comparative genomics and to uncover general principles of evolutionary processes. Such work can generally be termed evolution in silico. Complementary to these biologically-focused approaches, a now well-established field of computer science is Evolutionary Computations (ECs), in which highly efficient optimization techniques are inspired from evolutionary principles. In surveying biological simulation approaches, we discuss the considerations that must be taken with respect to: (a) the precision and completeness of the data (e.g. are the simulations for very close matches to anatomical data, or are they for more general exploration of evolutionary principles); (b) the level of detail to model (we proceed from 'coarse-grained' evolution of simple gene-gene interactions to 'fine-grained' evolution at the DNA sequence level); (c) to what degree is it important to include the genome's cellular context; and (d) the efficiency of computation. With respect to the latter, we argue that developments in computer science EC offer the means to perform more complete simulation searches, and will lead to more comprehensive biological predictions. Copyright © 2013 Elsevier Inc. All rights reserved.

A Numerical Analysis on the Effects of Self-Excited Tip Flow Unsteadiness and Upstream Blade Row Interactions on the Performance Predictions of a Transonic Compressor

NASA Astrophysics Data System (ADS)

Heberling, Brian

Computational fluid dynamics (CFD) simulations can offer a detailed view of the complex flow fields within an axial compressor and greatly aid the design process. However, the desire for quick turnaround times raises the question of how exact the model must be. At design conditions, steady CFD simulating an isolated blade row can accurately predict the performance of a rotor. However, as a compressor is throttled and mass flow rate decreased, axial flow becomes weaker making the capturing of unsteadiness, wakes, or other flow features more important. The unsteadiness of the tip clearance flow and upstream blade wake can have a significant impact on a rotor. At off-design conditions, time-accurate simulations or modeling multiple blade rows can become necessary in order to receive accurate performance predictions. Unsteady and multi- bladerow simulations are computationally expensive, especially when used in conjunction. It is important to understand which features are important to model in order to accurately capture a compressor's performance. CFD simulations of a transonic axial compressor throttling from the design point to stall are presented. The importance of capturing the unsteadiness of the rotor tip clearance flow versus capturing upstream blade-row interactions is examined through steady and unsteady, single- and multi-bladerow computations. It is shown that there are significant differences at near stall conditions between the different types of simulations.

Validation of High-Speed Turbulent Boundary Layer and Shock-Boundary Layer Interaction Computations with the OVERFLOW Code

NASA Technical Reports Server (NTRS)

Oliver, A. B.; Lillard, R. P.; Blaisdell, G. A.; Lyrintizis, A. S.

2006-01-01

The capability of the OVERFLOW code to accurately compute high-speed turbulent boundary layers and turbulent shock-boundary layer interactions is being evaluated. Configurations being investigated include a Mach 2.87 flat plate to compare experimental velocity profiles and boundary layer growth, a Mach 6 flat plate to compare experimental surface heat transfer,a direct numerical simulation (DNS) at Mach 2.25 for turbulent quantities, and several Mach 3 compression ramps to compare computations of shock-boundary layer interactions to experimental laser doppler velocimetry (LDV) data and hot-wire data. The present paper describes outlines the study and presents preliminary results for two of the flat plate cases and two small-angle compression corner test cases.

Evaluation of Pseudo-Haptic Interactions with Soft Objects in Virtual Environments.

PubMed

Li, Min; Sareh, Sina; Xu, Guanghua; Ridzuan, Maisarah Binti; Luo, Shan; Xie, Jun; Wurdemann, Helge; Althoefer, Kaspar

2016-01-01

This paper proposes a pseudo-haptic feedback method conveying simulated soft surface stiffness information through a visual interface. The method exploits a combination of two feedback techniques, namely visual feedback of soft surface deformation and control of the indenter avatar speed, to convey stiffness information of a simulated surface of a soft object in virtual environments. The proposed method was effective in distinguishing different sizes of virtual hard nodules integrated into the simulated soft bodies. To further improve the interactive experience, the approach was extended creating a multi-point pseudo-haptic feedback system. A comparison with regards to (a) nodule detection sensitivity and (b) elapsed time as performance indicators in hard nodule detection experiments to a tablet computer incorporating vibration feedback was conducted. The multi-point pseudo-haptic interaction is shown to be more time-efficient than the single-point pseudo-haptic interaction. It is noted that multi-point pseudo-haptic feedback performs similarly well when compared to a vibration-based feedback method based on both performance measures elapsed time and nodule detection sensitivity. This proves that the proposed method can be used to convey detailed haptic information for virtual environmental tasks, even subtle ones, using either a computer mouse or a pressure sensitive device as an input device. This pseudo-haptic feedback method provides an opportunity for low-cost simulation of objects with soft surfaces and hard inclusions, as, for example, occurring in ever more realistic video games with increasing emphasis on interaction with the physical environment and minimally invasive surgery in the form of soft tissue organs with embedded cancer nodules. Hence, the method can be used in many low-budget applications where haptic sensation is required, such as surgeon training or video games, either using desktop computers or portable devices, showing reasonably high fidelity in conveying stiffness perception to the user.

Data-Informed Large-Eddy Simulation of Coastal Land-Air-Sea Interactions

NASA Astrophysics Data System (ADS)

Calderer, A.; Hao, X.; Fernando, H. J.; Sotiropoulos, F.; Shen, L.

2016-12-01

The study of atmospheric flows in coastal areas has not been fully addressed due to the complex processes emerging from the land-air-sea interactions, e.g., abrupt change in land topography, strong current shear, wave shoaling, and depth-limited wave breaking. The available computational tools that have been applied to study such littoral regions are mostly based on open-ocean assumptions, which most times do not lead to reliable solutions. The goal of the present study is to better understand some of these near-shore processes, employing the advanced computational tools, developed in our research group. Our computational framework combines a large-eddy simulation (LES) flow solver for atmospheric flows, a sharp-interface immersed boundary method that can deal with real complex topographies (Calderer et al., J. Comp. Physics 2014), and a phase-resolved, depth-dependent, wave model (Yang and Shen, J. Comp. Physics 2011). Using real measured data taken in the FRF station in Duck, North Carolina, we validate and demonstrate the predictive capabilities of the present computational framework, which are shown to be in overall good agreement with the measured data under different wind-wave scenarios. We also analyse the effects of some of the complex processes captured by our simulation tools.

