An extension of the OpenModelica compiler for using Modelica models in a discrete event simulation

DOE PAGES

Nutaro, James

2014-11-03

In this article, a new back-end and run-time system is described for the OpenModelica compiler. This new back-end transforms a Modelica model into a module for the adevs discrete event simulation package, thereby extending adevs to encompass complex, hybrid dynamical systems. The new run-time system that has been built within the adevs simulation package supports models with state-events and time-events and that comprise differential-algebraic systems with high index. Finally, although the procedure for effecting this transformation is based on adevs and the Discrete Event System Specification, it can be adapted to any discrete event simulation package.

eSBMTools 1.0: enhanced native structure-based modeling tools.

PubMed

Lutz, Benjamin; Sinner, Claude; Heuermann, Geertje; Verma, Abhinav; Schug, Alexander

2013-11-01

Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints. We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2. http://sourceforge.net/projects/esbmtools/. alexander.schug@kit.edu. Supplementary data are available at Bioinformatics online.

Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

PubMed

Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

2017-01-01

Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

Molecular dynamics simulations of collision-induced absorption: Implementation in LAMMPS

NASA Astrophysics Data System (ADS)

Fakhardji, W.; Gustafsson, M.

2017-02-01

We pursue simulations of collision-induced absorption in a mixture of argon and xenon gas at room temperature by means of classical molecular dynamics. The established theoretical approach (Hartmann et al. 2011 J. Chem. Phys. 134 094316) is implemented with the molecular dynamics package LAMMPS. The bound state features in the absorption spectrum are well reproduced with the molecular dynamics simulation in comparison with a laboratory measurement. The magnitude of the computed absorption, however, is underestimated in a large part of the spectrum. We suggest some aspects of the simulation that could be improved.

Browndye: A Software Package for Brownian Dynamics

PubMed Central

McCammon, J. Andrew

2010-01-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. PMID:21132109

The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory

NASA Astrophysics Data System (ADS)

Lourderaj, Upakarasamy; Sun, Rui; Kohale, Swapnil C.; Barnes, George L.; de Jong, Wibe A.; Windus, Theresa L.; Hase, William L.

2014-03-01

The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling since the two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface that accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

Simulations of Operation Dynamics of Different Type GaN Particle Sensors

PubMed Central

Gaubas, Eugenijus; Ceponis, Tomas; Kalesinskas, Vidas; Pavlov, Jevgenij; Vysniauskas, Juozas

2015-01-01

The operation dynamics of the capacitor-type and PIN diode type detectors based on GaN have been simulated using the dynamic and drift-diffusion models. The drift-diffusion current simulations have been implemented by employing the software package Synopsys TCAD Sentaurus. The monopolar and bipolar drift regimes have been analyzed by using dynamic models based on the Shockley-Ramo theorem. The carrier multiplication processes determined by impact ionization have been considered in order to compensate carrier lifetime reduction due to introduction of radiation defects into GaN detector material. PMID:25751080

DNA Packaging in Bacteriophage: Is Twist Important?

PubMed Central

Spakowitz, Andrew James; Wang, Zhen-Gang

2005-01-01

We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with rotation exhibits a spool-like character that is consistent with experimental and previous theoretical work, whereas feeding without rotation results in a folded conformation inconsistent with a spool conformation. The chain segment density shows a layered structure, which is more pronounced for packaging with rotation. However, in both cases, the conformation is marked by frequent jumps of the polymer chain from layer to layer, potentially influencing the ability to disentangle during subsequent ejection. Ejection simulations with and without Brownian forces show that Brownian forces are necessary to achieve complete ejection of the polymer chain in the absence of external forces. PMID:15805174

DNA packaging in bacteriophage: is twist important?

PubMed

Spakowitz, Andrew James; Wang, Zhen-Gang

2005-06-01

We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with rotation exhibits a spool-like character that is consistent with experimental and previous theoretical work, whereas feeding without rotation results in a folded conformation inconsistent with a spool conformation. The chain segment density shows a layered structure, which is more pronounced for packaging with rotation. However, in both cases, the conformation is marked by frequent jumps of the polymer chain from layer to layer, potentially influencing the ability to disentangle during subsequent ejection. Ejection simulations with and without Brownian forces show that Brownian forces are necessary to achieve complete ejection of the polymer chain in the absence of external forces.

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.

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

Towards a Comprehensive Dynamic-chemistry Assimilation for Eos-Chem: Plans and Status in NASA's Data Assimilation Office

NASA Technical Reports Server (NTRS)

Pawson, Steven; Lin, Shian-Jiann; Rood, Richard B.; Stajner, Ivanka; Nebuda, Sharon; Nielsen, J. Eric; Douglass, Anne R.

2000-01-01

In order to support the EOS-Chem project, a comprehensive assimilation package for the coupled chemical-dynamical system is being developed by the Data Assimilation Office at NASA GSFC. This involves development of a coupled chemistry/meteorology model and of data assimilation techniques for trace species and meteorology. The model is being developed using the flux-form semi-Lagrangian dynamical core of Lin and Rood, the physical parameterizations from the NCAR Community Climate Model, and atmospheric chemistry modules from the Atmospheric Chemistry and Dynamics branch at NASA GSFC. To date the following results have been obtained: (i) multi-annual simulations with the dynamics-radiation model show the credibility of the package for atmospheric simulations; (ii) initial simulations including a limited number of middle atmospheric trace gases reveal the realistic nature of transport mechanisms, although there is still a need for some improvements. Samples of these results will be shown. A meteorological assimilation system is currently being constructed using the model; this will form the basis for the proposed meteorological/chemical assimilation package. The latter part of the presentation will focus on areas targeted for development in the near and far terms, with the objective of Providing a comprehensive assimilation package for the EOS-Chem science experiment. The first stage will target ozone assimilation. The plans also encompass a reanalysis (ReSTS) for the 1991-1995 period, which includes the Mt. Pinatubo eruption and the time when a large number of UARS observations were available. One of the most challenging aspects of future developments will be to couple theoretical advances in tracer assimilation with the practical considerations of a real environment and eventually a near-real-time assimilation system.

PLATSIM: An efficient linear simulation and analysis package for large-order flexible systems

NASA Technical Reports Server (NTRS)

Maghami, Periman; Kenny, Sean P.; Giesy, Daniel P.

1995-01-01

PLATSIM is a software package designed to provide efficient time and frequency domain analysis of large-order generic space platforms implemented with any linear time-invariant control system. Time domain analysis provides simulations of the overall spacecraft response levels due to either onboard or external disturbances. The time domain results can then be processed by the jitter analysis module to assess the spacecraft's pointing performance in a computationally efficient manner. The resulting jitter analysis algorithms have produced an increase in speed of several orders of magnitude over the brute force approach of sweeping minima and maxima. Frequency domain analysis produces frequency response functions for uncontrolled and controlled platform configurations. The latter represents an enabling technology for large-order flexible systems. PLATSIM uses a sparse matrix formulation for the spacecraft dynamics model which makes both the time and frequency domain operations quite efficient, particularly when a large number of modes are required to capture the true dynamics of the spacecraft. The package is written in MATLAB script language. A graphical user interface (GUI) is included in the PLATSIM software package. This GUI uses MATLAB's Handle graphics to provide a convenient way for setting simulation and analysis parameters.

DynamO: a free O(N) general event-driven molecular dynamics simulator.

PubMed

Bannerman, M N; Sargant, R; Lue, L

2011-11-30

Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo. Copyright © 2011 Wiley Periodicals, Inc.

Extensions to the Dynamic Aerospace Vehicle Exchange Markup Language

NASA Technical Reports Server (NTRS)

Brian, Geoffrey J.; Jackson, E. Bruce

2011-01-01

The Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML) is a syntactical language for exchanging flight vehicle dynamic model data. It provides a framework for encoding entire flight vehicle dynamic model data packages for exchange and/or long-term archiving. Version 2.0.1 of DAVE-ML provides much of the functionality envisioned for exchanging aerospace vehicle data; however, it is limited in only supporting scalar time-independent data. Additional functionality is required to support vector and matrix data, abstracting sub-system models, detailing dynamics system models (both discrete and continuous), and defining a dynamic data format (such as time sequenced data) for validation of dynamics system models and vehicle simulation packages. Extensions to DAVE-ML have been proposed to manage data as vectors and n-dimensional matrices, and record dynamic data in a compatible form. These capabilities will improve the clarity of data being exchanged, simplify the naming of parameters, and permit static and dynamic data to be stored using a common syntax within a single file; thereby enhancing the framework provided by DAVE-ML for exchanging entire flight vehicle dynamic simulation models.

Modelling robotic systems with DADS

NASA Technical Reports Server (NTRS)

Churchill, L. W.; Sharf, I.

1993-01-01

With the appearance of general off-the-shelf software packages for the simulation of mechanical systems, modelling and simulation of mechanisms has become an easier task. The authors have recently used one such package, DADS, to model the dynamics of rigid and flexible-link robotic manipulators. In this paper, we present this overview of our learning experiences with DADS, in the hope that it will shorten the learning process for others interested in this software.

Testing a structural model for viral DNA packaging motor function by optical tweezers measurements, site directed mutagenesis, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Keller, Nicholas A.; Migliori, Amy D.; Arya, Gaurav; Rao, Venigalla B.; Smith, Douglas E.

2013-09-01

Many double-stranded DNA viruses employ a molecular motor to package DNA into preformed capsid shells. Based on structures of phage T4 motor proteins determined by X-ray crystallography and cryo-electron microscopy, Rao, Rossmann and coworkers recently proposed a structural model for motor function. They proposed that DNA is ratcheted by a large conformational change driven by electrostatic interactions between charged residues at an interface between two globular domains of the motor protein. We have conducted experiments to test this model by studying the effect on packaging under applied load of site-directed changes altering these residues. We observe significant impairment of packaging activity including reductions in packaging rate, percent time packaging, and time active under high load. We show that these measured impairments correlate well with alterations in free energies associated with the conformational change predicted by molecular dynamics simulations.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

ATK-ForceField: a new generation molecular dynamics software package

NASA Astrophysics Data System (ADS)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

Dynamic simulation of train derailments

DOT National Transportation Integrated Search

2006-11-05

This paper describes a planar rigid-body model to examine the gross motions of rail cars in a train derailment. The model is implemented using a commercial software package called ADAMS (Automatic Dynamic Analysis of Mechanical Systems). The results ...

Preliminary Dynamic Feasibility and Analysis of a Spherical, Wind-Driven (Tumbleweed), Martian Rover

NASA Technical Reports Server (NTRS)

Flick, John J.; Toniolo, Matthew D.

2005-01-01

The process and findings are presented from a preliminary feasibility study examining the dynamics characteristics of a spherical wind-driven (or Tumbleweed) rover, which is intended for exploration of the Martian surface. The results of an initial feasibility study involving several worst-case mobility situations that a Tumbleweed rover might encounter on the surface of Mars are discussed. Additional topics include the evaluation of several commercially available analysis software packages that were examined as possible platforms for the development of a Monte Carlo Tumbleweed mission simulation tool. This evaluation lead to the development of the Mars Tumbleweed Monte Carlo Simulator (or Tumbleweed Simulator) using the Vortex physics software package from CM-Labs, Inc. Discussions regarding the development and evaluation of the Tumbleweed Simulator, as well as the results of a preliminary analysis using the tool are also presented. Finally, a brief conclusions section is presented.

Impact of the dynamical core on the direct simulation of tropical cyclones in a high-resolution global model

DOE PAGES

Reed, K. A.; Bacmeister, J. T.; Rosenbloom, N. A.; ...

2015-05-13

Our paper examines the impact of the dynamical core on the simulation of tropical cyclone (TC) frequency, distribution, and intensity. The dynamical core, the central fluid flow component of any general circulation model (GCM), is often overlooked in the analysis of a model's ability to simulate TCs compared to the impact of more commonly documented components (e.g., physical parameterizations). The Community Atmosphere Model version 5 is configured with multiple dynamics packages. This analysis demonstrates that the dynamical core has a significant impact on storm intensity and frequency, even in the presence of similar large-scale environments. In particular, the spectral elementmore » core produces stronger TCs and more hurricanes than the finite-volume core using very similar parameterization packages despite the latter having a slightly more favorable TC environment. Furthermore, these results suggest that more detailed investigations into the impact of the GCM dynamical core on TC climatology are needed to fully understand these uncertainties. Key Points The impact of the GCM dynamical core is often overlooked in TC assessments The CAM5 dynamical core has a significant impact on TC frequency and intensity A larger effort is needed to better understand this uncertainty« less

Substructured multibody molecular dynamics.

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

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

On Parallelizing Single Dynamic Simulation Using HPC Techniques and APIs of Commercial Software

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

Diao, Ruisheng; Jin, Shuangshuang; Howell, Frederic

Time-domain simulations are heavily used in today’s planning and operation practices to assess power system transient stability and post-transient voltage/frequency profiles following severe contingencies to comply with industry standards. Because of the increased modeling complexity, it is several times slower than real time for state-of-the-art commercial packages to complete a dynamic simulation for a large-scale model. With the growing stochastic behavior introduced by emerging technologies, power industry has seen a growing need for performing security assessment in real time. This paper presents a parallel implementation framework to speed up a single dynamic simulation by leveraging the existing stability model librarymore » in commercial tools through their application programming interfaces (APIs). Several high performance computing (HPC) techniques are explored such as parallelizing the calculation of generator current injection, identifying fast linear solvers for network solution, and parallelizing data outputs when interacting with APIs in the commercial package, TSAT. The proposed method has been tested on a WECC planning base case with detailed synchronous generator models and exhibits outstanding scalable performance with sufficient accuracy.« less

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

PubMed

Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

2017-09-30

GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Extended asymmetric hot region formation due to shockwave interactions following void collapse in shocked high explosive

NASA Astrophysics Data System (ADS)

Shan, Tzu-Ray; Wixom, Ryan R.; Thompson, Aidan P.

2016-08-01

In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed by coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. The formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

PubMed Central

Schöneberg, Johannes; Noé, Frank

2013-01-01

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics. PMID:24040218

Investigation of different modeling approaches for computational fluid dynamics simulation of high-pressure rocket combustors

NASA Astrophysics Data System (ADS)

Ivancic, B.; Riedmann, H.; Frey, M.; Knab, O.; Karl, S.; Hannemann, K.

2016-07-01

The paper summarizes technical results and first highlights of the cooperation between DLR and Airbus Defence and Space (DS) within the work package "CFD Modeling of Combustion Chamber Processes" conducted in the frame of the Propulsion 2020 Project. Within the addressed work package, DLR Göttingen and Airbus DS Ottobrunn have identified several test cases where adequate test data are available and which can be used for proper validation of the computational fluid dynamics (CFD) tools. In this paper, the first test case, the Penn State chamber (RCM1), is discussed. Presenting the simulation results from three different tools, it is shown that the test case can be computed properly with steady-state Reynolds-averaged Navier-Stokes (RANS) approaches. The achieved simulation results reproduce the measured wall heat flux as an important validation parameter very well but also reveal some inconsistencies in the test data which are addressed in this paper.

Particle-based simulations of self-motile suspensions

NASA Astrophysics Data System (ADS)

Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

2015-11-01

A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

Eddylicious: A Python package for turbulent inflow generation

NASA Astrophysics Data System (ADS)

Mukha, Timofey; Liefvendahl, Mattias

2018-01-01

A Python package for generating inflow for scale-resolving computer simulations of turbulent flow is presented. The purpose of the package is to unite existing inflow generation methods in a single code-base and make them accessible to users of various Computational Fluid Dynamics (CFD) solvers. The currently existing functionality consists of an accurate inflow generation method suitable for flows with a turbulent boundary layer inflow and input/output routines for coupling with the open-source CFD solver OpenFOAM.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.

PubMed

Yao, Kun; Herr, John E; Toth, David W; Mckintyre, Ryker; Parkhill, John

2018-02-28

Traditional force fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a data-driven approach is naturally inefficient for long-range interatomic forces that have simple physical formulas. In this manuscript we construct a hybrid model chemistry consisting of a nearsighted neural network potential with screened long-range electrostatic and van der Waals physics. This trained potential, simply dubbed "TensorMol-0.1", is offered in an open-source Python package capable of many of the simulation types commonly used to study chemistry: geometry optimizations, harmonic spectra, open or periodic molecular dynamics, Monte Carlo, and nudged elastic band calculations. We describe the robustness and speed of the package, demonstrating its millihartree accuracy and scalability to tens-of-thousands of atoms on ordinary laptops. We demonstrate the performance of the model by reproducing vibrational spectra, and simulating the molecular dynamics of a protein. Our comparisons with electronic structure theory and experimental data demonstrate that neural network molecular dynamics is poised to become an important tool for molecular simulation, lowering the resource barrier to simulating chemistry.

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

PubMed Central

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.

2015-01-01

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815

GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics.

PubMed

Blumers, Ansel L; Tang, Yu-Hang; Li, Zhen; Li, Xuejin; Karniadakis, George E

2017-08-01

Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

Extended asymmetric hot region formation due to shockwave interactions following void collapse in shocked high explosive

DOE PAGES

Shan, Tzu -Ray; Wixom, Ryan R.; Thompson, Aidan P.

2016-08-01

In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed bymore » coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. Furthermore, the formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.« less

Extended asymmetric hot region formation due to shockwave interactions following void collapse in shocked high explosive

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

Shan, Tzu -Ray; Wixom, Ryan R.; Thompson, Aidan P.

In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed bymore » coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. Furthermore, the formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.« less

Simulating the dynamics of complex plasmas.

PubMed

Schwabe, M; Graves, D B

2013-08-01

Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively coupled plasma with a fluid code written for the commercial package comsol. The output of this model is used to calculate forces on microparticles. The microparticles are modeled using the molecular dynamics package lammps, which we extended to include the forces from the plasma. Using this method, we are able to reproduce void formation, the separation of particles of different sizes into layers, lane formation, vortex formation, and other effects.

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

PubMed

Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A; Head-Gordon, Teresa

2017-06-05

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Cyber Physical System Modelling of Distribution Power Systems for Dynamic Demand Response

NASA Astrophysics Data System (ADS)

Chu, Xiaodong; Zhang, Rongxiang; Tang, Maosen; Huang, Haoyi; Zhang, Lei

2018-01-01

Dynamic demand response (DDR) is a package of control methods to enhance power system security. A CPS modelling and simulation platform for DDR in distribution power systems is presented in this paper. CPS modelling requirements of distribution power systems are analyzed. A coupled CPS modelling platform is built for assessing DDR in the distribution power system, which combines seamlessly modelling tools of physical power networks and cyber communication networks. Simulations results of IEEE 13-node test system demonstrate the effectiveness of the modelling and simulation platform.

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

USGS Publications Warehouse

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

2004-01-01

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

Packaging stiff polymers in small containers: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

2016-09-01

The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of the system—the DNA polymer and the spherical viral capsid—has been studied by molecular dynamics simulation. The results, involving longer polymers than in earlier work, show that as polymers become more rigid there is an increasing tendency to self-organize as spools that wrap from the inside out, rather than the inverse direction seen previously. In the final state, a substantial part of the polymer is packed into one or more coaxial spools, concentrically layered with different orientations, a form of packaging achievable without twisting the polymer.

ProtPOS: a python package for the prediction of protein preferred orientation on a surface.

PubMed

Ngai, Jimmy C F; Mak, Pui-In; Siu, Shirley W I

2016-08-15

Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein-surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined. Here, we present ProtPOS which is a lightweight and easy-to-use python package that can predict low-energy protein orientations on a surface of interest. It combines a fast conformational sampling algorithm with the energy calculation of GROMACS. The advantage of ProtPOS is it allows users to select any force fields suitable for the system at hand and provide structural output readily available for further simulation studies. ProtPOS is freely available for academic and non-profit uses at http://cbbio.cis.umac.mo/software/protpos Supplementary data are available at Bioinformatics online. shirleysiu@umac.mo. © The Author 2016. Published by Oxford University Press.