Use of Hilbert Curves in Parallelized CUDA code: Interaction of Interstellar Atoms with the Heliosphere

NASA Astrophysics Data System (ADS)

Destefano, Anthony; Heerikhuisen, Jacob

2015-04-01

Fully 3D particle simulations can be a computationally and memory expensive task, especially when high resolution grid cells are required. The problem becomes further complicated when parallelization is needed. In this work we focus on computational methods to solve these difficulties. Hilbert curves are used to map the 3D particle space to the 1D contiguous memory space. This method of organization allows for minimized cache misses on the GPU as well as a sorted structure that is equivalent to an octal tree data structure. This type of sorted structure is attractive for uses in adaptive mesh implementations due to the logarithm search time. Implementations using the Message Passing Interface (MPI) library and NVIDIA's parallel computing platform CUDA will be compared, as MPI is commonly used on server nodes with many CPU's. We will also compare static grid structures with those of adaptive mesh structures. The physical test bed will be simulating heavy interstellar atoms interacting with a background plasma, the heliosphere, simulated from fully consistent coupled MHD/kinetic particle code. It is known that charge exchange is an important factor in space plasmas, specifically it modifies the structure of the heliosphere itself. We would like to thank the Alabama Supercomputer Authority for the use of their computational resources.

Simulation tools for scattering corrections in spectrally resolved x-ray computed tomography using McXtrace

NASA Astrophysics Data System (ADS)

Busi, Matteo; Olsen, Ulrik L.; Knudsen, Erik B.; Frisvad, Jeppe R.; Kehres, Jan; Dreier, Erik S.; Khalil, Mohamad; Haldrup, Kristoffer

2018-03-01

Spectral computed tomography is an emerging imaging method that involves using recently developed energy discriminating photon-counting detectors (PCDs). This technique enables measurements at isolated high-energy ranges, in which the dominating undergoing interaction between the x-ray and the sample is the incoherent scattering. The scattered radiation causes a loss of contrast in the results, and its correction has proven to be a complex problem, due to its dependence on energy, material composition, and geometry. Monte Carlo simulations can utilize a physical model to estimate the scattering contribution to the signal, at the cost of high computational time. We present a fast Monte Carlo simulation tool, based on McXtrace, to predict the energy resolved radiation being scattered and absorbed by objects of complex shapes. We validate the tool through measurements using a CdTe single PCD (Multix ME-100) and use it for scattering correction in a simulation of a spectral CT. We found the correction to account for up to 7% relative amplification in the reconstructed linear attenuation. It is a useful tool for x-ray CT to obtain a more accurate material discrimination, especially in the high-energy range, where the incoherent scattering interactions become prevailing (>50 keV).

Direct Visuo-Haptic 4D Volume Rendering Using Respiratory Motion Models.

PubMed

Fortmeier, Dirk; Wilms, Matthias; Mastmeyer, Andre; Handels, Heinz

2015-01-01

This article presents methods for direct visuo-haptic 4D volume rendering of virtual patient models under respiratory motion. Breathing models are computed based on patient-specific 4D CT image data sequences. Virtual patient models are visualized in real-time by ray casting based rendering of a reference CT image warped by a time-variant displacement field, which is computed using the motion models at run-time. Furthermore, haptic interaction with the animated virtual patient models is provided by using the displacements computed at high rendering rates to translate the position of the haptic device into the space of the reference CT image. This concept is applied to virtual palpation and the haptic simulation of insertion of a virtual bendable needle. To this aim, different motion models that are applicable in real-time are presented and the methods are integrated into a needle puncture training simulation framework, which can be used for simulated biopsy or vessel puncture in the liver. To confirm real-time applicability, a performance analysis of the resulting framework is given. It is shown that the presented methods achieve mean update rates around 2,000 Hz for haptic simulation and interactive frame rates for volume rendering and thus are well suited for visuo-haptic rendering of virtual patients under respiratory motion.

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein-Protein Interactions.

PubMed

Tan, Yaw Sing; Spring, David R; Abell, Chris; Verma, Chandra S

2015-07-14

A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.

Collaborative voxel-based surgical virtual environments.

PubMed

Acosta, Eric; Muniz, Gilbert; Armonda, Rocco; Bowyer, Mark; Liu, Alan

2008-01-01

Virtual Reality-based surgical simulators can utilize Collaborative Virtual Environments (C-VEs) to provide team-based training. To support real-time interactions, C-VEs are typically replicated on each user's local computer and a synchronization method helps keep all local copies consistent. This approach does not work well for voxel-based C-VEs since large and frequent volumetric updates make synchronization difficult. This paper describes a method that allows multiple users to interact within a voxel-based C-VE for a craniotomy simulator being developed. Our C-VE method requires smaller update sizes and provides faster synchronization update rates than volumetric-based methods. Additionally, we address network bandwidth/latency issues to simulate networked haptic and bone drilling tool interactions with a voxel-based skull C-VE.

Formation of specific amino acid sequences during carbodiimide-mediated condensation of amino acids in aqueous solution, and computer-simulated sequence generation

NASA Astrophysics Data System (ADS)

Hartmann, Jürgen; Nawroth, Thomas; Dose, Klaus

1984-12-01

Carbodiimide-mediated peptide synthesis in aqueous solution has been studied with respect to self-ordering of amino acids. The copolymerisation of amino acids in the presence of glutamic acid or pyroglutamic acid leads to short pyroglutamyl peptides. Without pyroglutamic acid the formation of higher polymers is favoured. The interactions of the amino acids and the peptides, however, are very complex. Therefore, the experimental results are rather difficult to explain. Some of the experimental results, however, can be explained with the aid of computer simulation programs. Regarding only the tripeptide fraction the copolymerisation of pyroGlu, Ala and Leu, as well as the simulated copolymerisation lead to pyroGlu-Ala-Leu as the main reaction product. The amino acid composition of the insoluble peptides formed during the copolymerisation of Ser, Gly, Ala, Val, Phe, Leu and Ile corresponds in part to the computer-simulated copolymerisation data.

Incremental update of electrostatic interactions in adaptively restrained particle simulations.

PubMed

Edorh, Semeho Prince A; Redon, Stéphane

2018-04-06

The computation of long-range potentials is one of the demanding tasks in Molecular Dynamics. During the last decades, an inventive panoply of methods was developed to reduce the CPU time of this task. In this work, we propose a fast method dedicated to the computation of the electrostatic potential in adaptively restrained systems. We exploit the fact that, in such systems, only some particles are allowed to move at each timestep. We developed an incremental algorithm derived from a multigrid-based alternative to traditional Fourier-based methods. Our algorithm was implemented inside LAMMPS, a popular molecular dynamics simulation package. We evaluated the method on different systems. We showed that the new algorithm's computational complexity scales with the number of active particles in the simulated system, and is able to outperform the well-established Particle Particle Particle Mesh (P3M) for adaptively restrained simulations. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Rapid Human-Computer Interactive Conceptual Design of Mobile and Manipulative Robot Systems

DTIC Science & Technology

2015-05-19

algorithm based on Age-Fitness Pareto Optimization (AFPO) ([9]) with an additional user prefer- ence objective and a neural network-based user model, we...greater than 40, which is about 5 times further than any robot traveled in our experiments. 6 3.3 Methods The algorithm uses a client -server computational...architecture. The client here is an interactive pro- gram which takes a pair of controllers as input, simulates4 two copies of the robot with

Robot graphic simulation testbed

NASA Technical Reports Server (NTRS)

Cook, George E.; Sztipanovits, Janos; Biegl, Csaba; Karsai, Gabor; Springfield, James F.

1991-01-01

The objective of this research was twofold. First, the basic capabilities of ROBOSIM (graphical simulation system) were improved and extended by taking advantage of advanced graphic workstation technology and artificial intelligence programming techniques. Second, the scope of the graphic simulation testbed was extended to include general problems of Space Station automation. Hardware support for 3-D graphics and high processing performance make high resolution solid modeling, collision detection, and simulation of structural dynamics computationally feasible. The Space Station is a complex system with many interacting subsystems. Design and testing of automation concepts demand modeling of the affected processes, their interactions, and that of the proposed control systems. The automation testbed was designed to facilitate studies in Space Station automation concepts.

Dynamic and fluid-structure interaction simulations of bioprosthetic heart valves using parametric design with T-splines and Fung-type material models

NASA Astrophysics Data System (ADS)

Hsu, Ming-Chen; Kamensky, David; Xu, Fei; Kiendl, Josef; Wang, Chenglong; Wu, Michael C. H.; Mineroff, Joshua; Reali, Alessandro; Bazilevs, Yuri; Sacks, Michael S.

2015-06-01

This paper builds on a recently developed immersogeometric fluid-structure interaction (FSI) methodology for bioprosthetic heart valve (BHV) modeling and simulation. It enhances the proposed framework in the areas of geometry design and constitutive modeling. With these enhancements, BHV FSI simulations may be performed with greater levels of automation, robustness and physical realism. In addition, the paper presents a comparison between FSI analysis and standalone structural dynamics simulation driven by prescribed transvalvular pressure, the latter being a more common modeling choice for this class of problems. The FSI computation achieved better physiological realism in predicting the valve leaflet deformation than its standalone structural dynamics counterpart.

Simulation framework for intelligent transportation systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ewing, T.; Doss, E.; Hanebutte, U.

1996-10-01

A simulation framework has been developed for a large-scale, comprehensive, scaleable simulation of an Intelligent Transportation System (ITS). The simulator is designed for running on parallel computers and distributed (networked) computer systems, but can run on standalone workstations for smaller simulations. The simulator currently models instrumented smart vehicles with in-vehicle navigation units capable of optimal route planning and Traffic Management Centers (TMC). The TMC has probe vehicle tracking capabilities (display position and attributes of instrumented vehicles), and can provide two-way interaction with traffic to provide advisories and link times. Both the in-vehicle navigation module and the TMC feature detailed graphicalmore » user interfaces to support human-factors studies. Realistic modeling of variations of the posted driving speed are based on human factors studies that take into consideration weather, road conditions, driver personality and behavior, and vehicle type. The prototype has been developed on a distributed system of networked UNIX computers but is designed to run on parallel computers, such as ANL`s IBM SP-2, for large-scale problems. A novel feature of the approach is that vehicles are represented by autonomous computer processes which exchange messages with other processes. The vehicles have a behavior model which governs route selection and driving behavior, and can react to external traffic events much like real vehicles. With this approach, the simulation is scaleable to take advantage of emerging massively parallel processor (MPP) systems.« less

Development of MCNPX-ESUT computer code for simulation of neutron/gamma pulse height distribution

NASA Astrophysics Data System (ADS)

Abolfazl Hosseini, Seyed; Vosoughi, Naser; Zangian, Mehdi

2015-05-01

In this paper, the development of the MCNPX-ESUT (MCNPX-Energy Engineering of Sharif University of Technology) computer code for simulation of neutron/gamma pulse height distribution is reported. Since liquid organic scintillators like NE-213 are well suited and routinely used for spectrometry in mixed neutron/gamma fields, this type of detectors is selected for simulation in the present study. The proposed algorithm for simulation includes four main steps. The first step is the modeling of the neutron/gamma particle transport and their interactions with the materials in the environment and detector volume. In the second step, the number of scintillation photons due to charged particles such as electrons, alphas, protons and carbon nuclei in the scintillator material is calculated. In the third step, the transport of scintillation photons in the scintillator and lightguide is simulated. Finally, the resolution corresponding to the experiment is considered in the last step of the simulation. Unlike the similar computer codes like SCINFUL, NRESP7 and PHRESP, the developed computer code is applicable to both neutron and gamma sources. Hence, the discrimination of neutron and gamma in the mixed fields may be performed using the MCNPX-ESUT computer code. The main feature of MCNPX-ESUT computer code is that the neutron/gamma pulse height simulation may be performed without needing any sort of post processing. In the present study, the pulse height distributions due to a monoenergetic neutron/gamma source in NE-213 detector using MCNPX-ESUT computer code is simulated. The simulated neutron pulse height distributions are validated through comparing with experimental data (Gohil et al. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 664 (2012) 304-309.) and the results obtained from similar computer codes like SCINFUL, NRESP7 and Geant4. The simulated gamma pulse height distribution for a 137Cs source is also compared with the experimental data.

An Interactive, Physics-Based Unmanned Ground Vehicle Simulator Leveraging Open Source Gaming Technology: Progress in the Development and Application of the Virtual Autonomous Navigation Environment (VANE) Desktop

DTIC Science & Technology

2009-01-01

interface, mechatronics, video games 1. INTRODUCTION Engineering methods have substantially and continuously evolved over the past 40 years. In the past...1970s, video games have pioneered interactive simulation and laid the groundwork for inexpensive computing that individuals, corporations, and...purposes. This has not gone unnoticed, and software technology and techniques evolved for video games are beginning to have extraordinary impact in

3D liver volume reconstructed for palpation training.

PubMed

Tibamoso, Gerardo; Perez-Gutierrez, Byron; Uribe-Quevedo, Alvaro

2013-01-01

Virtual Reality systems for medical procedures such as the palpation of different organs, requires fast, robust, accurate and reliable computational methods for providing realism during interaction with the 3D biological models. This paper presents the segmentation, reconstruction and palpation simulation of a healthy liver volume as a tool for training. The chosen method considers the mechanical characteristics and liver properties for correctly simulating palpation interactions, which results appropriate as a complementary tool for training medical students in familiarizing with the liver anatomy.