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

PubMed

Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

2011-07-30

MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

ProtPOS: a python package for the prediction of protein preferred orientation on a surface

PubMed Central

Ngai, Jimmy C. F.; Mak, Pui-In; Siu, Shirley W. I.

2016-01-01

Summary: Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein–surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined. Here, we present ProtPOS which is a lightweight and easy-to-use python package that can predict low-energy protein orientations on a surface of interest. It combines a fast conformational sampling algorithm with the energy calculation of GROMACS. The advantage of ProtPOS is it allows users to select any force fields suitable for the system at hand and provide structural output readily available for further simulation studies. Availability and Implementation: ProtPOS is freely available for academic and non-profit uses at http://cbbio.cis.umac.mo/software/protpos Supplementary information: Supplementary data are available at Bioinformatics online. Contact: shirleysiu@umac.mo PMID:27153619

The Amber Biomolecular Simulation Programs

PubMed Central

CASE, DAVID A.; CHEATHAM, THOMAS E.; DARDEN, TOM; GOHLKE, HOLGER; LUO, RAY; MERZ, KENNETH M.; ONUFRIEV, ALEXEY; SIMMERLING, CARLOS; WANG, BING; WOODS, ROBERT J.

2006-01-01

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. PMID:16200636

A generic multibody simulation

NASA Technical Reports Server (NTRS)

Hopping, K. A.; Kohn, W.

1986-01-01

Described is a dynamic simulation package which can be configured for orbital test scenarios involving multiple bodies. The rotational and translational state integration methods are selectable for each individual body and may be changed during a run if necessary. Characteristics of the bodies are determined by assigning components consisting of mass properties, forces, and moments, which are the outputs of user-defined environmental models. Generic model implementation is facilitated by a transformation processor which performs coordinate frame inversions. Transformations are defined in the initialization file as part of the simulation configuration. The simulation package includes an initialization processor, which consists of a command line preprocessor, a general purpose grammar, and a syntax scanner. These permit specifications of the bodies, their interrelationships, and their initial states in a format that is not dependent on a particular test scenario.

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.

PubMed

Brackley, C A; Morozov, A N; Marenduzzo, D

2014-04-07

An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Finally, two possible implementations of the discretised model in the multi-purpose molecular dynamics software package LAMMPS are described.

BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems.

PubMed

Mcclenny, Levi D; Imani, Mahdi; Braga-Neto, Ulisses M

2017-11-25

Gene regulatory networks govern the function of key cellular processes, such as control of the cell cycle, response to stress, DNA repair mechanisms, and more. Boolean networks have been used successfully in modeling gene regulatory networks. In the Boolean network model, the transcriptional state of each gene is represented by 0 (inactive) or 1 (active), and the relationship among genes is represented by logical gates updated at discrete time points. However, the Boolean gene states are never observed directly, but only indirectly and incompletely through noisy measurements based on expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays. The Partially-Observed Boolean Dynamical System (POBDS) signal model is distinct from other deterministic and stochastic Boolean network models in removing the requirement of a directly observable Boolean state vector and allowing uncertainty in the measurement process, addressing the scenario encountered in practice in transcriptomic analysis. BoolFilter is an R package that implements the POBDS model and associated algorithms for state and parameter estimation. It allows the user to estimate the Boolean states, network topology, and measurement parameters from time series of transcriptomic data using exact and approximated (particle) filters, as well as simulate the transcriptomic data for a given Boolean network model. Some of its infrastructure, such as the network interface, is the same as in the previously published R package for Boolean Networks BoolNet, which enhances compatibility and user accessibility to the new package. We introduce the R package BoolFilter for Partially-Observed Boolean Dynamical Systems (POBDS). The BoolFilter package provides a useful toolbox for the bioinformatics community, with state-of-the-art algorithms for simulation of time series transcriptomic data as well as the inverse process of system identification from data obtained with various expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays.

Experiments in cooperative-arm object manipulation with a two-armed free-flying robot. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Koningstein, Ross

1990-01-01

Developing computed-torque controllers for complex manipulator systems using current techniques and tools is difficult because they address the issues pertinent to simulation, as opposed to control. A new formulation of computed-torque (CT) control that leads to an automated computer-torque robot controller program is presented. This automated tool is used for simulations and experimental demonstrations of endpoint and object control from a free-flying robot. A new computed-torque formulation states the multibody control problem in an elegant, homogeneous, and practical form. A recursive dynamics algorithm is presented that numerically evaluates kinematics and dynamics terms for multibody systems given a topological description. Manipulators may be free-flying, and may have closed-chain constraints. With the exception of object squeeze-force control, the algorithm does not deal with actuator redundancy. The algorithm is used to implement an automated 2D computed-torque dynamics and control package that allows joint, endpoint, orientation, momentum, and object squeeze-force control. This package obviates the need for hand-derivation of kinematics and dynamics, and is used for both simulation and experimental control. Endpoint control experiments are performed on a laboratory robot that has two arms to manipulate payloads, and uses an air bearing to achieve very-low drag characteristics. Simulations and experimental data for endpoint and object controllers are presented for the experimental robot - a complex dynamic system. There is a certain rather wide set of conditions under which CT endpoint controllers can neglect robot base accelerations (but not motions) and achieve comparable performance including base accelerations in the model. The regime over which this simplification holds is explored by simulation and experiment.

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

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

Felberg, Lisa E.; Brookes, David H.; Yap, Eng-Hui

2016-11-02

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmannmore » Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

A moist aquaplanet variant of the Held–Suarez test for atmospheric model dynamical cores

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

Thatcher, Diana R.; Jablonowski, Christiane

A moist idealized test case (MITC) for atmospheric model dynamical cores is presented. The MITC is based on the Held–Suarez (HS) test that was developed for dry simulations on “a flat Earth” and replaces the full physical parameterization package with a Newtonian temperature relaxation and Rayleigh damping of the low-level winds. This new variant of the HS test includes moisture and thereby sheds light on the nonlinear dynamics–physics moisture feedbacks without the complexity of full-physics parameterization packages. In particular, it adds simplified moist processes to the HS forcing to model large-scale condensation, boundary-layer mixing, and the exchange of latent and sensible heat betweenmore » the atmospheric surface and an ocean-covered planet. Using a variety of dynamical cores of the National Center for Atmospheric Research (NCAR)'s Community Atmosphere Model (CAM), this paper demonstrates that the inclusion of the moist idealized physics package leads to climatic states that closely resemble aquaplanet simulations with complex physical parameterizations. This establishes that the MITC approach generates reasonable atmospheric circulations and can be used for a broad range of scientific investigations. This paper provides examples of two application areas. First, the test case reveals the characteristics of the physics–dynamics coupling technique and reproduces coupling issues seen in full-physics simulations. In particular, it is shown that sudden adjustments of the prognostic fields due to moist physics tendencies can trigger undesirable large-scale gravity waves, which can be remedied by a more gradual application of the physical forcing. Second, the moist idealized test case can be used to intercompare dynamical cores. These examples demonstrate the versatility of the MITC approach and suggestions are made for further application areas. Furthermore, the new moist variant of the HS test can be considered a test case of intermediate complexity.« less

A moist aquaplanet variant of the Held–Suarez test for atmospheric model dynamical cores

DOE PAGES

Thatcher, Diana R.; Jablonowski, Christiane

2016-04-04

A moist idealized test case (MITC) for atmospheric model dynamical cores is presented. The MITC is based on the Held–Suarez (HS) test that was developed for dry simulations on “a flat Earth” and replaces the full physical parameterization package with a Newtonian temperature relaxation and Rayleigh damping of the low-level winds. This new variant of the HS test includes moisture and thereby sheds light on the nonlinear dynamics–physics moisture feedbacks without the complexity of full-physics parameterization packages. In particular, it adds simplified moist processes to the HS forcing to model large-scale condensation, boundary-layer mixing, and the exchange of latent and sensible heat betweenmore » the atmospheric surface and an ocean-covered planet. Using a variety of dynamical cores of the National Center for Atmospheric Research (NCAR)'s Community Atmosphere Model (CAM), this paper demonstrates that the inclusion of the moist idealized physics package leads to climatic states that closely resemble aquaplanet simulations with complex physical parameterizations. This establishes that the MITC approach generates reasonable atmospheric circulations and can be used for a broad range of scientific investigations. This paper provides examples of two application areas. First, the test case reveals the characteristics of the physics–dynamics coupling technique and reproduces coupling issues seen in full-physics simulations. In particular, it is shown that sudden adjustments of the prognostic fields due to moist physics tendencies can trigger undesirable large-scale gravity waves, which can be remedied by a more gradual application of the physical forcing. Second, the moist idealized test case can be used to intercompare dynamical cores. These examples demonstrate the versatility of the MITC approach and suggestions are made for further application areas. Furthermore, the new moist variant of the HS test can be considered a test case of intermediate complexity.« less

Langevin Dynamics Simulations of Genome Packing in Bacteriophage

PubMed Central

Forrey, Christopher; Muthukumar, M.

2006-01-01

We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general. PMID:16617089

Langevin dynamics simulations of genome packing in bacteriophage.

PubMed

Forrey, Christopher; Muthukumar, M

2006-07-01

We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general.

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

WavePacket: A Matlab package for numerical quantum dynamics. I: Closed quantum systems and discrete variable representations

NASA Astrophysics Data System (ADS)

Schmidt, Burkhard; Lorenz, Ulf

2017-04-01

WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. The graphical capabilities allow visualization of quantum dynamics 'on the fly', including Wigner phase space representations. Being easy to use and highly versatile, WavePacket is well suited for the teaching of quantum mechanics as well as for research projects in atomic, molecular and optical physics or in physical or theoretical chemistry. The present Part I deals with the description of closed quantum systems in terms of Schrödinger equations. The emphasis is on discrete variable representations for spatial discretization as well as various techniques for temporal discretization. The upcoming Part II will focus on open quantum systems and dimension reduction; it also describes the codes for optimal control of quantum dynamics. The present work introduces the MATLAB version of WavePacket 5.2.1 which is hosted at the Sourceforge platform, where extensive Wiki-documentation as well as worked-out demonstration examples can be found.

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package.

PubMed

Kaus, Joseph W; Pierce, Levi T; Walker, Ross C; McCammont, J Andrew

2013-09-10

Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license.

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

PubMed Central

Pierce, Levi T.; Walker, Ross C.; McCammont, J. Andrew

2013-01-01

Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license. PMID:24185531

Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

PubMed

Sieradzan, Adam K; Jakubowski, Rafał

2017-03-30

In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

MOlecular MAterials Property Prediction Package (MOMAP) 1.0: a software package for predicting the luminescent properties and mobility of organic functional materials

NASA Astrophysics Data System (ADS)

Niu, Yingli; Li, Wenqiang; Peng, Qian; Geng, Hua; Yi, Yuanping; Wang, Linjun; Nan, Guangjun; Wang, Dong; Shuai, Zhigang

2018-04-01

MOlecular MAterials Property Prediction Package (MOMAP) is a software toolkit for molecular materials property prediction. It focuses on luminescent properties and charge mobility properties. This article contains a brief descriptive introduction of key features, theoretical models and algorithms of the software, together with examples that illustrate the performance. First, we present the theoretical models and algorithms for molecular luminescent properties calculation, which includes the excited-state radiative/non-radiative decay rate constant and the optical spectra. Then, a multi-scale simulation approach and its algorithm for the molecular charge mobility are described. This approach is based on hopping model and combines with Kinetic Monte Carlo and molecular dynamics simulations, and it is especially applicable for describing a large category of organic semiconductors, whose inter-molecular electronic coupling is much smaller than intra-molecular charge reorganisation energy.

Active cooling of microvascular composites for battery packaging

NASA Astrophysics Data System (ADS)

Pety, Stephen J.; Chia, Patrick X. L.; Carrington, Stephen M.; White, Scott R.

2017-10-01

Batteries in electric vehicles (EVs) require a packaging system that provides both thermal regulation and crash protection. A novel packaging scheme is presented that uses active cooling of microvascular carbon fiber reinforced composites to accomplish this multifunctional objective. Microvascular carbon fiber/epoxy composite panels were fabricated and their cooling performance assessed over a range of thermal loads and experimental conditions. Tests were performed for different values of coolant flow rate, channel spacing, panel thermal conductivity, and applied heat flux. More efficient cooling occurs when the coolant flow rate is increased, channel spacing is reduced, and thermal conductivity of the host composite is increased. Computational fluid dynamics (CFD) simulations were also performed and correlate well with the experimental data. CFD simulations of a typical EV battery pack confirm that microvascular composite panels can adequately cool battery cells generating 500 W m-2 heat flux below 40 °C.

Modeling Impact-induced Failure of Polysilicon MEMS: A Multi-scale Approach.

PubMed

Mariani, Stefano; Ghisi, Aldo; Corigliano, Alberto; Zerbini, Sarah

2009-01-01

Failure of packaged polysilicon micro-electro-mechanical systems (MEMS) subjected to impacts involves phenomena occurring at several length-scales. In this paper we present a multi-scale finite element approach to properly allow for: (i) the propagation of stress waves inside the package; (ii) the dynamics of the whole MEMS; (iii) the spreading of micro-cracking in the failing part(s) of the sensor. Through Monte Carlo simulations, some effects of polysilicon micro-structure on the failure mode are elucidated.

Gromita: a fully integrated graphical user interface to gromacs 4.

PubMed

Sellis, Diamantis; Vlachakis, Dimitrios; Vlassi, Metaxia

2009-09-07

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Dakota Uncertainty Quantification Methods Applied to the CFD code Nek5000

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

Delchini, Marc-Olivier; Popov, Emilian L.; Pointer, William David

This report presents the state of advancement of a Nuclear Energy Advanced Modeling and Simulation (NEAMS) project to characterize the uncertainty of the computational fluid dynamics (CFD) code Nek5000 using the Dakota package for flows encountered in the nuclear engineering industry. Nek5000 is a high-order spectral element CFD code developed at Argonne National Laboratory for high-resolution spectral-filtered large eddy simulations (LESs) and unsteady Reynolds-averaged Navier-Stokes (URANS) simulations.

LAMMPS integrated materials engine (LIME) for efficient automation of particle-based simulations: application to equation of state generation

NASA Astrophysics Data System (ADS)

Barnes, Brian C.; Leiter, Kenneth W.; Becker, Richard; Knap, Jaroslaw; Brennan, John K.

2017-07-01

We describe the development, accuracy, and efficiency of an automation package for molecular simulation, the large-scale atomic/molecular massively parallel simulator (LAMMPS) integrated materials engine (LIME). Heuristics and algorithms employed for equation of state (EOS) calculation using a particle-based model of a molecular crystal, hexahydro-1,3,5-trinitro-s-triazine (RDX), are described in detail. The simulation method for the particle-based model is energy-conserving dissipative particle dynamics, but the techniques used in LIME are generally applicable to molecular dynamics simulations with a variety of particle-based models. The newly created tool set is tested through use of its EOS data in plate impact and Taylor anvil impact continuum simulations of solid RDX. The coarse-grain model results from LIME provide an approach to bridge the scales from atomistic simulations to continuum simulations.

A Process for the Creation of T-MATS Propulsion System Models from NPSS data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink (Math Works, Inc.) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

A Process for the Creation of T-MATS Propulsion System Models from NPSS Data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink(Trademark) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

A Process for the Creation of T-MATS Propulsion System Models from NPSS Data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink(Registered TradeMark) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

Analysis of helicopter flight dynamics through modeling and simulation of primary flight control actuation system

NASA Astrophysics Data System (ADS)

Nelson, Hunter Barton

A simplified second-order transfer function actuator model used in most flight dynamics applications cannot easily capture the effects of different actuator parameters. The present work integrates a nonlinear actuator model into a nonlinear state space rotorcraft model to determine the effect of actuator parameters on key flight dynamics. The completed actuator model was integrated with a swashplate kinematics where step responses were generated over a range of key hydraulic parameters. The actuator-swashplate system was then introduced into a nonlinear state space rotorcraft simulation where flight dynamics quantities such as bandwidth and phase delay analyzed. Frequency sweeps were simulated for unique actuator configurations using the coupled nonlinear actuator-rotorcraft system. The software package CIFER was used for system identification and compared directly to the linearized models. As the actuator became rate saturated, the effects on bandwidth and phase delay were apparent on the predicted handling qualities specifications.

Lightweight Object Oriented Structure analysis: Tools for building Tools to Analyze Molecular Dynamics Simulations

PubMed Central

Romo, Tod D.; Leioatts, Nicholas; Grossfield, Alan

2014-01-01

LOOS (Lightweight Object-Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 120 pre-built tools, including suites of tools for analyzing simulation convergence, 3D histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only 4 core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development. PMID:25327784

Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

PubMed

Romo, Tod D; Leioatts, Nicholas; Grossfield, Alan

2014-12-15

LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development. © 2014 Wiley Periodicals, Inc.

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

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

Grama, Ananth

2013-12-18

A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability.more » • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.« less

Sensitivity of a cloud parameterization package in the National Center for Atmospheric Research Community Climate Model

NASA Astrophysics Data System (ADS)

Kao, C.-Y. J.; Smith, W. S.

1999-05-01

A physically based cloud parameterization package, which includes the Arakawa-Schubert (AS) scheme for subgrid-scale convective clouds and the Sundqvist (SUN) scheme for nonconvective grid-scale layered clouds (hereafter referred to as the SUNAS cloud package), is incorporated into the National Center for Atmospheric Research (NCAR) Community Climate Model, Version 2 (CCM2). The AS scheme is used for a more reasonable heating distribution due to convective clouds and their associated precipitation. The SUN scheme allows for the prognostic computation of cloud water so that the cloud optical properties are more physically determined for shortwave and longwave radiation calculations. In addition, the formation of anvil-like clouds from deep convective systems is able to be simulated with the SUNAS package. A 10-year simulation spanning the period from 1980 to 1989 is conducted, and the effect of the cloud package on the January climate is assessed by comparing it with various available data sets and the National Center for Environmental Protection/NCAR reanalysis. Strengths and deficiencies of both the SUN and AS methods are identified and discussed. The AS scheme improves some aspects of the model dynamics and precipitation, especially with respect to the Pacific North America (PNA) pattern. CCM2's tendency to produce a westward bias of the 500 mbar stationary wave (time-averaged zonal anomalies) in the PNA sector is remedied apparently because of a less "locked-in" heating pattern in the tropics. The additional degree of freedom added by the prognostic calculation of cloud water in the SUN scheme produces interesting results in the modeled cloud and radiation fields compared with data. In general, too little cloud water forms in the tropics, while excessive cloud cover and cloud liquid water are simulated in midlatitudes. This results in a somewhat degraded simulation of the radiation budget. The overall simulated precipitation by the SUNAS package is, however, substantially improved over the original CCM2.

Benchmark tests for a Formula SAE Student car prototyping

NASA Astrophysics Data System (ADS)

Mariasiu, Florin

2011-12-01

Aerodynamic characteristics of a vehicle are important elements in its design and construction. A low drag coefficient brings significant fuel savings and increased engine power efficiency. In designing and developing vehicles trough computer simulation process to determine the vehicles aerodynamic characteristics are using dedicated CFD (Computer Fluid Dynamics) software packages. However, the results obtained by this faster and cheaper method, are validated by experiments in wind tunnels tests, which are expensive and were complex testing equipment are used in relatively high costs. Therefore, the emergence and development of new low-cost testing methods to validate CFD simulation results would bring great economic benefits for auto vehicles prototyping process. This paper presents the initial development process of a Formula SAE Student race-car prototype using CFD simulation and also present a measurement system based on low-cost sensors through which CFD simulation results were experimentally validated. CFD software package used for simulation was Solid Works with the FloXpress add-on and experimental measurement system was built using four piezoresistive force sensors FlexiForce type.

mizer: an R package for multispecies, trait-based and community size spectrum ecological modelling.