Organizational Adaptative Behavior: The Complex Perspective of Individuals-Tasks Interaction

NASA Astrophysics Data System (ADS)

Wu, Jiang; Sun, Duoyong; Hu, Bin; Zhang, Yu

Organizations with different organizational structures have different organizational behaviors when responding environmental changes. In this paper, we use a computational model to examine organizational adaptation on four dimensions: Agility, Robustness, Resilience, and Survivability. We analyze the dynamics of organizational adaptation by a simulation study from a complex perspective of the interaction between tasks and individuals in a sales enterprise. The simulation studies in different scenarios show that more flexible communication between employees and less hierarchy level with the suitable centralization can improve organizational adaptation.

Learning by Communicating in Natural Language with Conversational Agents

ERIC Educational Resources Information Center

Graesser, Arthur; Li, Haiying; Forsyth, Carol

2014-01-01

Learning is facilitated by conversational interactions both with human tutors and with computer agents that simulate human tutoring and ideal pedagogical strategies. In this article, we describe some intelligent tutoring systems (e.g., AutoTutor) in which agents interact with students in natural language while being sensitive to their cognitive…

A Computer Model of the Cardiovascular System for Effective Learning.

ERIC Educational Resources Information Center

Rothe, Carl F.

1980-01-01

Presents a model of the cardiovascular system which solves a set of interacting, possibly nonlinear, differential equations. Figures present a schematic diagram of the model and printouts that simulate normal conditions, exercise, hemorrhage, reduced contractility. The nine interacting equations used to describe the system are described in the…

Development and Evaluation of an Interactive Internet-Based Pharmacokinetic Teaching Module.

ERIC Educational Resources Information Center

Hedaya, Mohsen A.

1998-01-01

Describes an Internet-based, interactive, learner-centered, asynchronous instructional module for pharmacokinetics that requires minimal computer knowledge to operate. Main components are concept presentation, a simulation exercise, and self-assessment questions. The module has been found effective in teaching the steady state concept at the…

Theoretical, Experimental, and Computational Evaluation of Several Vane-Type Slow-Wave Structures

NASA Technical Reports Server (NTRS)

Wallett, Thomas M.; Qureshi, A. Haq

1994-01-01

Several types of periodic vane slow-wave structures were fabricated. The dispersion characteristics were found by theoretical analysis, experimental testing, and computer simulation using the MAFIA code. Computer-generated characteristics agreed to approximately within 2 percent of the experimental characteristics for all structures. The theoretical characteristics, however, deviated increasingly as the width to height ratio became smaller. Interaction impedances were also computed based on the experimental and computer-generated resonance frequency shifts due to the introduction of a perturbing dielectric rod.

Multi-Conformation Monte Carlo: A Method for Introducing Flexibility in Efficient Simulations of Many-Protein Systems.

PubMed

Prytkova, Vera; Heyden, Matthias; Khago, Domarin; Freites, J Alfredo; Butts, Carter T; Martin, Rachel W; Tobias, Douglas J

2016-08-25

We present a novel multi-conformation Monte Carlo simulation method that enables the modeling of protein-protein interactions and aggregation in crowded protein solutions. This approach is relevant to a molecular-scale description of realistic biological environments, including the cytoplasm and the extracellular matrix, which are characterized by high concentrations of biomolecular solutes (e.g., 300-400 mg/mL for proteins and nucleic acids in the cytoplasm of Escherichia coli). Simulation of such environments necessitates the inclusion of a large number of protein molecules. Therefore, computationally inexpensive methods, such as rigid-body Brownian dynamics (BD) or Monte Carlo simulations, can be particularly useful. However, as we demonstrate herein, the rigid-body representation typically employed in simulations of many-protein systems gives rise to certain artifacts in protein-protein interactions. Our approach allows us to incorporate molecular flexibility in Monte Carlo simulations at low computational cost, thereby eliminating ambiguities arising from structure selection in rigid-body simulations. We benchmark and validate the methodology using simulations of hen egg white lysozyme in solution, a well-studied system for which extensive experimental data, including osmotic second virial coefficients, small-angle scattering structure factors, and multiple structures determined by X-ray and neutron crystallography and solution NMR, as well as rigid-body BD simulation results, are available for comparison.

Simulations of Bluff Body Flow Interaction for Noise Source Modeling

NASA Technical Reports Server (NTRS)

Khorrami, Medi R.; Lockard David P.; Choudhari, Meelan M.; Jenkins, Luther N.; Neuhart, Dan H.; McGinley, Catherine B.

2006-01-01

The current study is a continuation of our effort to characterize the details of flow interaction between two cylinders in a tandem configuration. This configuration is viewed to possess many of the pertinent flow features of the highly interactive unsteady flow field associated with the main landing gear of large civil transports. The present effort extends our previous two-dimensional, unsteady, Reynolds Averaged Navier-Stokes computations to three dimensions using a quasilaminar, zonal approach, in conjunction with a two-equation turbulence model. Two distinct separation length-to-diameter ratios of L/D = 3.7 and 1.435, representing intermediate and short separation distances between the two cylinders, are simulated. The Mach 0.166 simulations are performed at a Reynolds number of Re = 1.66 105 to match the companion experiments at NASA Langley Research Center. Extensive comparisons with the measured steady and unsteady surface pressure and off-surface particle image velocimetry data show encouraging agreement. Both prominent and some of the more subtle trends in the mean and fluctuating flow fields are correctly predicted. Both computations and the measured data reveal a more robust and energetic shedding process at L/D = 3.7 in comparison with the weaker shedding in the shorter separation case of L/D = 1.435. The vortex shedding frequency based on the computed surface pressure spectra is in reasonable agreement with the measured Strouhal frequency.

Virtual Interactive Musculoskeletal System (VIMS) in orthopaedic research, education and clinical patient care.