PubMed

Scott, Finlay; Blanchard, Julia L; Andersen, Ken H

2014-10-01

Size spectrum ecological models are representations of a community of individuals which grow and change trophic level. A key emergent feature of these models is the size spectrum; the total abundance of all individuals that scales negatively with size. The models we focus on are designed to capture fish community dynamics useful for assessing the community impacts of fishing.We present mizer , an R package for implementing dynamic size spectrum ecological models of an entire aquatic community subject to fishing. Multiple fishing gears can be defined and fishing mortality can change through time making it possible to simulate a range of exploitation strategies and management options. mizer implements three versions of the size spectrum modelling framework: the community model, where individuals are only characterized by their size; the trait-based model, where individuals are further characterized by their asymptotic size; and the multispecies model where additional trait differences are resolved.A range of plot, community indicator and summary methods are available to inspect the results of the simulations.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks.

PubMed

Jenness, Samuel M; Goodreau, Steven M; Morris, Martina

2018-04-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel , designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel , designed to facilitate the exploration of novel research questions for advanced modelers.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks

PubMed Central

Jenness, Samuel M.; Goodreau, Steven M.; Morris, Martina

2018-01-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel, designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel, designed to facilitate the exploration of novel research questions for advanced modelers. PMID:29731699

Simulation of Escherichia coli O157:H7 behavior in fresh-cut lettuce under dynamic temperature conditions during distribution from processing to retail.

PubMed

McKellar, Robin C; LeBlanc, Denyse I; Lu, Jianbo; Delaquis, Pascal

2012-03-01

The temperature of packaged lettuce was recorded throughout a retail supply chain in Canada during the various stages of storage and shipping from the processor to retail. Temperatures were monitored in 27 cases of lettuce destined for three stores in three replicate trials conducted during the winter. A dynamic model that predicts the effect of temperature on the growth or die-off of Escherichia coli O157:H7 in packaged fresh-cut lettuce was applied to simulate the behavior of E. coli O157:H7 in the system. Simulations were carried out using distributions to account for variation in the temperature parameter and the die-off coefficient of the dynamic growth/death model. The results indicate that there was a predicted overall mean decline in cell numbers of 0.983 log cfu g⁻¹ and that the extent of cell death was proportional to the total time spent in the cold chain. Slight growth was predicted in a few instances when the dynamic temperature was above the permissive temperature of 5°C. These results suggest that generally there would be little or no growth of E. coli O157:H7 in product maintained at the proper temperature in the chain. Moreover, the predicted decline in cell numbers at refrigeration temperatures suggests that storage at 5°C or below prior to consumption would reduce populations of the pathogen in fresh-cut lettuce.

Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

PubMed

Richings, Gareth W; Habershon, Scott

2017-09-12

We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

NASA Astrophysics Data System (ADS)

Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

2017-01-01

The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

Multi-Purpose Crew Vehicle Camera Asset Planning: Imagery Previsualization

NASA Technical Reports Server (NTRS)

Beaulieu, K.

2014-01-01

Using JSC-developed and other industry-standard off-the-shelf 3D modeling, animation, and rendering software packages, the Image Science Analysis Group (ISAG) supports Orion Project imagery planning efforts through dynamic 3D simulation and realistic previsualization of ground-, vehicle-, and air-based camera output.

PyRETIS: A well-done, medium-sized python library for rare events.

PubMed

Lervik, Anders; Riccardi, Enrico; van Erp, Titus S

2017-10-30

Transition path sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, for example, chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. PyRETIS is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

PubMed

Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F; Harger, Matthew; Torabifard, Hedieh; Cisneros, G Andrés; Schnieders, Michael J; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y; Ponder, Jay W; Piquemal, Jean-Philip

2018-01-28

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.

Clustangles: An Open Library for Clustering Angular Data.

PubMed

Sargsyan, Karen; Hua, Yun Hao; Lim, Carmay

2015-08-24

Dihedral angles are good descriptors of the numerous conformations visited by large, flexible systems, but their analysis requires directional statistics. A single package including the various multivariate statistical methods for angular data that accounts for the distinct topology of such data does not exist. Here, we present a lightweight standalone, operating-system independent package called Clustangles to fill this gap. Clustangles will be useful in analyzing the ever-increasing number of structures in the Protein Data Bank and clustering the copious conformations from increasingly long molecular dynamics simulations.

Deployment Simulation of Ultra-Lightweight Inflatable Structures

NASA Technical Reports Server (NTRS)

Wang, John T.; Johnson, Arthur R.

2002-01-01

Dynamic deployment analyses of folded inflatable tubes are conducted to investigate modeling issues related to the deployment of solar sail booms. The analyses are necessary because ground tests include gravity effects and may poorly represent deployment in space. A control volume approach, available in the LS-DYNA nonlinear dynamic finite element code, and the ideal gas law are used to simulate the dynamic inflation deployment process. Three deployment issues are investigated for a tube packaged in a Z-fold configuration. The issues are the effect of the rate of inflation, the effect of residual air, and the effect of gravity. The results of the deployment analyses reveal that the time and amount of inflation gas required to achieve a full deployment are related to these issues.

QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS

NASA Astrophysics Data System (ADS)

Ma, Changru; Martin-Samos, Layla; Fabris, Stefano; Laio, Alessandro; Piccinin, Simone

2015-10-01

We present QMMMW, a new program aimed at performing Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics. The package operates as a wrapper that patches PWscf code included in the QUANTUM ESPRESSO distribution and LAMMPS Molecular Dynamics Simulator. It is designed with a paradigm based on three guidelines: (i) minimal amount of modifications on the parent codes, (ii) flexibility and computational efficiency of the communication layer and (iii) accuracy of the Hamiltonian describing the interaction between the QM and MM subsystems. These three features are seldom present simultaneously in other implementations of QMMM. The QMMMW project is hosted by qe-forge at

Numerical simulation of vessel dynamics in manoeuvrability and seakeeping problems

NASA Astrophysics Data System (ADS)

Blishchik, A. E.; Taranov, A. E.

2018-05-01

This paper deals with some examples of numerical modelling for ship's dynamics problems and data comparison with corresponding experimental results. It was considered two kinds of simulation: self-propelled turning motion of crude carrier KVLCC2 and changing position of container carrier S 175 due to wave loadings. Mesh generation and calculation were made in STAR-CCM+ package. URANS equations were used as system of equations closed by k-w SST turbulence model. The vessel had several degrees of freedom, which depend on task. Based on the results of this research, the conclusion was made concerning the applicability of used numerical methods.

LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

NASA Astrophysics Data System (ADS)

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

2018-07-01

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

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

Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications

PubMed Central

Miao, Yinglong; McCammon, J. Andrew

2018-01-01

A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of biomolecules. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of the biomolecules. Furthermore, by constructing a boost potential that follows a Gaussian distribution, accurate reweighting of GaMD simulations is achieved via cumulant expansion to the second order. The free energy profiles obtained from GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize biomolecular structural dynamics quantitatively. In this chapter, we present the theory of GaMD, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model system, protein folding, biomolecular large-scale conformational transitions and biomolecular recognition. PMID:29720925

A domain specific language for performance portable molecular dynamics algorithms

NASA Astrophysics Data System (ADS)

Saunders, William Robert; Grant, James; Müller, Eike Hermann

2018-03-01

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

All-atom molecular dynamics of virus capsids as drug targets

DOE PAGES

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...

2016-04-29

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

Molecular dynamics simulation on HP1 protein binding by histone H3 tail methylation and phosphorylation

NASA Astrophysics Data System (ADS)

Jiang, Yan-Ke; Zou, Jian-Wei; Wu, Yu-Qian; Zhang, Na; Yu, Qing-Sen; Jiang, Yong-Jun

Trimethylation of histone H3 lysine 9 is important for recruiting heterochromatin protein 1 (HP1) to discrete regions of the genome, thereby regulating gene expression, chromatin packaging, and heterochromatin formation. Phosphorylation of histone H3 has been linked with mitotic chromatin condensation. During mitosis in vivo, H3 lysine 9 methylation and serine 10 phosphorylation can occur concomitantly on the same histone tail, whereas the influence of phosphorylation to trimethylation H3 tail recruiting HP1 remains controversial. In this work, molecular dynamics simulation of HP1 complexed with both trimethylated and phosphorylated H3 tail were performed and compared with the results from the previous methylated H3-HP1 trajectory. It is clear from the 10-ns dynamics simulation that two adjacent posttranslational modifications directly increase the flexibility of the H3 tail and weaken HP1 binding to chromatin. A combinatorial readout of two adjacent posttranslational modifications-a stable methylation and a dynamic phosphorylation mark-establish a regulatory mechanism of protein-protein interactions.

All-atom molecular dynamics of virus capsids as drug targets

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

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

A time domain simulation of a beam control system

NASA Astrophysics Data System (ADS)

Mitchell, J. R.

1981-02-01

The Airborne Laser Laboratory (ALL) is being developed by the Air Force to investigate the integration and operation of high energy laser components in a dynamic airborne environment and to study the propagation of laser light from an airborne vehicle to an airborne target. The ALL is composed of several systems; among these are the Airborne Pointing and Tracking System (APT) and the Automatic Alignment System (AAS). This report presents the results of performing a time domain dynamic simulation for an integrated beam control system composed of the APT and AAS. The simulation is performed on a digital computer using the MIMIC language. It includes models of the dynamics of the system and of disturbances. Also presented in the report are the rationales and developments of these models. The data from the simulation code is summarized by several plots. In addition results from massaging the data with waveform analysis packages are presented. The results are discussed and conclusions are drawn.

Lightweight computational steering of very large scale molecular dynamics simulations

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

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less

Development and testing of a numerical simulation method for thermally nonequilibrium dissociating flows in ANSYS Fluent

NASA Astrophysics Data System (ADS)

Shoev, G. V.; Bondar, Ye. A.; Oblapenko, G. P.; Kustova, E. V.

2016-03-01

Various issues of numerical simulation of supersonic gas flows with allowance for thermochemical nonequilibrium on the basis of fluid dynamic equations in the two-temperature approximation are discussed. The computational tool for modeling flows with thermochemical nonequilibrium is the commercial software package ANSYS Fluent with an additional userdefined open-code module. A comparative analysis of results obtained by various models of vibration-dissociation coupling in binary gas mixtures of nitrogen and oxygen is performed. Results of numerical simulations are compared with available experimental data.

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

Stefek, T.; Daugherty, W.; Estochen, E.

Compaction of lower layers in the fiberboard assembly has been observed in 9975 packages that contain elevated moisture. Lab testing has resulted in a better understanding of the relationship between the fiberboard moisture level and compaction of the lower fiberboard assembly, and the behavior of the fiberboard during transport. In laboratory tests of cane fiberboard, higher moisture content has been shown to correspond to higher total compaction, greater rate of compaction, and continued compaction over a longer period of time. In addition, laboratory tests have shown that the application of a dynamic load results in higher fiberboard compaction compared tomore » a static load. The test conditions and sample geometric/loading configurations were chosen to simulate the regulatory requirements for 9975 package input dynamic loading. Dynamic testing was conducted to acquire immediate and cumulative changes in geometric data for various moisture levels. Two sample sets have undergone a complete dynamic test regimen, one set for 27 weeks, and the second set for 47 weeks. The dynamic input, data acquisition, test effects on sample dynamic parameters, and results from this test program are summarized and compared to regulatory specifications for dynamic loading. Compaction of the bottom fiberboard layers due to the accumulation of moisture is one possible cause of an increase in the axial gap at the top of the package. The net compaction of the bottom layers will directly add to the axial gap. The moisture which caused this compaction migrated from the middle region of the fiberboard assembly (which is typically the hottest). This will cause the middle region to shrink axially, which will also contribute directly to the axial gap. Measurement of the axial gap provides a screening tool for identifying significant change in the fiberboard condition. The data in this report provide a basis to evaluate the impact of moisture and fiberboard compaction on 9975 package performance during storage at the Savannah River Site (SRS).« less

Climate Simulations with an Isentropic Finite Volume Dynamical Core

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

Chen, Chih-Chieh; Rasch, Philip J.

2012-04-15

This paper discusses the impact of changing the vertical coordinate from a hybrid pressure to a hybrid-isentropic coordinate within the finite volume dynamical core of the Community Atmosphere Model (CAM). Results from a 20-year climate simulation using the new model coordinate configuration are compared to control simulations produced by the Eulerian spectral and FV dynamical cores of CAM which both use a pressure-based ({sigma}-p) coordinate. The same physical parameterization package is employed in all three dynamical cores. The isentropic modeling framework significantly alters the simulated climatology and has several desirable features. The revised model produces a better representation of heatmore » transport processes in the atmosphere leading to much improved atmospheric temperatures. We show that the isentropic model is very effective in reducing the long standing cold temperature bias in the upper troposphere and lower stratosphere, a deficiency shared among most climate models. The warmer upper troposphere and stratosphere seen in the isentropic model reduces the global coverage of high clouds which is in better agreement with observations. The isentropic model also shows improvements in the simulated wintertime mean sea-level pressure field in the northern hemisphere.« less

A Comparison of Three Approaches to Model Human Behavior

NASA Astrophysics Data System (ADS)

Palmius, Joel; Persson-Slumpi, Thomas

2010-11-01

One way of studying social processes is through the use of simulations. The use of simulations for this purpose has been established as its own field, social simulations, and has been used for studying a variety of phenomena. A simulation of a social setting can serve as an aid for thinking about that social setting, and for experimenting with different parameters and studying the outcomes caused by them. When using the simulation as an aid for thinking and experimenting, the chosen simulation approach will implicitly steer the simulationist towards thinking in a certain fashion in order to fit the model. To study the implications of model choice on the understanding of a setting where human anticipation comes into play, a simulation scenario of a coffee room was constructed using three different simulation approaches: Cellular Automata, Systems Dynamics and Agent-based modeling. The practical implementations of the models were done in three different simulation packages: Stella for Systems Dynamic, CaFun for Cellular automata and SesAM for Agent-based modeling. The models were evaluated both using Randers' criteria for model evaluation, and through introspection where the authors reflected upon how their understanding of the scenario was steered through the model choice. Further the software used for implementing the simulation models was evaluated, and practical considerations for the choice of software package are listed. It is concluded that the models have very different strengths. The Agent-based modeling approach offers the most intuitive support for thinking about and modeling a social setting where the behavior of the individual is in focus. The Systems Dynamics model would be preferable in situations where populations and large groups would be studied as wholes, but where individual behavior is of less concern. The Cellular Automata models would be preferable where processes need to be studied from the basis of a small set of very simple rules. It is further concluded that in most social simulation settings the Agent-based modeling approach would be the probable choice. This since the other models does not offer much in the way of supporting the modeling of the anticipatory behavior of humans acting in an organization.

Motion Law Analysis and Structural Optimization of the Ejection Device of Tray Seeder

NASA Astrophysics Data System (ADS)

Luo, Xin; Hu, Bin; Dong, Chunwang; Huang, Lili

An ejection mechanism consisting four reset springs, an electromagnet and a seed disk was designed for tray seeder. The motion conditions of seeds in the seed disk were theoretical analyzed and intensity and height of seed ejection were calculated. The motions of the seeds and seed disk were multi-body dynamic simulated using Cosmos modules plug-in SolidWorks software package. The simulation results showed the consistence with the theoretical analysis.

Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics

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

Kee, R.J.; Rupley, F.M.; Miller, J.A.

1989-09-01

This document is the user's manual for the second-generation Chemkin package. Chemkin is a software package for whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides an especially flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutinemore » Library. This library is a collection of about 100 highly modular Fortran subroutines that may be called to return information on equation of state, thermodynamic properties, and chemical production rates.« less

Optimizing legacy molecular dynamics software with directive-based offload

NASA Astrophysics Data System (ADS)

Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

2015-10-01

Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.

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

de Hatten, Xavier; Cournia, Zoe; Huc, Ivan

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostaticmore » potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C{sub 2}-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 {micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 {micro}s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.« less

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

De Hatten, Xavier; Cournia, Zoe; Smith, Jeremy C

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostaticmore » potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1{prime}-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1{micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline{prime}-1-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.« less

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

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

Walker, La Tonya Nicole; Malczynski, Leonard A.

DYNAMO is a computer program for building and running 'continuous' simulation models. It was developed by the Industrial Dynamics Group at the Massachusetts Institute of Technology for simulating dynamic feedback models of business, economic, and social systems. The history of the system dynamics method since 1957 includes many classic models built in DYANMO. It was not until the late 1980s that software was built to take advantage of the rise of personal computers and graphical user interfaces that DYNAMO was supplanted. There is much learning and insight to be gained from examining the DYANMO models and their accompanying research papers.more » We believe that it is a worthwhile exercise to convert DYNAMO models to more recent software packages. We have made an attempt to make it easier to turn these models into a more current system dynamics software language, Powersim © Studio produced by Powersim AS 2 of Bergen, Norway. This guide shows how to convert DYNAMO syntax into Studio syntax.« less

Deployment Simulation Methods for Ultra-Lightweight Inflatable Structures

NASA Technical Reports Server (NTRS)

Wang, John T.; Johnson, Arthur R.

2003-01-01

Two dynamic inflation simulation methods are employed for modeling the deployment of folded thin-membrane tubes. The simulations are necessary because ground tests include gravity effects and may poorly represent deployment in space. The two simulation methods are referred to as the Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method. They are available in the LS-DYNA nonlinear dynamic finite element code. Both methods are suitable for modeling the interactions between the inflation gas and the thin-membrane tube structures. The CV method only considers the pressure induced by the inflation gas in the simulation, while the ALE method models the actual flow of the inflation gas. Thus, the transient fluid properties at any location within the tube can be predicted by the ALE method. Deployment simulations of three packaged tube models; namely coiled, Z-folded, and telescopically-folded configurations, are performed. Results predicted by both methods for the telescopically-folded configuration are correlated and computational efficiency issues are discussed.

WavePacket: A Matlab package for numerical quantum dynamics.II: Open quantum systems, optimal control, and model reduction

NASA Astrophysics Data System (ADS)

Schmidt, Burkhard; Hartmann, Carsten

2018-07-01

WavePacket is an open-source program package for numeric simulations in quantum dynamics. It can solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows, e.g., to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semi-classical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. Being highly versatile and offering visualization of quantum dynamics 'on the fly', WavePacket is well suited for teaching or research projects in atomic, molecular and optical physics as well as in physical or theoretical chemistry. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] which dealt with closed quantum systems and discrete variable representations, the present Part II focuses on the dynamics of open quantum systems, with Lindblad operators modeling dissipation and dephasing. This part also describes the WavePacket function for optimal control of quantum dynamics, building on rapid monotonically convergent iteration methods. Furthermore, two different approaches to dimension reduction implemented in WavePacket are documented here. In the first one, a balancing transformation based on the concepts of controllability and observability Gramians is used to identify states that are neither well controllable nor well observable. Those states are either truncated or averaged out. In the other approach, the H2-error for a given reduced dimensionality is minimized by H2 optimal model reduction techniques, utilizing a bilinear iterative rational Krylov algorithm. The present work describes the MATLAB version of WavePacket 5.3.0 which is hosted and further developed at the Sourceforge platform, where also extensive Wiki-documentation as well as numerous worked-out demonstration examples with animated graphics can be found.

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.

Plane-Wave DFT Methods for Chemistry

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

Bylaska, Eric J.

A detailed description of modern plane-wave DFT methods and software (contained in the NWChem package) are described that allow for both geometry optimization and ab initio molecular dynamics simulations. Significant emphasis is placed on aspects of these methods that are of interest to computational chemists and useful for simulating chemistry, including techniques for calculating charged systems, exact exchange (i.e. hybrid DFT methods), and highly efficient AIMD/MM methods. Sample applications on the structure of the goethite+water interface and the hydrolysis of nitroaromatic molecules are described.

CCC7-119 Reactive Molecular Dynamics Simulations of Hot Spot Growth in Shocked Energetic Materials

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

Thompson, Aidan P.

2015-03-01

The purpose of this work is to understand how defects control initiation in energetic materials used in stockpile components; Sequoia gives us the core-count to run very large-scale simulations of up to 10 million atoms and; Using an OpenMP threaded implementation of the ReaxFF package in LAMMPS, we have been able to get good parallel efficiency running on 16k nodes of Sequoia, with 1 hardware thread per core.

Numerical simulation of deformation and failure processes of a complex technical object under impact loading

NASA Astrophysics Data System (ADS)

Kraus, E. I.; Shabalin, I. I.; Shabalin, T. I.

2018-04-01

The main points of development of numerical tools for simulation of deformation and failure of complex technical objects under nonstationary conditions of extreme loading are presented. The possibility of extending the dynamic method for construction of difference grids to the 3D case is shown. A 3D realization of discrete-continuum approach to the deformation and failure of complex technical objects is carried out. The efficiency of the existing software package for 3D modelling is shown.

Simulation Packages Expand Aircraft Design Options

NASA Technical Reports Server (NTRS)

2013-01-01

In 2001, NASA released a new approach to computational fluid dynamics that allows users to perform automated analysis on complex vehicle designs. In 2010, Palo Alto, California-based Desktop Aeronautics acquired a license from Ames Research Center to sell the technology. Today, the product assists organizations in the design of subsonic aircraft, space planes, spacecraft, and high speed commercial jets.

Virtual Reality Simulations and Animations in a Web-Based Interactive Manufacturing Engineering Module

ERIC Educational Resources Information Center

Ong, S. K.; Mannan, M. A.

2004-01-01

This paper presents a web-based interactive teaching package that provides a comprehensive and conducive yet dynamic and interactive environment for a module on automated machine tools in the Manufacturing Division at the National University of Singapore. The use of Internet technologies in this teaching tool makes it possible to conjure…

An Object-Oriented Serial DSMC Simulation Package

NASA Astrophysics Data System (ADS)

Liu, Hongli; Cai, Chunpei

2011-05-01

A newly developed three-dimensional direct simulation Monte Carlo (DSMC) simulation package, named GRASP ("Generalized Rarefied gAs Simulation Package"), is reported in this paper. This package utilizes the concept of simulation engine, many C++ features and software design patterns. The package has an open architecture which can benefit further development and maintenance of the code. In order to reduce the engineering time for three-dimensional models, a hybrid grid scheme, combined with a flexible data structure compiled by C++ language, are implemented in this package. This scheme utilizes a local data structure based on the computational cell to achieve high performance on workstation processors. This data structure allows the DSMC algorithm to be very efficiently parallelized with domain decomposition and it provides much flexibility in terms of grid types. This package can utilize traditional structured, unstructured or hybrid grids within the framework of a single code to model arbitrarily complex geometries and to simulate rarefied gas flows. Benchmark test cases indicate that this package has satisfactory accuracy for complex rarefied gas flows.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

PubMed

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

ICEG2D: An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils with Ice Accretion

NASA Technical Reports Server (NTRS)

Thompson, David S.; Soni, Bharat K.

2000-01-01

An integrated software package, ICEG2D, was developed to automate computational fluid dynamics (CFD) simulations for single-element airfoils with ice accretion. ICEG2D is designed to automatically perform three primary functions: (1) generating a grid-ready, surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generating a high-quality grid using the generated surface point distribution, and (3) generating the input and restart files needed to run the general purpose CFD solver NPARC. ICEG2D can be executed in batch mode using a script file or in an interactive mode by entering directives from a command line. This report summarizes activities completed in the first year of a three-year research and development program to address issues related to CFD simulations for aircraft components with ice accretion. Specifically, this document describes the technology employed in the software, the installation procedure, and a description of the operation of the software package. Validation of the geometry and grid generation modules of ICEG2D is also discussed.

airGRteaching: an R-package designed for teaching hydrology with lumped hydrological models

NASA Astrophysics Data System (ADS)

Thirel, Guillaume; Delaigue, Olivier; Coron, Laurent; Andréassian, Vazken; Brigode, Pierre

2017-04-01

Lumped hydrological models are useful and convenient tools for research, engineering and educational purposes. They propose catchment-scale representations of the precipitation-discharge relationship. Thanks to their limited data requirements, they can be easily implemented and run. With such models, it is possible to simulate a number of hydrological key processes over the catchment with limited structural and parametric complexity, typically evapotranspiration, runoff, underground losses, etc. The Hydrology Group at Irstea (Antony) has been developing a suite of rainfall-runoff models over the past 30 years. This resulted in a suite of models running at different time steps (from hourly to annual) applicable for various issues including water balance estimation, forecasting, simulation of impacts and scenario testing. Recently, Irstea has developed an easy-to-use R-package (R Core Team, 2016), called airGR (Coron et al., 2016, 2017), to make these models widely available. Although its initial target public was hydrological modellers, the package is already used for educational purposes. Indeed, simple models allow for rapidly visualising the effects of parameterizations and model components on flows hydrographs. In order to avoid the difficulties that students may have when manipulating R and datasets, we developed (Delaigue and Coron, 2016): - Three simplified functions to prepare data, calibrate a model and run a simulation - Simplified and dynamic plot functions - A shiny (Chang et al., 2016) interface that connects this R-package to a browser-based visualisation tool. On this interface, the students can use different hydrological models (including the possibility to use a snow-accounting model), manually modify their parameters and automatically calibrate their parameters with diverse objective functions. One of the visualisation tabs of the interface includes observed precipitation and temperature, simulated snowpack (if any), observed and simulated discharges, which are updated immediately (a calibration only needs a couple of seconds or less, a simulation is almost immediate). In addition, time series of internal variables, live-visualisation of internal variables evolution and performance statistics are provided. This interface allows for hands-on exercises that can include for instance the analysis by students of: - The effects of each parameter and model components on simulated discharge - The effects of objective functions based on high flows- or low flows-focused criteria on simulated discharge - The seasonality of the model components. References Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2016). shiny: Web Application Framework for R. R package version 0.13.2. https://CRAN.R-project.org/package=shiny Coron L., Thirel G., Perrin C., Delaigue O., Andréassian V., airGR: a suite of lumped hydrological models in an R-package, Environmental Modelling and software, 2017, submitted. Coron, L., Perrin, C. and Michel, C. (2016). airGR: Suite of GR hydrological models for precipitation-runoff modelling. R package version 1.0.3. https://webgr.irstea.fr/airGR/?lang=en. Olivier Delaigue and Laurent Coron (2016). airGRteaching: Tools to simplify the use of the airGR hydrological package by students. R package version 0.0.1. https://webgr.irstea.fr/airGR/?lang=en R Core Team (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Optimal segmentation and packaging process

DOEpatents

Kostelnik, Kevin M.; Meservey, Richard H.; Landon, Mark D.

1999-01-01

A process for improving packaging efficiency uses three dimensional, computer simulated models with various optimization algorithms to determine the optimal segmentation process and packaging configurations based on constraints including container limitations. The present invention is applied to a process for decontaminating, decommissioning (D&D), and remediating a nuclear facility involving the segmentation and packaging of contaminated items in waste containers in order to minimize the number of cuts, maximize packaging density, and reduce worker radiation exposure. A three-dimensional, computer simulated, facility model of the contaminated items are created. The contaminated items are differentiated. The optimal location, orientation and sequence of the segmentation and packaging of the contaminated items is determined using the simulated model, the algorithms, and various constraints including container limitations. The cut locations and orientations are transposed to the simulated model. The contaminated items are actually segmented and packaged. The segmentation and packaging may be simulated beforehand. In addition, the contaminated items may be cataloged and recorded.

MDplot: Visualise Molecular Dynamics.

PubMed

Margreitter, Christian; Oostenbrink, Chris

2017-05-10

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04531j

PubMed Central

Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F.; Harger, Matthew; Torabifard, Hedieh; Cisneros, G. Andrés; Schnieders, Michael J.; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y.; Ponder, Jay W.

2017-01-01

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed. PMID:29732110

Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS

PubMed Central

2011-01-01

We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the molecular motor F1-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique. PMID:21566696

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

PubMed

Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

2015-10-01

It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

PubMed Central

Dijkstra, Maurits J. J.; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

2015-01-01

It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

Analysis of the dynamic behavior of structures using the high-rate GNSS-PPP method combined with a wavelet-neural model: Numerical simulation and experimental tests

NASA Astrophysics Data System (ADS)

Kaloop, Mosbeh R.; Yigit, Cemal O.; Hu, Jong W.

2018-03-01

Recently, the high rate global navigation satellite system-precise point positioning (GNSS-PPP) technique has been used to detect the dynamic behavior of structures. This study aimed to increase the accuracy of the extraction oscillation properties of structural movements based on the high-rate (10 Hz) GNSS-PPP monitoring technique. A developmental model based on the combination of wavelet package transformation (WPT) de-noising and neural network prediction (NN) was proposed to improve the dynamic behavior of structures for GNSS-PPP method. A complicated numerical simulation involving highly noisy data and 13 experimental cases with different loads were utilized to confirm the efficiency of the proposed model design and the monitoring technique in detecting the dynamic behavior of structures. The results revealed that, when combined with the proposed model, GNSS-PPP method can be used to accurately detect the dynamic behavior of engineering structures as an alternative to relative GNSS method.

Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

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

1989-01-01

Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

Phi29 Connector-DNA Interactions Govern DNA Crunching and Rotation, Supporting the Check-Valve Model

PubMed Central

Kumar, Rajendra; Grubmüller, Helmut

2016-01-01

During replication of the ϕ29 bacteriophage inside a bacterial host cell, a DNA packaging motor transports the viral DNA into the procapsid against a pressure difference of up to 40 ± 20 atm. Several models have been proposed for the underlying molecular mechanism. Here we have used molecular dynamics simulations to examine the role of the connector part of the motor, and specifically the one-way revolution and the push-roll model. We have focused at the structure and intermolecular interactions between the DNA and the connector, for which a near-complete structure is available. The connector is found to induce considerable DNA deformations with respect to its canonical B-form. We further assessed by force-probe simulations to which extent the connector is able to prevent DNA leakage and found that the connector can act as a partial one-way valve by a check-valve mechanism via its mobile loops. Analysis of the geometry, flexibility, and energetics of channel lysine residues suggested that this arrangement of residues is incompatible with the observed DNA packaging step-size of ∼2.5 bp, such that the step-size is probably determined by the other components of the motor. Previously proposed DNA revolution and rolling motions inside the connector channel are both found implausible due to structural entanglement between the DNA and connector loops that have not been resolved in the crystal structure. Rather, in the simulations, the connector facilitates minor DNA rotation during the packaging process compatible with recent optical-tweezers experiments. Combined with the available experimental data, our simulation results suggest that the connector acts as a check-valve that prevents DNA leakage and induces DNA compression and rotation during DNA packaging. PMID:26789768

Space robot simulator vehicle

NASA Technical Reports Server (NTRS)

Cannon, R. H., Jr.; Alexander, H.

1985-01-01

A Space Robot Simulator Vehicle (SRSV) was constructed to model a free-flying robot capable of doing construction, manipulation and repair work in space. The SRSV is intended as a test bed for development of dynamic and static control methods for space robots. The vehicle is built around a two-foot-diameter air-cushion vehicle that carries batteries, power supplies, gas tanks, computer, reaction jets and radio equipment. It is fitted with one or two two-link manipulators, which may be of many possible designs, including flexible-link versions. Both the vehicle body and its first arm are nearly complete. Inverse dynamic control of the robot's manipulator has been successfully simulated using equations generated by the dynamic simulation package SDEXACT. In this mode, the position of the manipulator tip is controlled not by fixing the vehicle base through thruster operation, but by controlling the manipulator joint torques to achieve the desired tip motion, while allowing for the free motion of the vehicle base. One of the primary goals is to minimize use of the thrusters in favor of intelligent control of the manipulator. Ways to reduce the computational burden of control are described.

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

NASA Technical Reports Server (NTRS)

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

2012-01-01

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

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

PubMed Central

Zuckerman, Daniel M.; Chong, Lillian T.

2018-01-01

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling—the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes—protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation. PMID:28301772

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.

PubMed

Zuckerman, Daniel M; Chong, Lillian T

2017-05-22

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.

Screening for the Location of RNA using the Chloride Ion Distribution in Simulations of Virus Capsids.

PubMed

Larsson, Daniel S D; van der Spoel, David

2012-07-10

The complete structure of the genomic material inside a virus capsid remains elusive, although a limited amount of symmetric nucleic acid can be resolved in the crystal structure of 17 icosahedral viruses. The negatively charged sugar-phosphate backbone of RNA and DNA as well as the large positive charge of the interior surface of the virus capsids suggest that electrostatic complementarity is an important factor in the packaging of the genomes in these viruses. To test how much packing information is encoded by the electrostatic and steric envelope of the capsid interior, we performed extensive all-atom molecular dynamics (MD) simulations of virus capsids with explicit water molecules and solvent ions. The model systems were two small plant viruses in which significant amounts of RNA has been observed by X-ray crystallography: satellite tobacco mosaic virus (STMV, 62% RNA visible) and satellite tobacco necrosis virus (STNV, 34% RNA visible). Simulations of half-capsids of these viruses with no RNA present revealed that the binding sites of RNA correlated well with regions populated by chloride ions, suggesting that it is possible to screen for the binding sites of nucleic acids by determining the equilibrium distribution of negative ions. By including the crystallographically resolved RNA in addition to ions, we predicted the localization of the unresolved RNA in the viruses. Both viruses showed a hot-spot for RNA binding at the 5-fold symmetry axis. The MD simulations were compared to predictions of the chloride density based on nonlinear Poisson-Boltzmann equation (PBE) calculations with mobile ions. Although the predictions are superficially similar, the PBE calculations overestimate the ion concentration close to the capsid surface and underestimate it far away, mainly because protein dynamics is not taken into account. Density maps from chloride screening can be used to aid in building atomic models of packaged virus genomes. Knowledge of the principles of genome packaging might be exploited for both antiviral therapy and technological applications.

Eutectic-based wafer-level-packaging technique for piezoresistive MEMS accelerometers and bond characterization using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Aono, T.; Kazama, A.; Okada, R.; Iwasaki, T.; Isono, Y.

2018-03-01

We developed a eutectic-based wafer-level-packaging (WLP) technique for piezoresistive micro-electromechanical systems (MEMS) accelerometers on the basis of molecular dynamics analyses and shear tests of WLP accelerometers. The bonding conditions were experimentally and analytically determined to realize a high shear strength without solder material atoms diffusing to adhesion layers. Molecular dynamics (MD) simulations and energy dispersive x-ray (EDX) spectrometry done after the shear tests clarified the eutectic reaction of the solder materials used in this research. Energy relaxation calculations in MD showed that the diffusion of solder material atoms into the adhesive layer was promoted at a higher temperature. Tensile creep MD simulations also suggested that the local potential energy in a solder material model determined the fracture points of the model. These numerical results were supported by the shear tests and EDX analyses for WLP accelerometers. Consequently, a bonding load of 9.8 kN and temperature of 300 °C were found to be rational conditions because the shear strength was sufficient to endure the polishing process after the WLP process and there was little diffusion of solder material atoms to the adhesion layer. Also, eutectic-bonding-based WLP was effective for controlling the attenuation of the accelerometers by determining the thickness of electroplated solder materials that played the role of a cavity between the accelerometers and lids. If the gap distance between the two was less than 6.2 µm, the signal gains for x- and z-axis acceleration were less than 20 dB even at the resonance frequency due to air-damping.

FASTSIM2: a second-order accurate frictional rolling contact algorithm

NASA Astrophysics Data System (ADS)

Vollebregt, E. A. H.; Wilders, P.

2011-01-01

In this paper we consider the frictional (tangential) steady rolling contact problem. We confine ourselves to the simplified theory, instead of using full elastostatic theory, in order to be able to compute results fast, as needed for on-line application in vehicle system dynamics simulation packages. The FASTSIM algorithm is the leading technology in this field and is employed in all dominant railway vehicle system dynamics packages (VSD) in the world. The main contribution of this paper is a new version "FASTSIM2" of the FASTSIM algorithm, which is second-order accurate. This is relevant for VSD, because with the new algorithm 16 times less grid points are required for sufficiently accurate computations of the contact forces. The approach is based on new insights in the characteristics of the rolling contact problem when using the simplified theory, and on taking precise care of the contact conditions in the numerical integration scheme employed.

Progress Toward a Format Standard for Flight Dynamics Models

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Hildreth, Bruce L.

2006-01-01

In the beginning, there was FORTRAN, and it was... not so good. But it was universal, and all flight simulator equations of motion were coded with it. Then came ACSL, C, Ada, C++, C#, Java, FORTRAN-90, Matlab/Simulink, and a number of other programming languages. Since the halcyon punch card days of 1968, models of aircraft flight dynamics have proliferated in training devices, desktop engineering and development computers, and control design textbooks. With the rise of industry teaming and increased reliance on simulation for procurement decisions, aircraft and missile simulation models are created, updated, and exchanged with increasing frequency. However, there is no real lingua franca to facilitate the exchange of models from one simulation user to another. The current state-of-the-art is such that several staff-months if not staff-years are required to 'rehost' each release of a flight dynamics model from one simulation environment to another one. If a standard data package or exchange format were to be universally adopted, the cost and time of sharing and updating aerodynamics, control laws, mass and inertia, and other flight dynamic components of the equations of motion of an aircraft or spacecraft simulation could be drastically reduced. A 2002 paper estimated over $ 6 million in savings could be realized for one military aircraft type alone. This paper describes the efforts of the American Institute of Aeronautics and Astronautics (AIAA) to develop a standard flight dynamic model exchange standard based on XML and HDF-5 data formats.

Optimal segmentation and packaging process

DOEpatents

Kostelnik, K.M.; Meservey, R.H.; Landon, M.D.

1999-08-10

A process for improving packaging efficiency uses three dimensional, computer simulated models with various optimization algorithms to determine the optimal segmentation process and packaging configurations based on constraints including container limitations. The present invention is applied to a process for decontaminating, decommissioning (D and D), and remediating a nuclear facility involving the segmentation and packaging of contaminated items in waste containers in order to minimize the number of cuts, maximize packaging density, and reduce worker radiation exposure. A three-dimensional, computer simulated, facility model of the contaminated items are created. The contaminated items are differentiated. The optimal location, orientation and sequence of the segmentation and packaging of the contaminated items is determined using the simulated model, the algorithms, and various constraints including container limitations. The cut locations and orientations are transposed to the simulated model. The contaminated items are actually segmented and packaged. The segmentation and packaging may be simulated beforehand. In addition, the contaminated items may be cataloged and recorded. 3 figs.

Relationships between chromosome structure and chromosomal aberrations

NASA Astrophysics Data System (ADS)

Eidelman, Yuri; Andreev, Sergey

An interphase nucleus of human lymphocyte was simulated by the novel Monte Carlo tech-nique. The main features of interphase chromosome structure and packaging were taken into account: different levels of chromatin organisation; nonrandom localisation of chromosomes within a nucleus; chromosome loci dynamics. All chromosomes in a nucleus were modelled as polymer globules. A dynamic pattern of intra/interchromosomal contacts was simulated. The detailed information about chromosomal contacts, such as distribution of intrachromoso-mal contacts over the length of each chromosome and dependence of contact probability on genomic separation between chromosome loci, were calculated and compared to the new exper-imental data obtained by the Hi-C technique. Types and frequencies of simple and complex radiation-induced chromosomal exchange aberrations (CA) induced by X-rays were predicted with taking formation and decay of chromosomal contacts into account. Distance dependence of exchange formation probability was calculated directly. mFISH data for human lymphocytes were analysed. The calculated frequencies of simple CA agreed with the experimental data. Complex CA were underestimated despite the dense packaging of chromosome territories within a nucleus. Possible influence of chromosome-nucleus structural organisation on the frequency and spectrum of radiation-induced chromosome aberrations is discussed.

Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides.

PubMed

Yu, Hua; Wang, Mao-jun; Xuan, Nan-xia; Shang, Zhi-cai; Wu, Jun

2015-10-01

To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding. van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues.

CFD simulation and experimental validation of a GM type double inlet pulse tube refrigerator

NASA Astrophysics Data System (ADS)

Banjare, Y. P.; Sahoo, R. K.; Sarangi, S. K.