PubMed

Chao, Edmund Y S; Armiger, Robert S; Yoshida, Hiroaki; Lim, Jonathan; Haraguchi, Naoki

2007-03-08

The ability to combine physiology and engineering analyses with computer sciences has opened the door to the possibility of creating the "Virtual Human" reality. This paper presents a broad foundation for a full-featured biomechanical simulator for the human musculoskeletal system physiology. This simulation technology unites the expertise in biomechanical analysis and graphic modeling to investigate joint and connective tissue mechanics at the structural level and to visualize the results in both static and animated forms together with the model. Adaptable anatomical models including prosthetic implants and fracture fixation devices and a robust computational infrastructure for static, kinematic, kinetic, and stress analyses under varying boundary and loading conditions are incorporated on a common platform, the VIMS (Virtual Interactive Musculoskeletal System). Within this software system, a manageable database containing long bone dimensions, connective tissue material properties and a library of skeletal joint system functional activities and loading conditions are also available and they can easily be modified, updated and expanded. Application software is also available to allow end-users to perform biomechanical analyses interactively. Examples using these models and the computational algorithms in a virtual laboratory environment are used to demonstrate the utility of these unique database and simulation technology. This integrated system, model library and database will impact on orthopaedic education, basic research, device development and application, and clinical patient care related to musculoskeletal joint system reconstruction, trauma management, and rehabilitation.

Virtual interactive musculoskeletal system (VIMS) in orthopaedic research, education and clinical patient care

PubMed Central

Chao, Edmund YS; Armiger, Robert S; Yoshida, Hiroaki; Lim, Jonathan; Haraguchi, Naoki

2007-01-01

The ability to combine physiology and engineering analyses with computer sciences has opened the door to the possibility of creating the "Virtual Human" reality. This paper presents a broad foundation for a full-featured biomechanical simulator for the human musculoskeletal system physiology. This simulation technology unites the expertise in biomechanical analysis and graphic modeling to investigate joint and connective tissue mechanics at the structural level and to visualize the results in both static and animated forms together with the model. Adaptable anatomical models including prosthetic implants and fracture fixation devices and a robust computational infrastructure for static, kinematic, kinetic, and stress analyses under varying boundary and loading conditions are incorporated on a common platform, the VIMS (Virtual Interactive Musculoskeletal System). Within this software system, a manageable database containing long bone dimensions, connective tissue material properties and a library of skeletal joint system functional activities and loading conditions are also available and they can easily be modified, updated and expanded. Application software is also available to allow end-users to perform biomechanical analyses interactively. Examples using these models and the computational algorithms in a virtual laboratory environment are used to demonstrate the utility of these unique database and simulation technology. This integrated system, model library and database will impact on orthopaedic education, basic research, device development and application, and clinical patient care related to musculoskeletal joint system reconstruction, trauma management, and rehabilitation. PMID:17343764

Biocellion: accelerating computer simulation of multicellular biological system models.

PubMed

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-11-01

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Simulation of deterministic energy-balance particle agglomeration in turbulent liquid-solid flows

NASA Astrophysics Data System (ADS)

Njobuenwu, Derrick O.; Fairweather, Michael

2017-08-01

An efficient technique to simulate turbulent particle-laden flow at high mass loadings within the four-way coupled simulation regime is presented. The technique implements large-eddy simulation, discrete particle simulation, a deterministic treatment of inter-particle collisions, and an energy-balanced particle agglomeration model. The algorithm to detect inter-particle collisions is such that the computational costs scale linearly with the number of particles present in the computational domain. On detection of a collision, particle agglomeration is tested based on the pre-collision kinetic energy, restitution coefficient, and van der Waals' interactions. The performance of the technique developed is tested by performing parametric studies on the influence of the restitution coefficient (en = 0.2, 0.4, 0.6, and 0.8), particle size (dp = 60, 120, 200, and 316 μm), Reynolds number (Reτ = 150, 300, and 590), and particle concentration (αp = 5.0 × 10-4, 1.0 × 10-3, and 5.0 × 10-3) on particle-particle interaction events (collision and agglomeration). The results demonstrate that the collision frequency shows a linear dependency on the restitution coefficient, while the agglomeration rate shows an inverse dependence. Collisions among smaller particles are more frequent and efficient in forming agglomerates than those of coarser particles. The particle-particle interaction events show a strong dependency on the shear Reynolds number Reτ, while increasing the particle concentration effectively enhances particle collision and agglomeration whilst having only a minor influence on the agglomeration rate. Overall, the sensitivity of the particle-particle interaction events to the selected simulation parameters is found to influence the population and distribution of the primary particles and agglomerates formed.

PHREEQCI; a graphical user interface for the geochemical computer program PHREEQC

USGS Publications Warehouse

Charlton, Scott R.; Macklin, Clifford L.; Parkhurst, David L.

1997-01-01

PhreeqcI is a Windows-based graphical user interface for the geochemical computer program PHREEQC. PhreeqcI provides the capability to generate and edit input data files, run simulations, and view text files containing simulation results, all within the framework of a single interface. PHREEQC is a multipurpose geochemical program that can perform speciation, inverse, reaction-path, and 1D advective reaction-transport modeling. Interactive access to all of the capabilities of PHREEQC is available with PhreeqcI. The interface is written in Visual Basic and will run on personal computers under the Windows(3.1), Windows95, and WindowsNT operating systems.

Projective simulation for artificial intelligence

NASA Astrophysics Data System (ADS)

Briegel, Hans J.; de Las Cuevas, Gemma

2012-05-01

We propose a model of a learning agent whose interaction with the environment is governed by a simulation-based projection, which allows the agent to project itself into future situations before it takes real action. Projective simulation is based on a random walk through a network of clips, which are elementary patches of episodic memory. The network of clips changes dynamically, both due to new perceptual input and due to certain compositional principles of the simulation process. During simulation, the clips are screened for specific features which trigger factual action of the agent. The scheme is different from other, computational, notions of simulation, and it provides a new element in an embodied cognitive science approach to intelligent action and learning. Our model provides a natural route for generalization to quantum-mechanical operation and connects the fields of reinforcement learning and quantum computation.

Projective simulation for artificial intelligence

PubMed Central

Briegel, Hans J.; De las Cuevas, Gemma

2012-01-01

We propose a model of a learning agent whose interaction with the environment is governed by a simulation-based projection, which allows the agent to project itself into future situations before it takes real action. Projective simulation is based on a random walk through a network of clips, which are elementary patches of episodic memory. The network of clips changes dynamically, both due to new perceptual input and due to certain compositional principles of the simulation process. During simulation, the clips are screened for specific features which trigger factual action of the agent. The scheme is different from other, computational, notions of simulation, and it provides a new element in an embodied cognitive science approach to intelligent action and learning. Our model provides a natural route for generalization to quantum-mechanical operation and connects the fields of reinforcement learning and quantum computation. PMID:22590690

Modelling of Dispersed Gas-Liquid Flow using LBGK and LPT Approach

NASA Astrophysics Data System (ADS)

Agarwal, Alankar; Prakash, Akshay; Ravindra, B.

2017-11-01

The dynamics of gas bubbles play a significant, if not crucial, role in a large variety of industrial process that involves using reactors. Many of these processes are still not well understood in terms of optimal scale-up strategies.An accurate modeling of bubbles and bubble swarms become important for high fidelity bioreactor simulations. This study is a part of the development of robust bubble fluid interaction modules for simulation of industrial-scale reactors. The work presents the simulation of a single bubble rising in a quiescent water tank using current models presented in the literature for bubble-fluid interaction. In this multiphase benchmark problem, the continuous phase (water) is discretized using the Lattice Bhatnagar-Gross and Krook (LBGK) model of Lattice Boltzmann Method (LBM), while the dispersed gas phase (i.e. air-bubble) modeled with the Lagrangian particle tracking (LPT) approach. The cheap clipped fourth order polynomial function is used to model the interaction between two phases. The model is validated by comparing the simulation results for terminal velocity of a bubble at varying bubble diameter and the influence of bubble motion in liquid velocity with the theoretical and previously available experimental data. This work is supported by the ``Centre for Development of Advanced Computing (C-DAC), Pune'' by providing the advanced computational facility in PARAM Yuva-II.

Distributed interactive communication in simulated space-dwelling groups.

PubMed

Brady, Joseph V; Hienz, Robert D; Hursh, Steven R; Ragusa, Leonard C; Rouse, Charles O; Gasior, Eric D

2004-03-01

This report describes the development and preliminary application of an experimental test bed for modeling human behavior in the context of a computer generated environment to analyze the effects of variations in communication modalities, incentives and stressful conditions. In addition to detailing the methodological development of a simulated task environment that provides for electronic monitoring and recording of individual and group behavior, the initial substantive findings from an experimental analysis of distributed interactive communication in simulated space dwelling groups are described. Crews of three members each (male and female) participated in simulated "planetary missions" based upon a synthetic scenario task that required identification, collection, and analysis of geologic specimens with a range of grade values. The results of these preliminary studies showed clearly that cooperative and productive interactions were maintained between individually isolated and distributed individuals communicating and problem-solving effectively in a computer-generated "planetary" environment over extended time intervals without benefit of one another's physical presence. Studies on communication channel constraints confirmed the functional interchangeability between available modalities with the highest degree of interchangeability occurring between Audio and Text modes of communication. The effects of task-related incentives were determined by the conditions under which they were available with Positive Incentives effectively attenuating decrements in performance under stressful time pressure. c2003 Elsevier Ltd. All rights reserved.

Theoretical Study of Wave Particle Correlation Measurement via 1-D Electromagnetic Particle Simulation

NASA Astrophysics Data System (ADS)

Ueda, Yoshikatsu; Omura, Yoshiharu; Kojima, Hiro

Spacecraft observation is essentially "one-point measurement", while numerical simulation can reproduce a whole system of physical processes on a computer. By performing particle simulations of plasma wave instabilities and calculating correlation of waves and particles observed at a single point, we examine how well we can infer the characteristics of the whole system by a one-point measurement. We perform various simulation runs with different plasma parameters using one-dimensional electromagnetic particle code (KEMPO1) and calculate 'E dot v' or other moments at a single point. We find good correlation between the measurement and the macroscopic fluctuations of the total simulation region. We make use of the results of the computer experiments in our system design of new instruments 'One-chip Wave Particle Interaction Analyzer (OWPIA)'.

Meso-scale Computational Investigation of Polyurea Microstructure and Its Role in Shockwave Attenuation/dispersion

DTIC Science & Technology

2015-07-01

grained simulations of the formation of meso-segregated microstructure and its interaction with the shockwave is analyzed in the present work. It is...help identify these phenomena and processes, meso-scale coarse-grained simulations of the formation of meso-segregated microstructure and its...of shockwave-induced hard-domain densification. Keywords: Polyurea; Meso-scale; Coarse-grained simulations ; Shockwave attenuation; shockwave

Tetrahedral-Mesh Simulation of Turbulent Flows with the Space-Time Conservative Schemes

NASA Technical Reports Server (NTRS)

Chang, Chau-Lyan; Venkatachari, Balaji; Cheng, Gary C.

2015-01-01

Direct numerical simulations of turbulent flows are predominantly carried out using structured, hexahedral meshes despite decades of development in unstructured mesh methods. Tetrahedral meshes offer ease of mesh generation around complex geometries and the potential of an orientation free grid that would provide un-biased small-scale dissipation and more accurate intermediate scale solutions. However, due to the lack of consistent multi-dimensional numerical formulations in conventional schemes for triangular and tetrahedral meshes at the cell interfaces, numerical issues exist when flow discontinuities or stagnation regions are present. The space-time conservative conservation element solution element (CESE) method - due to its Riemann-solver-free shock capturing capabilities, non-dissipative baseline schemes, and flux conservation in time as well as space - has the potential to more accurately simulate turbulent flows using unstructured tetrahedral meshes. To pave the way towards accurate simulation of shock/turbulent boundary-layer interaction, a series of wave and shock interaction benchmark problems that increase in complexity, are computed in this paper with triangular/tetrahedral meshes. Preliminary computations for the normal shock/turbulence interactions are carried out with a relatively coarse mesh, by direct numerical simulations standards, in order to assess other effects such as boundary conditions and the necessity of a buffer domain. The results indicate that qualitative agreement with previous studies can be obtained for flows where, strong shocks co-exist along with unsteady waves that display a broad range of scales, with a relatively compact computational domain and less stringent requirements for grid clustering near the shock. With the space-time conservation properties, stable solutions without any spurious wave reflections can be obtained without a need for buffer domains near the outflow/farfield boundaries. Computational results for the isotropic turbulent flow decay, at a relatively high turbulent Mach number, show a nicely behaved spectral decay rate for medium to high wave numbers. The high-order CESE schemes offer very robust solutions even with the presence of strong shocks or widespread shocklets. The explicit formulation in conjunction with a close to unity theoretical upper Courant number bound has the potential to offer an efficient numerical framework for general compressible turbulent flow simulations with unstructured meshes.