2010-04-01

Pulse tube refrigerator has the advantages of long life and low vibration over the conventional cryocoolers, such as GM and stirling coolers because of the absence of moving parts in low temperature. This paper performs a three-dimensional computational fluid dynamic (CFD) simulation of a GM type double inlet pulse tube refrigerator (DIPTR) vertically aligned, operating under a variety of thermal boundary conditions. A commercial computational fluid dynamics (CFD) software package, Fluent 6.1 is used to model the oscillating flow inside a pulse tube refrigerator. The simulation represents fully coupled systems operating in steady-periodic mode. The externally imposed boundary conditions are sinusoidal pressure inlet by user defined function at one end of the tube and constant temperature or heat flux boundaries at the external walls of the cold-end heat exchangers. The experimental method to evaluate the optimum parameters of DIPTR is difficult. On the other hand, developing a computer code for CFD analysis is equally complex. The objectives of the present investigations are to ascertain the suitability of CFD based commercial package, Fluent for study of energy and fluid flow in DIPTR and to validate the CFD simulation results with available experimental data. The general results, such as the cool down behaviours of the system, phase relation between mass flow rate and pressure at cold end, the temperature profile along the wall of the cooler and refrigeration load are presented for different boundary conditions of the system. The results confirm that CFD based Fluent simulations are capable of elucidating complex periodic processes in DIPTR. The results also show that there is an excellent agreement between CFD simulation results and experimental results.

Optimizing legacy molecular dynamics software with directive-based offload

DOE PAGES

Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; ...

2015-05-14

The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less

Multiscale equation-free algorithms for molecular dynamics

NASA Astrophysics Data System (ADS)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Advanced functional network analysis in the geosciences: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Runge, Jakob; Schultz, Hanna C. H.; Wiedermann, Marc; Zech, Alraune; Feldhoff, Jan; Rheinwalt, Aljoscha; Kutza, Hannes; Radebach, Alexander; Marwan, Norbert; Kurths, Jürgen

2013-04-01

Functional networks are a powerful tool for analyzing large geoscientific datasets such as global fields of climate time series originating from observations or model simulations. pyunicorn (pythonic unified complex network and recurrence analysis toolbox) is an open-source, fully object-oriented and easily parallelizable package written in the language Python. It allows for constructing functional networks (aka climate networks) representing the structure of statistical interrelationships in large datasets and, subsequently, investigating this structure using advanced methods of complex network theory such as measures for networks of interacting networks, node-weighted statistics or network surrogates. Additionally, pyunicorn allows to study the complex dynamics of geoscientific systems as recorded by time series by means of recurrence networks and visibility graphs. The range of possible applications of the package is outlined drawing on several examples from climatology.

Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions.

PubMed

Krajniak, Jakub; Zhang, Zidan; Pandiyan, Sudharsan; Nies, Eric; Samaey, Giovanni

2018-06-11

We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non-bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse-grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain-specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Single-pass incremental force updates for adaptively restrained molecular dynamics.

PubMed

Singh, Krishna Kant; Redon, Stephane

2018-03-30

Adaptively restrained molecular dynamics (ARMD) allows users to perform more integration steps in wall-clock time by switching on and off positional degrees of freedoms. This article presents new, single-pass incremental force updates algorithms to efficiently simulate a system using ARMD. We assessed different algorithms for speedup measurements and implemented them in the LAMMPS MD package. We validated the single-pass incremental force update algorithm on four different benchmarks using diverse pair potentials. The proposed algorithm allows us to perform simulation of a system faster than traditional MD in both NVE and NVT ensembles. Moreover, ARMD using the new single-pass algorithm speeds up the convergence of observables in wall-clock time. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Development and Use of an Open-Source, User-Friendly Package to Simulate Voltammetry Experiments

ERIC Educational Resources Information Center

Wang, Shuo; Wang, Jing; Gao, Yanjing

2017-01-01

An open-source electrochemistry simulation package has been developed that simulates the electrode processes of four reaction mechanisms and two typical electroanalysis techniques: cyclic voltammetry and chronoamperometry. Unlike other open-source simulation software, this package balances the features with ease of learning and implementation and…

Kinematics Simulation Analysis of Packaging Robot with Joint Clearance

NASA Astrophysics Data System (ADS)

Zhang, Y. W.; Meng, W. J.; Wang, L. Q.; Cui, G. H.

2018-03-01

Considering the influence of joint clearance on the motion error, repeated positioning accuracy and overall position of the machine, this paper presents simulation analysis of a packaging robot — 2 degrees of freedom(DOF) planar parallel robot based on the characteristics of high precision and fast speed of packaging equipment. The motion constraint equation of the mechanism is established, and the analysis and simulation of the motion error are carried out in the case of turning the revolute clearance. The simulation results show that the size of the joint clearance will affect the movement accuracy and packaging efficiency of the packaging robot. The analysis provides a reference point of view for the packaging equipment design and selection criteria and has a great significance on the packaging industry automation.

Characteristics of 3-D transport simulations of the stratosphere and mesosphere

NASA Technical Reports Server (NTRS)

Fairlie, T. D. A.; Siskind, D. E.; Turner, R. E.; Fisher, M.

1992-01-01

A 3D mechanistic, primitive-equation model of the stratosphere and mesosphere is coupled to an offline spectral transport model. The dynamics model is initialized with and forced by observations so that the coupled models may be used to study specific episodes. Results are compared with those obtained by transport online in the dynamics model. Although some differences are apparent, the results suggest that coupling of the models to a comprehensive photochemical package will provide a useful tool for studying the evolution of constituents in the middle atmosphere during specific episodes.

Development of a non-linear simulation for generic hypersonic vehicles - ASUHS1

NASA Technical Reports Server (NTRS)

Salas, Juan; Lovell, T. Alan; Schmidt, David K.

1993-01-01

A nonlinear simulation is developed to model the longitudinal motion of a vehicle in hypersonic flight. The equations of motion pertinent to this study are presented. Analytic expressions for the aerodynamic forces acting on a hypersonic vehicle which were obtained from Newtonian Impact Theory are further developed. The control surface forces are further examined to incorporate vehicle elastic motion. The purpose is to establish feasible equations of motion which combine rigid body, elastic, and aeropropulsive dynamics for use in nonlinear simulations. The software package SIMULINK is used to implement the simulation. Also discussed are issues needing additional attention and potential problems associated with the implementation (with proposed solutions).

Modeling of radiation damage recovery in particle detectors based on GaN

NASA Astrophysics Data System (ADS)

Gaubas, E.; Ceponis, T.; Pavlov, J.

2015-12-01

The pulsed characteristics of the capacitor-type and PIN diode type detectors based on GaN have been simulated using the dynamic and drift-diffusion models. The drift-diffusion current simulations have been implemented by employing the commercial software package Synopsys TCAD Sentaurus. The bipolar drift regime has been analyzed. The possible internal gain in charge collection through carrier multiplication processes determined by impact ionization has been considered in order to compensate carrier lifetime reduction due to radiation defects introduced into GaN material of detector.

Prediction of glass transition temperature of freeze-dried formulations by molecular dynamics simulation.

PubMed

Yoshioka, Sumie; Aso, Yukio; Kojima, Shigeo

2003-06-01

To examine whether the glass transition temperature (Tg) of freeze-dried formulations containing polymer excipients can be accurately predicted by molecular dynamics simulation using software currently available on the market. Molecular dynamics simulations were carried out for isomaltodecaose, a fragment of dextran, and alpha-glucose, the repeated unit of dextran. in the presence or absence of water molecules. Estimated values of Tg were compared with experimental values obtained by differential scanning calorimetry (DSC). Isothermal-isobaric molecular dynamics simulations (NPTMD) and isothermal molecular dynamics simulations at a constant volume (NVTMD) were carried out using the software package DISCOVER (Material Studio) with the Polymer Consortium Force Field. Mean-squared displacement and radial distribution function were calculated. NVTMD using the values of density obtained by NPTMD provided the diffusivity of glucose-ring oxygen and water oxygen in amorphous alpha-glucose and isomaltodecaose, which exhibited a discontinuity in temperature dependence due to glass transition. Tg was estimated to be approximately 400K and 500K for pure amorphous a-glucose and isomaltodecaose, respectively, and in the presence of one water molecule per glucose unit, Tg was 340K and 360K, respectively. Estimated Tg values were higher than experimentally determined values because of the very fast cooling rates in the simulations. However, decreases in Tg on hydration and increases in Tg associated with larger fragment size could be demonstrated. The results indicate that molecular dynamics simulation is a useful method for investigating the effects of hydration and molecular weight on the Tg of lyophilized formulations containing polymer excipients. although the relationship between cooling rates and Tg must first be elucidated to predict Tg vales observed by DSC measurement. January 16.

Evolutionary behaviour, trade-offs and cyclic and chaotic population dynamics.

PubMed

Hoyle, Andy; Bowers, Roger G; White, Andy

2011-05-01

Many studies of the evolution of life-history traits assume that the underlying population dynamical attractor is stable point equilibrium. However, evolutionary outcomes can change significantly in different circumstances. We present an analysis based on adaptive dynamics of a discrete-time demographic model involving a trade-off whose shape is also an important determinant of evolutionary behaviour. We derive an explicit expression for the fitness in the cyclic region and consequently present an adaptive dynamic analysis which is algebraic. We do this fully in the region of 2-cycles and (using a symbolic package) almost fully for 4-cycles. Simulations illustrate and verify our results. With equilibrium population dynamics, trade-offs with accelerating costs produce a continuously stable strategy (CSS) whereas trade-offs with decelerating costs produce a non-ES repellor. The transition to 2-cycles produces a discontinuous change: the appearance of an intermediate region in which branching points occur. The size of this region decreases as we move through the region of 2-cycles. There is a further discontinuous fall in the size of the branching region during the transition to 4-cycles. We extend our results numerically and with simulations to higher-period cycles and chaos. Simulations show that chaotic population dynamics can evolve from equilibrium and vice-versa.

Simulation of transverse modes with their intrinsic Landau damping for bunched beams in the presence of space charge

DOE PAGES

Macridin, Alexandru; Burov, Alexey; Stern, Eric; ...

2015-07-22

Transverse dipole modes in bunches with space charge are simulated using the synergia accelerator modeling package and analyzed with dynamic mode decomposition. The properties of the first three space charge modes, including their shape, damping rates, and tune shifts are described over the entire range of space charge strength. As a result, the intrinsic Landau damping predicted and estimated in 2009 by one of the authors is confirmed with a reasonable scaling factor of ≃2.4. For the KV distribution, very good agreement with PATRIC simulations performed by Kornilov and Boine-Frankenheim is obtained.

A gene network simulator to assess reverse engineering algorithms.

PubMed

Di Camillo, Barbara; Toffolo, Gianna; Cobelli, Claudio

2009-03-01

In the context of reverse engineering of biological networks, simulators are helpful to test and compare the accuracy of different reverse-engineering approaches in a variety of experimental conditions. A novel gene-network simulator is presented that resembles some of the main features of transcriptional regulatory networks related to topology, interaction among regulators of transcription, and expression dynamics. The simulator generates network topology according to the current knowledge of biological network organization, including scale-free distribution of the connectivity and clustering coefficient independent of the number of nodes in the network. It uses fuzzy logic to represent interactions among the regulators of each gene, integrated with differential equations to generate continuous data, comparable to real data for variety and dynamic complexity. Finally, the simulator accounts for saturation in the response to regulation and transcription activation thresholds and shows robustness to perturbations. It therefore provides a reliable and versatile test bed for reverse engineering algorithms applied to microarray data. Since the simulator describes regulatory interactions and expression dynamics as two distinct, although interconnected aspects of regulation, it can also be used to test reverse engineering approaches that use both microarray and protein-protein interaction data in the process of learning. A first software release is available at http://www.dei.unipd.it/~dicamill/software/netsim as an R programming language package.

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

PubMed

Serçinoglu, Onur; Ozbek, Pemra

2018-05-25

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Prediction of pressure drop in fluid tuned mounts using analytical and computational techniques

NASA Technical Reports Server (NTRS)

Lasher, William C.; Khalilollahi, Amir; Mischler, John; Uhric, Tom

1993-01-01

A simplified model for predicting pressure drop in fluid tuned isolator mounts was developed. The model is based on an exact solution to the Navier-Stokes equations and was made more general through the use of empirical coefficients. The values of these coefficients were determined by numerical simulation of the flow using the commercial computational fluid dynamics (CFD) package FIDAP.

Simulating botulinum neurotoxin with constant pH molecular dynamics in Generalized Born implicit solvent

NASA Astrophysics Data System (ADS)

Chen, Yongzhi; Chen, Xin; Deng, Yuefan

2007-07-01

A new method was proposed by Mongan et al. for constant pH molecular dynamics simulation and was implemented in AMBER 8 package. Protonation states are modeled with different charge sets, and titrating residues are sampled from a Boltzmann distribution of protonation states. The simulation periodically adopts Monte Carlo sampling based on Generalized Born (GB) derived energies. However, when this approach was applied to a bio-toxin, Botulinum Neurotoxin Type A (BoNT/A) at pH 4.4, 4.7, 5.0, 6.8 and 7.2, the pK predictions yielded by the method were inconsistent with the experimental values. The systems being simulated were divergent. Furthermore, the system behaviors in a very weak acidic solution (pH 6.8) and in a very weak basic solution (pH 7.2) were significantly different from the neutral case (pH 7.0). Hence, we speculate this method may require further study for modeling large biomolecule.

Molecular-dynamic simulations of the thermophysical properties of hexanitrohexaazaisowurtzitane single crystal at high pressures and temperatures

NASA Astrophysics Data System (ADS)

Kozlova, S. A.; Gubin, S. A.; Maklashova, I. V.; Selezenev, A. A.

2017-11-01

Molecular dynamic simulations of isothermal compression parameters are performed for a hexanitrohexaazaisowurtzitane single crystal (C6H6O12N12) using a modified ReaxFF-log reactive force field. It is shown that the pressure-compression ratio curve for a single C6H6O12N12 crystal at constant temperature T = 300 K in pressure range P = 0.05-40 GPa is in satisfactory agreement with experimental compression isotherms obtained for a single C6H6O12N12 crystal. Hugoniot molecular-dynamic simulations of the shock-wave hydrostatic compression of a single C6H6O12N12 crystal are performed. Along with Hugoniot temperature-pressure curves, calculated shock-wave pressure-compression ratios for a single C6H6O12N12 crystal are obtained for a wide pressure range of P = 1-40 GPa. It is established that the percussive adiabat obtained for a single C6H6O12N12 crystal is in a good agreement with the experimental data. All calculations are performed using a LAMMPS molecular dynamics simulation software package that provides a ReaxFF-lg reactive force field to support the approach.

Bee++: An Object-Oriented, Agent-Based Simulator for Honey Bee Colonies

PubMed Central

Betti, Matthew; LeClair, Josh; Wahl, Lindi M.; Zamir, Mair

2017-01-01

We present a model and associated simulation package (www.beeplusplus.ca) to capture the natural dynamics of a honey bee colony in a spatially-explicit landscape, with temporally-variable, weather-dependent parameters. The simulation tracks bees of different ages and castes, food stores within the colony, pollen and nectar sources and the spatial position of individual foragers outside the hive. We track explicitly the intake of pesticides in individual bees and their ability to metabolize these toxins, such that the impact of sub-lethal doses of pesticides can be explored. Moreover, pathogen populations (in particular, Nosema apis, Nosema cerenae and Varroa mites) have been included in the model and may be introduced at any time or location. The ability to study interactions among pesticides, climate, biodiversity and pathogens in this predictive framework should prove useful to a wide range of researchers studying honey bee populations. To this end, the simulation package is written in open source, object-oriented code (C++) and can be easily modified by the user. Here, we demonstrate the use of the model by exploring the effects of sub-lethal pesticide exposure on the flight behaviour of foragers. PMID:28287445

Molecular Dynamics Simulations of Creatine Kinase and Adenine Nucleotide Translocase in Mitochondrial Membrane Patch*

PubMed Central

Karo, Jaanus; Peterson, Pearu; Vendelin, Marko

2012-01-01

Interaction between mitochondrial creatine kinase (MtCK) and adenine nucleotide translocase (ANT) can play an important role in determining energy transfer pathways in the cell. Although the functional coupling between MtCK and ANT has been demonstrated, the precise mechanism of the coupling is not clear. To study the details of the coupling, we turned to molecular dynamics simulations. We introduce a new coarse-grained molecular dynamics model of a patch of the mitochondrial inner membrane containing a transmembrane ANT and an MtCK above the membrane. The membrane model consists of three major types of lipids (phosphatidylcholine, phosphatidylethanolamine, and cardiolipin) in a roughly 2:1:1 molar ratio. A thermodynamics-based coarse-grained force field, termed MARTINI, has been used together with the GROMACS molecular dynamics package for all simulated systems in this work. Several physical properties of the system are reproduced by the model and are in agreement with known data. This includes membrane thickness, dimension of the proteins, and diffusion constants. We have studied the binding of MtCK to the membrane and demonstrated the effect of cardiolipin on the stabilization of the binding. In addition, our simulations predict which part of the MtCK protein sequence interacts with the membrane. Taken together, the model has been verified by dynamical and structural data and can be used as the basis for further studies. PMID:22241474

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

SPICE Work Package 3: Modelling the Effects of Stratospheric Aerosol Geoengineering

NASA Astrophysics Data System (ADS)

Driscoll, Simon

2015-04-01

This talk presents the results of the SPICE Work Package 3. There is an obvious need for methods to verify the accuracy of geoengineering given no observations of a geoengineering programme. Accordingly, model ability in reproducing the observed dynamical response to volcanic eruptions is discussed using analysis of CMIP5 data and different configurations of the HadGEM2 model. With the HadGEM2-L60 model shown to be substantially better in reproducing the observed dynamical response to volcanic eruptions, simulations of GeoMIP's G4 scenario are performed. Simulated impacts of geoengineering are described, and asymmetries between the immediate onset and immediate cessation ('termination') of geoengineering are analysed. Whilst a rapid large increase in stratospheric sulphate aerosols (such as from volcanic eruptions) can cause substantial damage, most volcanic eruptions in general are not catastrophic. One may therefore suspect that an 'equal but opposite' change in radiative forcing from termination may therefore not be catastrophic, if the climatic response is simulated to be symmetric. HadGEM2 simulations reveal a substantially more rapid change in variables such as near-surface temperature and precipitation following termination than the onset, indicating that termination may be substantially more damaging and even catastrophic. Some suggestions for hemispherically asymmetric geoengineering have been proposed as a way to reduce Northern Hemisphere sea ice, for example, with lesser impacts on the rest of the climate. However, HadGEM2 simulations are performed and observations analysed following volcanic eruptions. Both indicate substantial averse consequences from hemispherically asymmetric loading of stratospheric loading on precipitation in the Sahelian region - a vulnerable region where drought has caused hundreds of thousands of deaths and created millions of refugees in the past.

Investigation of migrant-polymer interaction in pharmaceutical packaging material using the linear interaction energy algorithm.

PubMed

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2014-10-01

The interaction between drug products and polymeric packaging materials is an important topic in the pharmaceutical industry and often associated with high costs because of the required elaborative interaction studies. Therefore, a theoretical prediction of such interactions would be beneficial. Often, material parameters such as the octanol water partition coefficient are used to predict the partitioning of migrant molecules between a solvent and a polymeric packaging material. Here, we present the investigation of the partitioning of various migrant molecules between polymers and solvents using molecular dynamics simulations for the calculation of interaction energies. Our results show that the use of a model for the interaction between the migrant and the polymer at atomistic detail can yield significantly better results when predicting the polymer solvent partitioning than a model based on the octanol water partition coefficient. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Simulating Freak Waves in the Ocean with CFD Modeling

NASA Astrophysics Data System (ADS)

Manolidis, M.; Orzech, M.; Simeonov, J.