In vitro flow assessment: from PC-MRI to computational fluid dynamics including fluid-structure interaction

NASA Astrophysics Data System (ADS)

Kratzke, Jonas; Rengier, Fabian; Weis, Christian; Beller, Carsten J.; Heuveline, Vincent

2016-04-01

Initiation and development of cardiovascular diseases can be highly correlated to specific biomechanical parameters. To examine and assess biomechanical parameters, numerical simulation of cardiovascular dynamics has the potential to complement and enhance medical measurement and imaging techniques. As such, computational fluid dynamics (CFD) have shown to be suitable to evaluate blood velocity and pressure in scenarios, where vessel wall deformation plays a minor role. However, there is a need for further validation studies and the inclusion of vessel wall elasticity for morphologies being subject to large displacement. In this work, we consider a fluid-structure interaction (FSI) model including the full elasticity equation to take the deformability of aortic wall soft tissue into account. We present a numerical framework, in which either a CFD study can be performed for less deformable aortic segments or an FSI simulation for regions of large displacement such as the aortic root and arch. Both of the methods are validated by means of an aortic phantom experiment. The computational results are in good agreement with 2D phase-contrast magnetic resonance imaging (PC-MRI) velocity measurements as well as catheter-based pressure measurements. The FSI simulation shows a characteristic vessel compliance effect on the flow field induced by the elasticity of the vessel wall, which the CFD model is not capable of. The in vitro validated FSI simulation framework can enable the computation of complementary biomechanical parameters such as the stress distribution within the vessel wall.

Aeroelastic-Acoustics Simulation of Flight Systems

NASA Technical Reports Server (NTRS)

Gupta, kajal K.; Choi, S.; Ibrahim, A.

2009-01-01

This paper describes the details of a numerical finite element (FE) based analysis procedure and a resulting code for the simulation of the acoustics phenomenon arising from aeroelastic interactions. Both CFD and structural simulations are based on FE discretization employing unstructured grids. The sound pressure level (SPL) on structural surfaces is calculated from the root mean square (RMS) of the unsteady pressure and the acoustic wave frequencies are computed from a fast Fourier transform (FFT) of the unsteady pressure distribution as a function of time. The resulting tool proves to be unique as it is designed to analyze complex practical problems, involving large scale computations, in a routine fashion.

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

Monte Carlo simulation of biomolecular systems with BIOMCSIM

NASA Astrophysics Data System (ADS)

Kamberaj, H.; Helms, V.

2001-12-01

A new Monte Carlo simulation program, BIOMCSIM, is presented that has been developed in particular to simulate the behaviour of biomolecular systems, leading to insights and understanding of their functions. The computational complexity in Monte Carlo simulations of high density systems, with large molecules like proteins immersed in a solvent medium, or when simulating the dynamics of water molecules in a protein cavity, is enormous. The program presented in this paper seeks to provide these desirable features putting special emphasis on simulations in grand canonical ensembles. It uses different biasing techniques to increase the convergence of simulations, and periodic load balancing in its parallel version, to maximally utilize the available computer power. In periodic systems, the long-ranged electrostatic interactions can be treated by Ewald summation. The program is modularly organized, and implemented using an ANSI C dialect, so as to enhance its modifiability. Its performance is demonstrated in benchmark applications for the proteins BPTI and Cytochrome c Oxidase.

Routine Discovery of Complex Genetic Models using Genetic Algorithms

PubMed Central

Moore, Jason H.; Hahn, Lance W.; Ritchie, Marylyn D.; Thornton, Tricia A.; White, Bill C.

2010-01-01

Simulation studies are useful in various disciplines for a number of reasons including the development and evaluation of new computational and statistical methods. This is particularly true in human genetics and genetic epidemiology where new analytical methods are needed for the detection and characterization of disease susceptibility genes whose effects are complex, nonlinear, and partially or solely dependent on the effects of other genes (i.e. epistasis or gene-gene interaction). Despite this need, the development of complex genetic models that can be used to simulate data is not always intuitive. In fact, only a few such models have been published. We have previously developed a genetic algorithm approach to discovering complex genetic models in which two single nucleotide polymorphisms (SNPs) influence disease risk solely through nonlinear interactions. In this paper, we extend this approach for the discovery of high-order epistasis models involving three to five SNPs. We demonstrate that the genetic algorithm is capable of routinely discovering interesting high-order epistasis models in which each SNP influences risk of disease only through interactions with the other SNPs in the model. This study opens the door for routine simulation of complex gene-gene interactions among SNPs for the development and evaluation of new statistical and computational approaches for identifying common, complex multifactorial disease susceptibility genes. PMID:20948983

Testing the Two-Layer Model for Correcting Near Cloud Reflectance Enhancement Using LES SHDOM Simulated Radiances

NASA Technical Reports Server (NTRS)

Wen, Guoyong; Marshak, Alexander; Varnai, Tamas; Levy, Robert

2016-01-01

A transition zone exists between cloudy skies and clear sky; such that, clouds scatter solar radiation into clear-sky regions. From a satellite perspective, it appears that clouds enhance the radiation nearby. We seek a simple method to estimate this enhancement, since it is so computationally expensive to account for all three-dimensional (3-D) scattering processes. In previous studies, we developed a simple two-layer model (2LM) that estimated the radiation scattered via cloud-molecular interactions. Here we have developed a new model to account for cloud-surface interaction (CSI). We test the models by comparing to calculations provided by full 3-D radiative transfer simulations of realistic cloud scenes. For these scenes, the Moderate Resolution Imaging Spectroradiometer (MODIS)-like radiance fields were computed from the Spherical Harmonic Discrete Ordinate Method (SHDOM), based on a large number of cumulus fields simulated by the University of California, Los Angeles (UCLA) large eddy simulation (LES) model. We find that the original 2LM model that estimates cloud-air molecule interactions accounts for 64 of the total reflectance enhancement and the new model (2LM+CSI) that also includes cloud-surface interactions accounts for nearly 80. We discuss the possibility of accounting for cloud-aerosol radiative interactions in 3-D cloud-induced reflectance enhancement, which may explain the remaining 20 of enhancements. Because these are simple models, these corrections can be applied to global satellite observations (e.g., MODIS) and help to reduce biases in aerosol and other clear-sky retrievals.

Synchronization Of Parallel Discrete Event Simulations

NASA Technical Reports Server (NTRS)

Steinman, Jeffrey S.

1992-01-01

Adaptive, parallel, discrete-event-simulation-synchronization algorithm, Breathing Time Buckets, developed in Synchronous Parallel Environment for Emulation and Discrete Event Simulation (SPEEDES) operating system. Algorithm allows parallel simulations to process events optimistically in fluctuating time cycles that naturally adapt while simulation in progress. Combines best of optimistic and conservative synchronization strategies while avoiding major disadvantages. Algorithm processes events optimistically in time cycles adapting while simulation in progress. Well suited for modeling communication networks, for large-scale war games, for simulated flights of aircraft, for simulations of computer equipment, for mathematical modeling, for interactive engineering simulations, and for depictions of flows of information.