2017-12-01

Rogue, or freak, waves constitute an active topic of research within the world scientific community, as various maritime authorities around the globe seek to better understand and more accurately assess the risks that the occurrence of such phenomena entail. Several experimental studies have shed some light on the mechanics of rogue wave formation. In our work we numerically simulate the formation of such waves in oceanic conditions by means of Computational Fluid Dynamics (CFD) software. For this purpose we implement the NHWAVE and OpenFOAM software packages. Both are non-hydrostatic, turbulent flow solvers, but NHWAVE implements a shock-capturing scheme at the free surface-interface, while OpenFOAM utilizes the Volume Of Fluid (VOF) method. NHWAVE has been shown to accurately reproduce highly nonlinear surface wave phenomena, such as soliton propagation and wave shoaling. We conducted a range of tests simulating rogue wave formation and horizontally varying currents to evaluate and compare the capabilities of the two software packages. Then we used each model to investigate the effect of ocean currents and current gradients on the formation of rogue waves. We present preliminary results.

Function Package for Computing Quantum Resource Measures

NASA Astrophysics Data System (ADS)

Huang, Zhiming

2018-05-01

In this paper, we present a function package for to calculate quantum resource measures and dynamics of open systems. Our package includes common operators and operator lists, frequently-used functions for computing quantum entanglement, quantum correlation, quantum coherence, quantum Fisher information and dynamics in noisy environments. We briefly explain the functions of the package and illustrate how to use the package with several typical examples. We expect that this package is a useful tool for future research and education.

A musculoskeletal model of the upper extremity for use in the development of neuroprosthetic systems

PubMed Central

Blana, Dimitra; Hincapie, Juan G.; Chadwick, Edward K.; Kirsch, Robert F.

2008-01-01

Upper extremity neuroprostheses use functional electrical stimulation (FES) to restore arm motor function to individuals with cervical level spinal cord injury. For the design and testing of these systems, a biomechanical model of the shoulder and elbow has been developed, to be used as a substitute for the human arm. It can be used to design and evaluate specific implementations of FES systems, as well as FES controllers. The model can be customized to simulate a variety of pathological conditions. For example, by adjusting the maximum force the muscles can produce, the model can be used to simulate an individual with tetraplegia and to explore the effects of FES of different muscle sets. The model comprises six bones, five joints, nine degrees of freedom, and 29 shoulder and arm muscles. It was developed using commercial, graphics-based modeling and simulation packages that are easily accessible to other researchers and can be readily interfaced to other analysis packages. It can be used for both forward-dynamic (inputs: muscle activation and external load; outputs:motions) and inverse-dynamic (inputs: motions and external load; outputs: muscle activation) simulations. Our model was verified by comparing the model-calculated muscle activations to electromyographic signals recorded from shoulder and arm muscles of five subjects. As an example of its application to neuroprosthesis design, the model was used to demonstrate the importance of rotator cuff muscle stimulation when aiming to restore humeral elevation. It is concluded that this model is a useful tool in the development and implementation of upper extremity neuroprosthetic systems. PMID:18420213

A musculoskeletal model of the upper extremity for use in the development of neuroprosthetic systems.

PubMed

Blana, Dimitra; Hincapie, Juan G; Chadwick, Edward K; Kirsch, Robert F

2008-01-01

Upper extremity neuroprostheses use functional electrical stimulation (FES) to restore arm motor function to individuals with cervical level spinal cord injury. For the design and testing of these systems, a biomechanical model of the shoulder and elbow has been developed, to be used as a substitute for the human arm. It can be used to design and evaluate specific implementations of FES systems, as well as FES controllers. The model can be customized to simulate a variety of pathological conditions. For example, by adjusting the maximum force the muscles can produce, the model can be used to simulate an individual with tetraplegia and to explore the effects of FES of different muscle sets. The model comprises six bones, five joints, nine degrees of freedom, and 29 shoulder and arm muscles. It was developed using commercial, graphics-based modeling and simulation packages that are easily accessible to other researchers and can be readily interfaced to other analysis packages. It can be used for both forward-dynamic (inputs: muscle activation and external load; outputs: motions) and inverse-dynamic (inputs: motions and external load; outputs: muscle activation) simulations. Our model was verified by comparing the model calculated muscle activations to electromyographic signals recorded from shoulder and arm muscles of five subjects. As an example of its application to neuroprosthesis design, the model was used to demonstrate the importance of rotator cuff muscle stimulation when aiming to restore humeral elevation. It is concluded that this model is a useful tool in the development and implementation of upper extremity neuroprosthetic systems.

An analytical study of electric vehicle handling dynamics

NASA Technical Reports Server (NTRS)

Greene, J. E.; Segal, D. J.

1979-01-01

Hypothetical electric vehicle configurations were studied by applying available analytical methods. Elementary linearized models were used in addition to a highly sophisticated vehicle dynamics computer simulation technique. Physical properties of specific EV's were defined for various battery and powertrain packaging approaches applied to a range of weight distribution and inertial properties which characterize a generic class of EV's. Computer simulations of structured maneuvers were performed for predicting handling qualities in the normal driving range and during various extreme conditions related to accident avoidance. Results indicate that an EV with forward weight bias will possess handling qualities superior to a comparable EV that is rear-heavy or equally balanced. The importance of properly matching tires, suspension systems, and brake system front/rear torque proportioning to a given EV configuration during the design stage is demonstrated.

Understanding the interfacial chain dynamics of fiber-reinforced polymer composite

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Carrillo, Jan-Michael; Naskar, Amit; Sumpter, Bobby

The polymer-fiber interface plays a major role in determining the structural and dynamical properties of fiber reinforced composite materials. We utilized LAMMPS MD package to understand the interfacial properties at the nanoscale. Coarse-grained flexible polymer chains are introduced to compare the various structures and dynamics of the polymer chains. Our preliminary simulation study shows that the rigidity of the polymer chain affects the interfacial morphology and dynamics of the chain on a flat surface. In this work, we identified the `immobile inter-phase' morphology and relate it to rheological properties. We calculated the viscoelastic properties, e.g., shear modulus and storage modulus, which are compared with experiments. MD simulations are used to show the variation of viscoelastic properties with polymer volume fraction. The nanoscale segmental and chain relaxation are calculated from the MD simulations and compared to the experimental data. These observations will be able to identify the fundamental physics behind the effect of the polymer-fiber interactions and orientation of the fiber to the overall rheological properties of the fiber reinforced polymer matrix. Funding for the project was provided by ORNLs Laboratory Directed Research and Development (LDRD) program.

Development of a High Fidelity Dynamic Module of the Advanced Resistive Exercise Device (ARED) Using Adams

NASA Technical Reports Server (NTRS)

Humphreys, B. T.; Thompson, W. K.; Lewandowski, B. E.; Cadwell, E. E.; Newby, N. J.; Fincke, R. S.; Sheehan, C.; Mulugeta, L.

2012-01-01

NASA's Digital Astronaut Project (DAP) implements well-vetted computational models to predict and assess spaceflight health and performance risks, and enhance countermeasure development. DAP provides expertise and computation tools to its research customers for model development, integration, or analysis. DAP is currently supporting the NASA Exercise Physiology and Countermeasures (ExPC) project by integrating their biomechanical models of specific exercise movements with dynamic models of the devices on which the exercises were performed. This presentation focuses on the development of a high fidelity dynamic module of the Advanced Resistive Exercise Device (ARED) on board the ISS. The ARED module, illustrated in the figure below, was developed using the Adams (MSC Santa Ana, California) simulation package. The Adams package provides the capabilities to perform multi rigid body, flexible body, and mixed dynamic analyses of complex mechanisms. These capabilities were applied to accurately simulate: Inertial and mass properties of the device such as the vibration isolation system (VIS) effects and other ARED components, Non-linear joint friction effects, The gas law dynamics of the vacuum cylinders and VIS components using custom written differential state equations, The ARED flywheel dynamics, including torque limiting clutch. Design data from the JSC ARED Engineering team was utilized in developing the model. This included solid modeling geometry files, component/system specifications, engineering reports and available data sets. The Adams ARED module is importable into LifeMOD (Life Modeler, Inc., San Clemente, CA) for biomechanical analyses of different resistive exercises such as squat and dead-lift. Using motion capture data from ground test subjects, the ExPC developed biomechanical exercise models in LifeMOD. The Adams ARED device module was then integrated with the exercise subject model into one integrated dynamic model. This presentation will describe the development of the Adams ARED module including its capabilities, limitations, and assumptions. Preliminary results, validation activities, and a practical application of the module to inform the relative effect of the flywheels on exercise will be discussed.

Integrating neuroinformatics tools in TheVirtualBrain.

PubMed

Woodman, M Marmaduke; Pezard, Laurent; Domide, Lia; Knock, Stuart A; Sanz-Leon, Paula; Mersmann, Jochen; McIntosh, Anthony R; Jirsa, Viktor

2014-01-01

TheVirtualBrain (TVB) is a neuroinformatics Python package representing the convergence of clinical, systems, and theoretical neuroscience in the analysis, visualization and modeling of neural and neuroimaging dynamics. TVB is composed of a flexible simulator for neural dynamics measured across scales from local populations to large-scale dynamics measured by electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI), and core analytic and visualization functions, all accessible through a web browser user interface. A datatype system modeling neuroscientific data ties together these pieces with persistent data storage, based on a combination of SQL and HDF5. These datatypes combine with adapters allowing TVB to integrate other algorithms or computational systems. TVB provides infrastructure for multiple projects and multiple users, possibly participating under multiple roles. For example, a clinician might import patient data to identify several potential lesion points in the patient's connectome. A modeler, working on the same project, tests these points for viability through whole brain simulation, based on the patient's connectome, and subsequent analysis of dynamical features. TVB also drives research forward: the simulator itself represents the culmination of several simulation frameworks in the modeling literature. The availability of the numerical methods, set of neural mass models and forward solutions allows for the construction of a wide range of brain-scale simulation scenarios. This paper briefly outlines the history and motivation for TVB, describing the framework and simulator, giving usage examples in the web UI and Python scripting.

Integrating neuroinformatics tools in TheVirtualBrain

PubMed Central

Woodman, M. Marmaduke; Pezard, Laurent; Domide, Lia; Knock, Stuart A.; Sanz-Leon, Paula; Mersmann, Jochen; McIntosh, Anthony R.; Jirsa, Viktor

2014-01-01

TheVirtualBrain (TVB) is a neuroinformatics Python package representing the convergence of clinical, systems, and theoretical neuroscience in the analysis, visualization and modeling of neural and neuroimaging dynamics. TVB is composed of a flexible simulator for neural dynamics measured across scales from local populations to large-scale dynamics measured by electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI), and core analytic and visualization functions, all accessible through a web browser user interface. A datatype system modeling neuroscientific data ties together these pieces with persistent data storage, based on a combination of SQL and HDF5. These datatypes combine with adapters allowing TVB to integrate other algorithms or computational systems. TVB provides infrastructure for multiple projects and multiple users, possibly participating under multiple roles. For example, a clinician might import patient data to identify several potential lesion points in the patient's connectome. A modeler, working on the same project, tests these points for viability through whole brain simulation, based on the patient's connectome, and subsequent analysis of dynamical features. TVB also drives research forward: the simulator itself represents the culmination of several simulation frameworks in the modeling literature. The availability of the numerical methods, set of neural mass models and forward solutions allows for the construction of a wide range of brain-scale simulation scenarios. This paper briefly outlines the history and motivation for TVB, describing the framework and simulator, giving usage examples in the web UI and Python scripting. PMID:24795617

MaMiCo: Transient multi-instance molecular-continuum flow simulation on supercomputers

NASA Astrophysics Data System (ADS)

Neumann, Philipp; Bian, Xin

2017-11-01

We present extensions of the macro-micro-coupling tool MaMiCo, which was designed to couple continuum fluid dynamics solvers with discrete particle dynamics. To enable local extraction of smooth flow field quantities especially on rather short time scales, sampling over an ensemble of molecular dynamics simulations is introduced. We provide details on these extensions including the transient coupling algorithm, open boundary forcing, and multi-instance sampling. Furthermore, we validate the coupling in Couette flow using different particle simulation software packages and particle models, i.e. molecular dynamics and dissipative particle dynamics. Finally, we demonstrate the parallel scalability of the molecular-continuum simulations by using up to 65 536 compute cores of the supercomputer Shaheen II located at KAUST. Program Files doi:http://dx.doi.org/10.17632/w7rgdrhb85.1 Licensing provisions: BSD 3-clause Programming language: C, C++ External routines/libraries: For compiling: SCons, MPI (optional) Subprograms used: ESPResSo, LAMMPS, ls1 mardyn, waLBerla For installation procedures of the MaMiCo interfaces, see the README files in the respective code directories located in coupling/interface/impl. Journal reference of previous version: P. Neumann, H. Flohr, R. Arora, P. Jarmatz, N. Tchipev, H.-J. Bungartz. MaMiCo: Software design for parallel molecular-continuum flow simulations, Computer Physics Communications 200: 324-335, 2016 Does the new version supersede the previous version?: Yes. The functionality of the previous version is completely retained in the new version. Nature of problem: Coupled molecular-continuum simulation for multi-resolution fluid dynamics: parts of the domain are resolved by molecular dynamics or another particle-based solver whereas large parts are covered by a mesh-based CFD solver, e.g. a lattice Boltzmann automaton. Solution method: We couple existing MD and CFD solvers via MaMiCo (macro-micro coupling tool). Data exchange and coupling algorithmics are abstracted and incorporated in MaMiCo. Once an algorithm is set up in MaMiCo, it can be used and extended, even if other solvers are used (as soon as the respective interfaces are implemented/available). Reasons for the new version: We have incorporated a new algorithm to simulate transient molecular-continuum systems and to automatically sample data over multiple MD runs that can be executed simultaneously (on, e.g., a compute cluster). MaMiCo has further been extended by an interface to incorporate boundary forcing to account for open molecular dynamics boundaries. Besides support for coupling with various MD and CFD frameworks, the new version contains a test case that allows to run molecular-continuum Couette flow simulations out-of-the-box. No external tools or simulation codes are required anymore. However, the user is free to switch from the included MD simulation package to LAMMPS. For details on how to run the transient Couette problem, see the file README in the folder coupling/tests, Remark on MaMiCo V1.1. Summary of revisions: Open boundary forcing; Multi-instance MD sampling; support for transient molecular-continuum systems Restrictions: Currently, only single-centered systems are supported. For access to the LAMMPS-based implementation of DPD boundary forcing, please contact Xin Bian, xin.bian@tum.de. Additional comments: Please see file license_mamico.txt for further details regarding distribution and advertising of this software.

Monte Carlo Methodology Serves Up a Software Success

NASA Technical Reports Server (NTRS)

2003-01-01

Widely used for the modeling of gas flows through the computation of the motion and collisions of representative molecules, the Direct Simulation Monte Carlo method has become the gold standard for producing research and engineering predictions in the field of rarefied gas dynamics. Direct Simulation Monte Carlo was first introduced in the early 1960s by Dr. Graeme Bird, a professor at the University of Sydney, Australia. It has since proved to be a valuable tool to the aerospace and defense industries in providing design and operational support data, as well as flight data analysis. In 2002, NASA brought to the forefront a software product that maintains the same basic physics formulation of Dr. Bird's method, but provides effective modeling of complex, three-dimensional, real vehicle simulations and parallel processing capabilities to handle additional computational requirements, especially in areas where computational fluid dynamics (CFD) is not applicable. NASA's Direct Simulation Monte Carlo Analysis Code (DAC) software package is now considered the Agency s premier high-fidelity simulation tool for predicting vehicle aerodynamics and aerothermodynamic environments in rarified, or low-density, gas flows.

Molecular Dynamics Simulation of Mahkota Dewa (Phaleria Macrocarpa) Extract in Subcritical Water Extraction Process

NASA Astrophysics Data System (ADS)

Hashim, N. A.; Mudalip, S. K. Abdul; Harun, N.; Che Man, R.; Sulaiman, S. Z.; Arshad, Z. I. M.; Shaarani, S. M.

2018-05-01

Mahkota Dewa (Phaleria Macrocarpa), a good source of saponin, flavanoid, polyphenol, alkaloid, and mangiferin has an extensive range of medicinal effects. The intermolecular interactions between solute and solvents such as hydrogen bonding considered as an important factor that affect the extraction of bioactive compounds. In this work, molecular dynamics simulation was performed to elucidate the hydrogen bonding exists between Mahkota Dewa extracts and water during subcritical extraction process. A bioactive compound in the Mahkota Dewa extract, namely mangiferin was selected as a model compound. The simulation was performed at 373 K and 4.0 MPa using COMPASS force field and Ewald summation method available in Material Studio 7.0 simulation package. The radial distribution functions (RDF) between mangiferin and water signify the presence of hydrogen bonding in the extraction process. The simulation of the binary mixture of mangiferin:water shows that strong hydrogen bonding was formed. It is suggested that, the intermolecular interaction between OH2O••HMR4(OH1) has been identified to be responsible for the mangiferin extraction process.

Efficient and Robust Optimization for Building Energy Simulation

PubMed Central

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-01-01

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell’s Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell’s method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell’s Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell’s Hybrid method presently used in HVACSIM+. PMID:27325907

Efficient and Robust Optimization for Building Energy Simulation.

PubMed

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-06-15

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell's Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell's method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell's Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell's Hybrid method presently used in HVACSIM+.

The Effect of C-Terminal Helix on the Stability of FF Domain Studied by Molecular Dynamics Simulation

PubMed Central

Zhao, Liling; Cao, Zanxia; Wang, Jihua

2012-01-01

To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain. PMID:22408419

The atomic simulation environment-a Python library for working with atoms.

PubMed

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The atomic simulation environment—a Python library for working with atoms

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

2017-07-01

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Simulation of magnetic particles in microfluidic channels

NASA Astrophysics Data System (ADS)

Gusenbauer, Markus; Schrefl, Thomas

2018-01-01

In the field of biomedicine the applications of magnetic beads have increased immensely in the last decade. Drug delivery, magnetic resonance imaging, bioseparation or hyperthermia are only a small excerpt of their usage. Starting from microscaled particles the research is focusing more and more on nanoscaled particles. We are investigating and validating a method for simulating magnetic beads in a microfluidic flow which will help to manipulate beads in a controlled and reproducible manner. We are using the soft-matter simulation package ESPResSo to simulate magnetic particle dynamics in a lattice Boltzmann flow and applied external magnetic fields. Laminar as well as turbulent flow conditions in microfluidic systems can be analyzed while particles tend to agglomerate due to magnetic interactions. The proposed simulation methods are validated with experiments from literature.

Simulating star clusters with the AMUSE software framework. I. Dependence of cluster lifetimes on model assumptions and cluster dissolution modes

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

Whitehead, Alfred J.; McMillan, Stephen L. W.; Vesperini, Enrico

2013-12-01

We perform a series of simulations of evolving star clusters using the Astrophysical Multipurpose Software Environment (AMUSE), a new community-based multi-physics simulation package, and compare our results to existing work. These simulations model a star cluster beginning with a King model distribution and a selection of power-law initial mass functions and contain a tidal cutoff. They are evolved using collisional stellar dynamics and include mass loss due to stellar evolution. After studying and understanding that the differences between AMUSE results and results from previous studies are understood, we explored the variation in cluster lifetimes due to the random realization noisemore » introduced by transforming a King model to specific initial conditions. This random realization noise can affect the lifetime of a simulated star cluster by up to 30%. Two modes of star cluster dissolution were identified: a mass evolution curve that contains a runaway cluster dissolution with a sudden loss of mass, and a dissolution mode that does not contain this feature. We refer to these dissolution modes as 'dynamical' and 'relaxation' dominated, respectively. For Salpeter-like initial mass functions, we determined the boundary between these two modes in terms of the dynamical and relaxation timescales.« less

An undergraduate laboratory activity on molecular dynamics simulations.

PubMed

Spitznagel, Benjamin; Pritchett, Paige R; Messina, Troy C; Goadrich, Mark; Rodriguez, Juan

2016-01-01

Vision and Change [AAAS, 2011] outlines a blueprint for modernizing biology education by addressing conceptual understanding of key concepts, such as the relationship between structure and function. The document also highlights skills necessary for student success in 21st century Biology, such as the use of modeling and simulation. Here we describe a laboratory activity that allows students to investigate the dynamic nature of protein structure and function through the use of a modeling technique known as molecular dynamics (MD). The activity takes place over two lab periods that are 3 hr each. The first lab period unpacks the basic approach behind MD simulations, beginning with the kinematic equations that all bioscience students learn in an introductory physics course. During this period students are taught rudimentary programming skills in Python while guided through simple modeling exercises that lead up to the simulation of the motion of a single atom. In the second lab period students extend concepts learned in the first period to develop skills in the use of expert MD software. Here students simulate and analyze changes in protein conformation resulting from temperature change, solvation, and phosphorylation. The article will describe how these activities can be carried out using free software packages, including Abalone and VMD/NAMD. © 2016 The International Union of Biochemistry and Molecular Biology.

Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides* #

PubMed Central

Yu, Hua; Wang, Mao-Jun; Xuan, Nan-Xia; Shang, Zhi-Cai; Wu, Jun

2015-01-01

Objective: To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Methods: Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. Results: The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding. Conclusions: van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues. PMID:26465136

`spup' - An R Package for Analysis of Spatial Uncertainty Propagation and Application to Trace Gas Emission Simulations

NASA Astrophysics Data System (ADS)

Sawicka, K.; Breuer, L.; Houska, T.; Santabarbara Ruiz, I.; Heuvelink, G. B. M.

2016-12-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Advances in uncertainty propagation analysis and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the `spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo techniques, as well as several uncertainty visualization functions. Here we will demonstrate that the 'spup' package is an effective and easy-to-use tool to be applied even in a very complex study case, and that it can be used in multi-disciplinary research and model-based decision support. As an example, we use the ecological LandscapeDNDC model to analyse propagation of uncertainties associated with spatial variability of the model driving forces such as rainfall, nitrogen deposition and fertilizer inputs. The uncertainty propagation is analysed for the prediction of emissions of N2O and CO2 for a German low mountainous, agriculturally developed catchment. The study tests the effect of spatial correlations on spatially aggregated model outputs, and could serve as an advice for developing best management practices and model improvement strategies.

ALI: A CSSL/multiprocessor software interface

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

Makoui, A.; Karplus, W.J.

ALI (A Language Interface) is a software package which translates simulation models expressed in one of the higher-level languages, CSSL-IV or ACSL, into sequences of instructions for each processor of a network of microprocessors. The partitioning of the source program among the processors is automatically accomplished. The code is converted into a data flow graph, analyzed and divided among the processors to minimize the overall execution time in the presence of interprocessor communication delays. This paper describes ALI from the user's point of view and includes a detailed example of the application of ALI to a specific dynamic system simulation.

Simulation Environment for Orion Launch Abort System Control Design Studies

NASA Technical Reports Server (NTRS)

McMinn, J. Dana; Jackson, E. Bruce; Christhilf, David M.

2007-01-01

The development and use of an interactive environment to perform control system design and analysis of the proposed Crew Exploration Vehicle Launch Abort System is described. The environment, built using a commercial dynamic systems design package, includes use of an open-source configuration control software tool and a collaborative wiki to coordinate between the simulation developers, control law developers and users. A method for switching between multiple candidate control laws and vehicle configurations is described. Aerodynamic models, especially in a development program, change rapidly, so a means for automating the implementation of new aerodynamic models is described.

Simulation and Analyses of Multi-Body Separation in Launch Vehicle Staging Environment

NASA Technical Reports Server (NTRS)

Pamadi, Bandu N.; Hotchko, Nathaniel J.; Samareh, Jamshid; Covell, Peter F.; Tartabini, Paul V.

2006-01-01

The development of methodologies, techniques, and tools for analysis and simulation of multi-body separation is critically needed for successful design and operation of next generation launch vehicles. As a part of this activity, ConSep simulation tool is being developed. ConSep is a generic MATLAB-based front-and-back-end to the commercially available ADAMS. solver, an industry standard package for solving multi-body dynamic problems. This paper discusses the 3-body separation capability in ConSep and its application to the separation of the Shuttle Solid Rocket Boosters (SRBs) from the External Tank (ET) and the Orbiter. The results are compared with STS-1 flight data.

Robotics On-Board Trainer (ROBoT)

NASA Technical Reports Server (NTRS)

Johnson, Genevieve; Alexander, Greg

2013-01-01

ROBoT is an on-orbit version of the ground-based Dynamics Skills Trainer (DST) that astronauts use for training on a frequent basis. This software consists of two primary software groups. The first series of components is responsible for displaying the graphical scenes. The remaining components are responsible for simulating the Mobile Servicing System (MSS), the Japanese Experiment Module Remote Manipulator System (JEMRMS), and the H-II Transfer Vehicle (HTV) Free Flyer Robotics Operations. The MSS simulation software includes: Robotic Workstation (RWS) simulation, a simulation of the Space Station Remote Manipulator System (SSRMS), a simulation of the ISS Command and Control System (CCS), and a portion of the Portable Computer System (PCS) software necessary for MSS operations. These components all run under the CentOS4.5 Linux operating system. The JEMRMS simulation software includes real-time, HIL, dynamics, manipulator multi-body dynamics, and a moving object contact model with Tricks discrete time scheduling. The JEMRMS DST will be used as a functional proficiency and skills trainer for flight crews. The HTV Free Flyer Robotics Operations simulation software adds a functional simulation of HTV vehicle controllers, sensors, and data to the MSS simulation software. These components are intended to support HTV ISS visiting vehicle analysis and training. The scene generation software will use DOUG (Dynamic On-orbit Ubiquitous Graphics) to render the graphical scenes. DOUG runs on a laptop running the CentOS4.5 Linux operating system. DOUG is an Open GL-based 3D computer graphics rendering package. It uses pre-built three-dimensional models of on-orbit ISS and space shuttle systems elements, and provides realtime views of various station and shuttle configurations.

Pizza.py Toolkit

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

Plimpton, Steve; Jones, Matt; Crozier, Paul

2006-01-01

Pizza.py is a loosely integrated collection of tools, many of which provide support for the LAMMPS molecular dynamics and ChemCell cell modeling packages. There are tools to create input files. convert between file formats, process log and dump files, create plots, and visualize and animate simulation snapshots. Software packages that are wrapped by Pizza.py. so they can invoked from within Python, include GnuPlot, MatLab, Raster3d. and RasMol. Pizza.py is written in Python and runs on any platform that supports Python. Pizza.py enhances the standard Python interpreter in a few simple ways. Its tools are Python modules which can be invokedmore » interactively, from scripts, or from GUIs when appropriate. Some of the tools require additional Python packages to be installed as part of the users Python. Others are wrappers on software packages (as listed above) which must be available on the users system. It is easy to modify or extend Pizza.py with new functionality or new tools, which need not have anything to do with LAMMPS or ChemCell.« less

HNBody: A Simulation Package for Hierarchical N-Body Systems

NASA Astrophysics Data System (ADS)

Rauch, Kevin P.

2018-04-01

HNBody (http://www.hnbody.org/) is an extensible software package forintegrating the dynamics of N-body systems. Although general purpose, itincorporates several features and algorithms particularly well-suited tosystems containing a hierarchy (wide dynamic range) of masses. HNBodyversion 1 focused heavily on symplectic integration of nearly-Kepleriansystems. Here I describe the capabilities of the redesigned and expandedpackage version 2, which includes: symplectic integrators up to eighth order(both leap frog and Wisdom-Holman type methods), with symplectic corrector andclose encounter support; variable-order, variable-timestep Bulirsch-Stoer andStörmer integrators; post-Newtonian and multipole physics options; advancedround-off control for improved long-term stability; multi-threading and SIMDvectorization enhancements; seamless availability of extended precisionarithmetic for all calculations; extremely flexible configuration andoutput. Tests of the physical correctness of the algorithms are presentedusing JPL Horizons ephemerides (https://ssd.jpl.nasa.gov/?horizons) andpreviously published results for reference. The features and performanceof HNBody are also compared to several other freely available N-body codes,including MERCURY (Chambers), SWIFT (Levison & Duncan) and WHFAST (Rein &Tamayo).

Optimizing the Performance of Reactive Molecular Dynamics Simulations for Multi-core Architectures

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

Aktulga, Hasan Metin; Coffman, Paul; Shan, Tzu-Ray

2015-12-01

Hybrid parallelism allows high performance computing applications to better leverage the increasing on-node parallelism of modern supercomputers. In this paper, we present a hybrid parallel implementation of the widely used LAMMPS/ReaxC package, where the construction of bonded and nonbonded lists and evaluation of complex ReaxFF interactions are implemented efficiently using OpenMP parallelism. Additionally, the performance of the QEq charge equilibration scheme is examined and a dual-solver is implemented. We present the performance of the resulting ReaxC-OMP package on a state-of-the-art multi-core architecture Mira, an IBM BlueGene/Q supercomputer. For system sizes ranging from 32 thousand to 16.6 million particles, speedups inmore » the range of 1.5-4.5x are observed using the new ReaxC-OMP software. Sustained performance improvements have been observed for up to 262,144 cores (1,048,576 processes) of Mira with a weak scaling efficiency of 91.5% in larger simulations containing 16.6 million particles.« less

Effect of train vibration on settlement of soil: A numerical analysis

NASA Astrophysics Data System (ADS)

Tiong, Kah-Yong; Ling, Felix Ngee-Leh; Talib, Zaihasra Abu

2017-10-01

The drastic development of transit system caused the influence of ground-borne vibrations induced by train on ground settlement became concern problem nowadays. The purpose of this study is to investigate soil settlement caused by train vibration. To facilitate this study, computer simulation of soil dynamic response using commercial finite element package - PLAXIS 2D was performed to simulate track-subgrade system together with dynamic train load under three different conditions. The results of simulation analysis established the facts that the soil deformation increased with raising in water level. This phenomenon happens because the increasing water level not only induced greater excess pore water pressure but also reduced stiffness of soil. Furthermore, the simulation analysis also deduced that the soil settlement was reduced by placing material with high stiffness between the subgrade and the ballast layer since material with high stiffness was able to dissipate energy efficiently due to its high bearing capacity, thus protecting the subgrade from deteriorating. The simulation analysis result also showed that the soil dynamic response increased with the increase in the speed of train and a noticeable amplification in soil deformation occurred as the train speed approaches the Rayleigh wave velocity of the track subgrade system. This is due to the fact that dynamic train load depend on both the self-weight of the train and the dynamic component due to inertial effects associated with the train speed. Thus, controlling the train speeds under critical velocity of track-subgrade system is able to ensure the safety of train operation as it prevents track-ground resonance and dramatic ground.

Modeling Nitrogen Dynamics in a Waste Stabilization Pond System Using Flexible Modeling Environment with MCMC.

PubMed

Mukhtar, Hussnain; Lin, Yu-Pin; Shipin, Oleg V; Petway, Joy R

2017-07-12

This study presents an approach for obtaining realization sets of parameters for nitrogen removal in a pilot-scale waste stabilization pond (WSP) system. The proposed approach was designed for optimal parameterization, local sensitivity analysis, and global uncertainty analysis of a dynamic simulation model for the WSP by using the R software package Flexible Modeling Environment (R-FME) with the Markov chain Monte Carlo (MCMC) method. Additionally, generalized likelihood uncertainty estimation (GLUE) was integrated into the FME to evaluate the major parameters that affect the simulation outputs in the study WSP. Comprehensive modeling analysis was used to simulate and assess nine parameters and concentrations of ON-N, NH₃-N and NO₃-N. Results indicate that the integrated FME-GLUE-based model, with good Nash-Sutcliffe coefficients (0.53-0.69) and correlation coefficients (0.76-0.83), successfully simulates the concentrations of ON-N, NH₃-N and NO₃-N. Moreover, the Arrhenius constant was the only parameter sensitive to model performances of ON-N and NH₃-N simulations. However, Nitrosomonas growth rate, the denitrification constant, and the maximum growth rate at 20 °C were sensitive to ON-N and NO₃-N simulation, which was measured using global sensitivity.

Signalling product healthiness through symbolic package cues: Effects of package shape and goal congruence on consumer behaviour.

PubMed

van Ooijen, Iris; Fransen, Marieke L; Verlegh, Peeter W J; Smit, Edith G

2017-02-01

Three studies show that product packaging shape serves as a cue that communicates healthiness of food products. Inspired by embodiment accounts, we show that packaging that simulates a slim body shape acts as a symbolic cue for product healthiness (e.g., low in calories), as opposed to packaging that simulates a wide body shape. Furthermore, we show that the effect of slim package shape on consumer behaviour is goal dependent. Whereas simulation of a slim (vs. wide) body shape increases choice likelihood and product attitude when consumers have a health-relevant shopping goal, packaging shape does not affect these outcomes when consumers have a hedonic shopping goal. In Study 3, we adopt a realistic shopping paradigm using a shelf with authentic products, and find that a slim (as opposed to wide) package shape increases on-shelf product recognition and increases product attitude for healthy products. We discuss results and implications regarding product positioning and the packaging design process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Influence of different materials on the thermal behavior of a CDIP-8 ceramic package

NASA Astrophysics Data System (ADS)

Weide, Kirsten; Keck, Christian

1999-08-01

The temperature distribution inside a package is determined by the heat transfer from the package to the ambient, depending on the heat conductivities of the different used materials. With the help of finite element simulations the thermal behavior of the package can be characterized. In precise simulations convection and radiation effects have to be taken into account. In this paper the influence of different materials like the ceramic, the pin and die attach material and adhesive material between the chip and the die attach on the thermal resistance of the ceramic package will be investigated. A finite element model of the ceramic package including a voltage regulator on the chip was created. The simulations were carried out with the finite element program ANSYS. An easy way to take the radiation effect into account, which normally is difficult to handle in the simulation, will be shown. The results of the simulations are verified by infrared measurements. A comparison of the thermal resistance between the best case and worst case for different package materials was done. The thermal conductivity of the ceramic material shows the strongest influence on the thermal resistance.

Dynamic rupture scenarios from Sumatra to Iceland - High-resolution earthquake source physics on natural fault systems

NASA Astrophysics Data System (ADS)

Gabriel, A. A.; Madden, E. H.; Ulrich, T.; Wollherr, S.

2016-12-01

Capturing the observed complexity of earthquake sources in dynamic rupture simulations may require: non-linear fault friction, thermal and fluid effects, heterogeneous fault stress and strength initial conditions, fault curvature and roughness, on- and off-fault non-elastic failure. All of these factors have been independently shown to alter dynamic rupture behavior and thus possibly influence the degree of realism attainable via simulated ground motions. In this presentation we will show examples of high-resolution earthquake scenarios, e.g. based on the 2004 Sumatra-Andaman Earthquake and a potential rupture of the Husavik-Flatey fault system in Northern Iceland. The simulations combine a multitude of representations of source complexity at the necessary spatio-temporal resolution enabled by excellent scalability on modern HPC systems. Such simulations allow an analysis of the dominant factors impacting earthquake source physics and ground motions given distinct tectonic settings or distinct focuses of seismic hazard assessment. Across all simulations, we find that fault geometry concurrently with the regional background stress state provide a first order influence on source dynamics and the emanated seismic wave field. The dynamic rupture models are performed with SeisSol, a software package based on an ADER-Discontinuous Galerkin scheme for solving the spontaneous dynamic earthquake rupture problem with high-order accuracy in space and time. Use of unstructured tetrahedral meshes allows for a realistic representation of the non-planar fault geometry, subsurface structure and bathymetry. The results presented highlight the fact that modern numerical methods are essential to further our understanding of earthquake source physics and complement both physic-based ground motion research and empirical approaches in seismic hazard analysis.

Dynamic rupture scenarios from Sumatra to Iceland - High-resolution earthquake source physics on natural fault systems

NASA Astrophysics Data System (ADS)

Gabriel, Alice-Agnes; Madden, Elizabeth H.; Ulrich, Thomas; Wollherr, Stephanie

2017-04-01

Capturing the observed complexity of earthquake sources in dynamic rupture simulations may require: non-linear fault friction, thermal and fluid effects, heterogeneous fault stress and fault strength initial conditions, fault curvature and roughness, on- and off-fault non-elastic failure. All of these factors have been independently shown to alter dynamic rupture behavior and thus possibly influence the degree of realism attainable via simulated ground motions. In this presentation we will show examples of high-resolution earthquake scenarios, e.g. based on the 2004 Sumatra-Andaman Earthquake, the 1994 Northridge earthquake and a potential rupture of the Husavik-Flatey fault system in Northern Iceland. The simulations combine a multitude of representations of source complexity at the necessary spatio-temporal resolution enabled by excellent scalability on modern HPC systems. Such simulations allow an analysis of the dominant factors impacting earthquake source physics and ground motions given distinct tectonic settings or distinct focuses of seismic hazard assessment. Across all simulations, we find that fault geometry concurrently with the regional background stress state provide a first order influence on source dynamics and the emanated seismic wave field. The dynamic rupture models are performed with SeisSol, a software package based on an ADER-Discontinuous Galerkin scheme for solving the spontaneous dynamic earthquake rupture problem with high-order accuracy in space and time. Use of unstructured tetrahedral meshes allows for a realistic representation of the non-planar fault geometry, subsurface structure and bathymetry. The results presented highlight the fact that modern numerical methods are essential to further our understanding of earthquake source physics and complement both physic-based ground motion research and empirical approaches in seismic hazard analysis.

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

PubMed

Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

2012-05-01

MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

Space life support engineering program

NASA Technical Reports Server (NTRS)

Seagrave, Richard C.

1992-01-01

A comprehensive study to develop software to simulate the dynamic operation of water reclamation systems in long-term closed-loop life support systems is being carried out as part of an overall program for the design of systems for a moon station or a Mars voyage. This project is being done in parallel with a similar effort in the Department of Chemistry to develop durable accurate low-cost sensors for monitoring of trace chemical and biological species in recycled water supplies. Aspen-Plus software is being used on a group of high-performance work stations to develop the steady state descriptions for a number of existing technologies. Following completion, a dynamic simulation package will be developed for determining the response of such systems to changes in the metabolic needs of the crew and to upsets in system hardware performance.

Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Karpusenka, Vadzim; Moradi, Mahmoud; Roland, Christopher; Sagui, Celeste

We discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential. It is characterized by a small number of control parameters and an O(t) numerical cost with simulation time t. The method naturally allows for extensions based on multiple walkers and replica exchange mechanism. The workings of the method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short β-turn peptide. ABMD has been implemented into the latest version (Case et al., AMBER 10; University of California: San Francisco, 2008) of the AMBER software package and is freely available to the simulation community.

Dynamic Modeling and Control of Nuclear Reactors Coupled to Closed-Loop Brayton Cycle Systems using SIMULINK{sup TM}

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

Wright, Steven A.; Sanchez, Travis

2005-02-06

The operation of space reactors for both in-space and planetary operations will require unprecedented levels of autonomy and control. Development of these autonomous control systems will require dynamic system models, effective control methodologies, and autonomous control logic. This paper briefly describes the results of reactor, power-conversion, and control models that are implemented in SIMULINK{sup TM} (Simulink, 2004). SIMULINK{sup TM} is a development environment packaged with MatLab{sup TM} (MatLab, 2004) that allows the creation of dynamic state flow models. Simulation modules for liquid metal, gas cooled reactors, and electrically heated systems have been developed, as have modules for dynamic power-conversion componentsmore » such as, ducting, heat exchangers, turbines, compressors, permanent magnet alternators, and load resistors. Various control modules for the reactor and the power-conversion shaft speed have also been developed and simulated. The modules are compiled into libraries and can be easily connected in different ways to explore the operational space of a number of potential reactor, power-conversion system configurations, and control approaches. The modularity and variability of these SIMULINK{sup TM} models provides a way to simulate a variety of complete power generation systems. To date, both Liquid Metal Reactors (LMR), Gas Cooled Reactors (GCR), and electric heaters that are coupled to gas-dynamics systems and thermoelectric systems have been simulated and are used to understand the behavior of these systems. Current efforts are focused on improving the fidelity of the existing SIMULINK{sup TM} modules, extending them to include isotopic heaters, heat pipes, Stirling engines, and on developing state flow logic to provide intelligent autonomy. The simulation code is called RPC-SIM (Reactor Power and Control-Simulator)« less

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

PubMed

Noel, Jeffrey K; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L; Onuchic, José N; Whitford, Paul C

2016-03-01

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

NiftySim: A GPU-based nonlinear finite element package for simulation of soft tissue biomechanics.