Simulating Sand Behavior through Terrain Subdivision and Particle Refinement

NASA Astrophysics Data System (ADS)

Clothier, M.

2013-12-01

Advances in computer graphics, GPUs, and parallel processing hardware have provided researchers with new methods to visualize scientific data. In fact, these advances have spurred new research opportunities between computer graphics and other disciplines, such as Earth sciences. Through collaboration, Earth and planetary scientists have benefited by using these advances in hardware technology to process large amounts of data for visualization and analysis. At Oregon State University, we are collaborating with the Oregon Space Grant and IGERT Ecosystem Informatics programs to investigate techniques for simulating the behavior of sand. In addition, we have also been collaborating with the Jet Propulsion Laboratory's DARTS Lab to exchange ideas on our research. The DARTS Lab specializes in the simulation of planetary vehicles, such as the Mars rovers. One aspect of their work is testing these vehicles in a virtual "sand box" to test their performance in different environments. Our research builds upon this idea to create a sand simulation framework to allow for more complex and diverse environments. As a basis for our framework, we have focused on planetary environments, such as the harsh, sandy regions on Mars. To evaluate our framework, we have used simulated planetary vehicles, such as a rover, to gain insight into the performance and interaction between the surface sand and the vehicle. Unfortunately, simulating the vast number of individual sand particles and their interaction with each other has been a computationally complex problem in the past. However, through the use of high-performance computing, we have developed a technique to subdivide physically active terrain regions across a large landscape. To achieve this, we only subdivide terrain regions where sand particles are actively participating with another object or force, such as a rover wheel. This is similar to a Level of Detail (LOD) technique, except that the density of subdivisions are determined by their proximity to the interacting object or force with the sand. To illustrate an example, as a rover wheel moves forward and approaches a particular sand region, that region will continue to subdivide until individual sand particles are represented. Conversely, if the rover wheel moves away, previously subdivided sand regions will recombine. Thus, individual sand particles are available when an interacting force is present but stored away if there is not. As such, this technique allows for many particles to be represented without the computational complexity. We have also further generalized these subdivision regions in our sand framework into any volumetric area suitable for use in the simulation. This allows for more compact subdivision regions and has fine-tuned our framework so that more emphasis can be placed on regions of actively participating sand. We feel that this increases the framework's usefulness across scientific applications and can provide for other research opportunities within the earth and planetary sciences. Through continued collaboration with our academic partners, we continue to build upon our sand simulation framework and look for other opportunities to utilize this research.

Electrostatic interactions in soft particle systems: mesoscale simulations of ionic liquids.

PubMed

Wang, Yong-Lei; Zhu, You-Liang; Lu, Zhong-Yuan; Laaksonen, Aatto

2018-05-21

Computer simulations provide a unique insight into the microscopic details, molecular interactions and dynamic behavior responsible for many distinct physicochemical properties of ionic liquids. Due to the sluggish and heterogeneous dynamics and the long-ranged nanostructured nature of ionic liquids, coarse-grained meso-scale simulations provide an indispensable complement to detailed first-principles calculations and atomistic simulations allowing studies over extended length and time scales with a modest computational cost. Here, we present extensive coarse-grained simulations on a series of ionic liquids of the 1-alkyl-3-methylimidazolium (alkyl = butyl, heptyl-, and decyl-) family with Cl, [BF4], and [PF6] counterions. Liquid densities, microstructures, translational diffusion coefficients, and re-orientational motion of these model ionic liquid systems have been systematically studied over a wide temperature range. The addition of neutral beads in cationic models leads to a transition of liquid morphologies from dispersed apolar beads in a polar framework to that characterized by bi-continuous sponge-like interpenetrating networks in liquid matrices. Translational diffusion coefficients of both cations and anions decrease upon lengthening of the neutral chains in the cationic models and by enlarging molecular sizes of the anionic groups. Similar features are observed in re-orientational motion and time scales of different cationic models within the studied temperature range. The comparison of the liquid properties of the ionic systems with their neutral counterparts indicates that the distinctive microstructures and dynamical quantities of the model ionic liquid systems are intrinsically related to Coulombic interactions. Finally, we compared the computational efficiencies of three linearly scaling O(N log N) Ewald summation methods, the particle-particle particle-mesh method, the particle-mesh Ewald summation method, and the Ewald summation method based on a non-uniform fast Fourier transform technique, to calculate electrostatic interactions. Coarse-grained simulations were performed using the GALAMOST and the GROMACS packages and hardware efficiently utilizing graphics processing units on a set of extended [1-decyl-3-methylimidazolium][BF4] ionic liquid systems of up to 131 072 ion pairs.

TH-A-19A-08: Intel Xeon Phi Implementation of a Fast Multi-Purpose Monte Carlo Simulation for Proton Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Souris, K; Lee, J; Sterpin, E

2014-06-15

Purpose: Recent studies have demonstrated the capability of graphics processing units (GPUs) to compute dose distributions using Monte Carlo (MC) methods within clinical time constraints. However, GPUs have a rigid vectorial architecture that favors the implementation of simplified particle transport algorithms, adapted to specific tasks. Our new, fast, and multipurpose MC code, named MCsquare, runs on Intel Xeon Phi coprocessors. This technology offers 60 independent cores, and therefore more flexibility to implement fast and yet generic MC functionalities, such as prompt gamma simulations. Methods: MCsquare implements several models and hence allows users to make their own tradeoff between speed andmore » accuracy. A 200 MeV proton beam is simulated in a heterogeneous phantom using Geant4 and two configurations of MCsquare. The first one is the most conservative and accurate. The method of fictitious interactions handles the interfaces and secondary charged particles emitted in nuclear interactions are fully simulated. The second, faster configuration simplifies interface crossings and simulates only secondary protons after nuclear interaction events. Integral depth-dose and transversal profiles are compared to those of Geant4. Moreover, the production profile of prompt gammas is compared to PENH results. Results: Integral depth dose and transversal profiles computed by MCsquare and Geant4 are within 3%. The production of secondaries from nuclear interactions is slightly inaccurate at interfaces for the fastest configuration of MCsquare but this is unlikely to have any clinical impact. The computation time varies between 90 seconds for the most conservative settings to merely 59 seconds in the fastest configuration. Finally prompt gamma profiles are also in very good agreement with PENH results. Conclusion: Our new, fast, and multi-purpose Monte Carlo code simulates prompt gammas and calculates dose distributions in less than a minute, which complies with clinical time constraints. It has been successfully validated with Geant4. This work has been financialy supported by InVivoIGT, a public/private partnership between UCL and IBA.« less