PubMed

Johnsen, Stian F; Taylor, Zeike A; Clarkson, Matthew J; Hipwell, John; Modat, Marc; Eiben, Bjoern; Han, Lianghao; Hu, Yipeng; Mertzanidou, Thomy; Hawkes, David J; Ourselin, Sebastien

2015-07-01

NiftySim, an open-source finite element toolkit, has been designed to allow incorporation of high-performance soft tissue simulation capabilities into biomedical applications. The toolkit provides the option of execution on fast graphics processing unit (GPU) hardware, numerous constitutive models and solid-element options, membrane and shell elements, and contact modelling facilities, in a simple to use library. The toolkit is founded on the total Lagrangian explicit dynamics (TLEDs) algorithm, which has been shown to be efficient and accurate for simulation of soft tissues. The base code is written in C[Formula: see text], and GPU execution is achieved using the nVidia CUDA framework. In most cases, interaction with the underlying solvers can be achieved through a single Simulator class, which may be embedded directly in third-party applications such as, surgical guidance systems. Advanced capabilities such as contact modelling and nonlinear constitutive models are also provided, as are more experimental technologies like reduced order modelling. A consistent description of the underlying solution algorithm, its implementation with a focus on GPU execution, and examples of the toolkit's usage in biomedical applications are provided. Efficient mapping of the TLED algorithm to parallel hardware results in very high computational performance, far exceeding that available in commercial packages. The NiftySim toolkit provides high-performance soft tissue simulation capabilities using GPU technology for biomechanical simulation research applications in medical image computing, surgical simulation, and surgical guidance applications.

Guidelines for the analysis of free energy calculations.

PubMed

Klimovich, Pavel V; Shirts, Michael R; Mobley, David L

2015-05-01

Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.

Numerical Study of Damage Propagation and Dynamic Fracture in Sapphire

DTIC Science & Technology

2016-08-30

NOTICES Disclaimers The findings in this report are not to be construed as an official Department of the Army position unless so...package by using three- dimensional, 180 degrees (reflective) modeling and simulation. This study reports on the ability and the modification of...existing strength and failure material models of Al2O3 to be used as sapphire models for duplication of the experimental fracture and wave propagation in

A new force field including charge directionality for TMAO in aqueous solution

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

Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes

We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O{sub TMAO}) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O{sub TMAO} to mimic the O{sub TMAO} lone pairs and we migrate the negative charge on the O{sub TMAO} to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasingmore » TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.« less

Numerical simulations of earthquakes and the dynamics of fault systems using the Finite Element method.

NASA Astrophysics Data System (ADS)

Kettle, L. M.; Mora, P.; Weatherley, D.; Gross, L.; Xing, H.

2006-12-01

Simulations using the Finite Element method are widely used in many engineering applications and for the solution of partial differential equations (PDEs). Computational models based on the solution of PDEs play a key role in earth systems simulations. We present numerical modelling of crustal fault systems where the dynamic elastic wave equation is solved using the Finite Element method. This is achieved using a high level computational modelling language, escript, available as open source software from ACcESS (Australian Computational Earth Systems Simulator), the University of Queensland. Escript is an advanced geophysical simulation software package developed at ACcESS which includes parallel equation solvers, data visualisation and data analysis software. The escript library was implemented to develop a flexible Finite Element model which reliably simulates the mechanism of faulting and the physics of earthquakes. Both 2D and 3D elastodynamic models are being developed to study the dynamics of crustal fault systems. Our final goal is to build a flexible model which can be applied to any fault system with user-defined geometry and input parameters. To study the physics of earthquake processes, two different time scales must be modelled, firstly the quasi-static loading phase which gradually increases stress in the system (~100years), and secondly the dynamic rupture process which rapidly redistributes stress in the system (~100secs). We will discuss the solution of the time-dependent elastic wave equation for an arbitrary fault system using escript. This involves prescribing the correct initial stress distribution in the system to simulate the quasi-static loading of faults to failure; determining a suitable frictional constitutive law which accurately reproduces the dynamics of the stick/slip instability at the faults; and using a robust time integration scheme. These dynamic models generate data and information that can be used for earthquake forecasting.

Ground Simulation of an Autonomous Satellite Rendezvous and Tracking System Using Dual Robotic Systems

NASA Technical Reports Server (NTRS)

Trube, Matthew J.; Hyslop, Andrew M.; Carignan, Craig R.; Easley, Joseph W.

2012-01-01

A hardware-in-the-loop ground system was developed for simulating a robotic servicer spacecraft tracking a target satellite at short range. A relative navigation sensor package "Argon" is mounted on the end-effector of a Fanuc 430 manipulator, which functions as the base platform of the robotic spacecraft servicer. Machine vision algorithms estimate the pose of the target spacecraft, mounted on a Rotopod R-2000 platform, relay the solution to a simulation of the servicer spacecraft running in "Freespace", which performs guidance, navigation and control functions, integrates dynamics, and issues motion commands to a Fanuc platform controller so that it tracks the simulated servicer spacecraft. Results will be reviewed for several satellite motion scenarios at different ranges. Key words: robotics, satellite, servicing, guidance, navigation, tracking, control, docking.

Thermal conductance at atomically clean and disordered silicon/aluminum interfaces: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Ih Choi, Woon; Kim, Kwiseon; Narumanchi, Sreekant

2012-09-01

Thermal resistance between layers impedes effective heat dissipation in electronics packaging applications. Thermal conductance for clean and disordered interfaces between silicon (Si) and aluminum (Al) was computed using realistic Si/Al interfaces and classical molecular dynamics with the modified embedded atom method potential. These realistic interfaces, which include atomically clean as well as disordered interfaces, were obtained using density functional theory. At 300 K, the magnitude of interfacial conductance due to phonon-phonon scattering obtained from the classical molecular dynamics simulations was approximately five times higher than the conductance obtained using analytical elastic diffuse mismatch models. Interfacial disorder reduced the thermal conductance due to increased phonon scattering with respect to the atomically clean interface. Also, the interfacial conductance, due to electron-phonon scattering at the interface, was greater than the conductance due to phonon-phonon scattering. This indicates that phonon-phonon scattering is the bottleneck for interfacial transport at the semiconductor/metal interfaces. The molecular dynamics modeling predictions for interfacial thermal conductance for a 5-nm disordered interface between Si/Al were in-line with recent experimental data in the literature.

Molecular Dynamics Simulation and Analysis of the Antimicrobial Peptide-Lipid Bilayer Interactions.

PubMed

Arasteh, Shima; Bagheri, Mojtaba

2017-01-01

A great deal of research has been undertaken in order to discover antimicrobial peptides (AMPs) with unexploited mechanisms of action to counteract the health-threatening issues associated with bacterial resistance. The intrinsic effectiveness of AMPs is strongly influenced by their initial interactions with the bacterial cell membrane. Understanding these interactions in the atomistic details is important for the design of the less prone bacteria-resistant peptides. However, these studies always require labor-intensive and difficult steps. With this regard, modeling studies of the AMPs binding to simple lipid membrane systems, e.g., lipid bilayers, is of great advantage. In this chapter, we present an applicable step-by-step protocol to run the molecular dynamics (MD) simulation of the interaction between cyclo-RRWFWR (c-WFW) (a small cyclic AMP) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer using the Groningen machine for chemical simulations (GROMACS) package. The protocol as described here may simply be optimized for other peptide-lipid systems of interest.

A dynamic simulation based water resources education tool.

PubMed

Williams, Alison; Lansey, Kevin; Washburne, James

2009-01-01

Educational tools to assist the public in recognizing impacts of water policy in a realistic context are not generally available. This project developed systems with modeling-based educational decision support simulation tools to satisfy this need. The goal of this model is to teach undergraduate students and the general public about the implications of common water management alternatives so that they can better understand or become involved in water policy and make more knowledgeable personal or community decisions. The model is based on Powersim, a dynamic simulation software package capable of producing web-accessible, intuitive, graphic, user-friendly interfaces. Modules are included to represent residential, agricultural, industrial, and turf uses, as well as non-market values, water quality, reservoir, flow, and climate conditions. Supplementary materials emphasize important concepts and lead learners through the model, culminating in an open-ended water management project. The model is used in a University of Arizona undergraduate class and within the Arizona Master Watershed Stewards Program. Evaluation results demonstrated improved understanding of concepts and system interactions, fulfilling the project's objectives.

Molecular-dynamics simulations of crosslinking and confinement effects on structure, segmental mobility and mechanics of filled elastomers

NASA Astrophysics Data System (ADS)

Davris, Theodoros; Lyulin, Alexey V.

2016-05-01

The significant drop of the storage modulus under uniaxial deformation (Payne effect) restrains the performance of the elastomer-based composites and the development of possible new applications. In this paper molecular-dynamics (MD) computer simulations using LAMMPS MD package have been performed to study the mechanical properties of a coarse-grained model of this family of nanocomposite materials. Our goal is to provide simulational insights into the viscoelastic properties of filled elastomers, and try to connect the macroscopic mechanics with composite microstructure, the strength of the polymer-filler interactions and the polymer mobility at different scales. To this end we simulate random copolymer films capped between two infinite solid (filler aggregate) walls. We systematically vary the strength of the polymer-substrate adhesion interactions, degree of polymer confinement (film thickness), polymer crosslinking density, and study their influence on the equilibrium and non-equilibrium structure, segmental dynamics, and the mechanical properties of the simulated systems. The glass-transition temperature increases once the mesh size became smaller than the chain radius of gyration; otherwise it remained invariant to mesh-size variations. This increase in the glass-transition temperature was accompanied by a monotonic slowing-down of segmental dynamics on all studied length scales. This observation is attributed to the correspondingly decreased width of the bulk density layer that was obtained in films whose thickness was larger than the end-to-end distance of the bulk polymer chains. To test this hypothesis additional simulations were performed in which the crystalline walls were replaced with amorphous or rough walls.

Dynamics and Solubility of He and CO 2 in Brine

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

Ho, Tuan Anh; Tenney, Craig M.

2016-09-01

Molecular dynamics simulation was implemented using LAMMPS simulation package (1) to study the diffusivity of He 3 and CO 2 in NaCl aqueous solution. To simulate at infinite dilute gas concentration, we placed one He 3 or CO 2 molecule in an initial simulation box of 24x24x33Å 3 containing 512 water molecules and a certain number of NaCl molecules depending on the concentration. Initial configuration was set up by placing water, NaCl, and gas molecules into different regions in the simulation box. Calculating diffusion coefficient for one He or CO 2 molecule consistently yields poor results. To overcome this, formore » each simulation at specific conditions (i.e., temperature, pressure, and NaCl concentration), we conducted 50 simulations initiated from 50 different configurations. These configurations are obtained by performing the simulation starting from the initial configuration mentioned above in the NVE ensemble (i.e., constant number of particles, volume, and energy). for 100,000 time steps and collecting one configuration every 2,000 times step. The output temperature of this simulation is about 500K. The collected configurations were then equilibrated for 2ns in the NPT ensemble (i.e., constant number of particles, pressure, and temperature) followed by 9ns simulations in the NVT ensemble (i.e., constant number of particles, volume, and temperature). The time step is 1fs for all simulations.« less

pysimm: A Python Package for Simulation of Molecular Systems

NASA Astrophysics Data System (ADS)

Fortunato, Michael; Colina, Coray

pysimm, short for python simulation interface for molecular modeling, is a python package designed to facilitate the structure generation and simulation of molecular systems through convenient and programmatic access to object-oriented representations of molecular system data. This poster presents core features of pysimm and design philosophies that highlight a generalized methodology for incorporation of third-party software packages through API interfaces. The integration with the LAMMPS simulation package is explained to demonstrate this methodology. pysimm began as a back-end python library that powered a cloud-based application on nanohub.org for amorphous polymer simulation. The extension from a specific application library to general purpose simulation interface is explained. Additionally, this poster highlights the rapid development of new applications to construct polymer chains capable of controlling chain morphology such as molecular weight distribution and monomer composition.

Study of silicon crystal surface formation based on molecular dynamics simulation results

NASA Astrophysics Data System (ADS)

Barinovs, G.; Sabanskis, A.; Muiznieks, A.

2014-04-01

The equilibrium shape of <110>-oriented single crystal silicon nanowire, 8 nm in cross-section, was found from molecular dynamics simulations using LAMMPS molecular dynamics package. The calculated shape agrees well to the shape predicted from experimental observations of nanocavities in silicon crystals. By parametrization of the shape and scaling to a known value of {111} surface energy, Wulff form for solid-vapor interface was obtained. The Wulff form for solid-liquid interface was constructed using the same model of the shape as for the solid-vapor interface. The parameters describing solid-liquid interface shape were found using values of surface energies in low-index directions known from published molecular dynamics simulations. Using an experimental value of the liquid-vapor interface energy for silicon and graphical solution of Herring's equation, we constructed angular diagram showing relative equilibrium orientation of solid-liquid, liquid-vapor and solid-vapor interfaces at the triple phase line. The diagram gives quantitative predictions about growth angles for different growth directions and formation of facets on the solid-liquid and solid-vapor interfaces. The diagram can be used to describe growth ridges appearing on the crystal surface grown from a melt. Qualitative comparison to the ridges of a Float zone silicon crystal cone is given.

INDOOR AIR QUALITY AND INHALATION EXPOSURE - SIMULATION TOOL KIT

EPA Science Inventory

A Microsoft Windows-based indoor air quality (IAQ) simulation software package is presented. Named Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short, this package complements and supplements existing IAQ simulation programs and is desi...

Effectiveness of combination packages for HIV-1 prevention in sub-Saharan Africa depends on partnership network structure: a mathematical modelling study.

PubMed

Jenness, Samuel M; Goodreau, Steven M; Morris, Martina; Cassels, Susan

2016-12-01

Combination packages for HIV prevention can leverage the effectiveness of biomedical and behavioural elements to lower disease incidence with realistic targets for individual and population risk reduction. We investigated how sexual network structures can maximise the effectiveness of a package targeting sexually active adults in sub-Saharan Africa (SSA) with intervention components for medical male circumcision (MMC) and sexual partnership concurrency (having >1 ongoing partner). Network-based mathematical models of HIV type 1 (HIV-1) transmission dynamics among heterosexual couples were used to explore how changes to MMC alone and in combination with changes to concurrency impacted endemic HIV-1 prevalence and incidence. Starting from a base model parameterised from empirical data from West Africa, we simulated the prevalence of circumcision from 10% to 90% and concurrency was modelled at four discrete levels corresponding to values observed across SSA. MMC and concurrency could contribute to the empirical variation in HIV-1 disease prevalence across SSA. Small reductions in concurrency resulted in large declines in HIV-1 prevalence. Scaling up circumcision in low-concurrency settings yields a greater relative benefit, but the absolute number of infections averted depends on both the circumcision coverage and baseline incidence. Epidemic extinction with this package will require substantial scale-up of MMC in low-concurrency settings. Dynamic sexual network structure should be considered in the design and targeting of MMC within combination HIV-1 prevention packages. Realistic levels of coverage for these packages within southern Africa could lead to a reduction of incidence to the low levels observed in western Africa, and possibly, epidemic extinction. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

NASA Astrophysics Data System (ADS)

Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

2015-12-01

We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

PubMed

Heo, Lim; Feig, Michael

2018-03-15

Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. feig@msu.edu. Supplementary data are available at Bioinformatics online.

Simulation of the Tsunami Resulting from the M 9.2 2004 Sumatra-Andaman Earthquake - Dynamic Rupture vs. Seismic Inversion Source Model

NASA Astrophysics Data System (ADS)

Vater, Stefan; Behrens, Jörn

2017-04-01

Simulations of historic tsunami events such as the 2004 Sumatra or the 2011 Tohoku event are usually initialized using earthquake sources resulting from inversion of seismic data. Also, other data from ocean buoys etc. is sometimes included in the derivation of the source model. The associated tsunami event can often be well simulated in this way, and the results show high correlation with measured data. However, it is unclear how the derived source model compares to the particular earthquake event. In this study we use the results from dynamic rupture simulations obtained with SeisSol, a software package based on an ADER-DG discretization solving the spontaneous dynamic earthquake rupture problem with high-order accuracy in space and time. The tsunami model is based on a second-order Runge-Kutta discontinuous Galerkin (RKDG) scheme on triangular grids and features a robust wetting and drying scheme for the simulation of inundation events at the coast. Adaptive mesh refinement enables the efficient computation of large domains, while at the same time it allows for high local resolution and geometric accuracy. The results are compared to measured data and results using earthquake sources based on inversion. With the approach of using the output of actual dynamic rupture simulations, we can estimate the influence of different earthquake parameters. Furthermore, the comparison to other source models enables a thorough comparison and validation of important tsunami parameters, such as the runup at the coast. This work is part of the ASCETE (Advanced Simulation of Coupled Earthquake and Tsunami Events) project, which aims at an improved understanding of the coupling between the earthquake and the generated tsunami event.

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

PubMed

Adalsteinsson, David; McMillen, David; Elston, Timothy C

2004-03-08

Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

MODFLOW-OWHM v2: The next generation of fully integrated hydrologic simulation software

NASA Astrophysics Data System (ADS)

Boyce, S. E.; Hanson, R. T.; Ferguson, I. M.; Reimann, T.; Henson, W.; Mehl, S.; Leake, S.; Maddock, T.

2016-12-01

The One-Water Hydrologic Flow Model (One-Water) is a MODFLOW-based integrated hydrologic flow model designed for the analysis of a broad range of conjunctive-use and climate-related issues. One-Water fully links the movement and use of groundwater, surface water, and imported water for consumption by agriculture and natural vegetation on the landscape, and for potable and other uses within a supply-and-demand framework. One-Water includes linkages for deformation-, flow-, and head-dependent flows; additional observation and parameter options for higher-order calibrations; and redesigned code for facilitation of self-updating models and faster simulation run times. The next version of One-Water, currently under development, will include a new surface-water operations module that simulates dynamic reservoir operations, a new sustainability analysis package that facilitates the estimation and simulation of reduced storage depletion and captured discharge, a conduit-flow process for karst aquifers and leaky pipe networks, a soil zone process that adds an enhanced infiltration process, interflow, deep percolation and soil moisture, and a new subsidence and aquifer compaction package. It will also include enhancements to local grid refinement, and additional features to facilitate easier model updates, faster execution, better error messages, and more integration/cross communication between the traditional MODFLOW packages. By retaining and tracking the water within the hydrosphere, One-Water accounts for "all of the water everywhere and all of the time." This philosophy provides more confidence in the water accounting by the scientific community and provides the public a foundation needed to address wider classes of problems. Ultimately, more complex questions are being asked about water resources, so they require a more complete answer about conjunctive-use and climate-related issues.

'spup' - an R package for uncertainty propagation in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2016-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected static and interactive visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

'spup' - an R package for uncertainty propagation analysis in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2017-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability and being able to deal with case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

Shuttle Communications and Tracking Systems Modeling and TDRSS Link Simulations Studies

NASA Technical Reports Server (NTRS)

Chie, C. M.; Dessouky, K.; Lindsey, W. C.; Tsang, C. S.; Su, Y. T.

1985-01-01

An analytical simulation package (LinCsim) which allows the analytical verification of data transmission performance through TDRSS satellites was modified. The work involved the modeling of the user transponder, TDRS, TDRS ground terminal, and link dynamics for forward and return links based on the TDRSS performance specifications (4) and the critical design reviews. The scope of this effort has recently been expanded to include the effects of radio frequency interference (RFI) on the bit error rate (BER) performance of the S-band return links. The RFI environment and the modified TDRSS satellite and ground station hardware are being modeled in accordance with their description in the applicable documents.

PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

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

Kylasa, S.B., E-mail: skylasa@purdue.edu; Aktulga, H.M., E-mail: hmaktulga@lbl.gov; Grama, A.Y., E-mail: ayg@cs.purdue.edu

2014-09-01

We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques wemore » developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.« less

Suggested Courseware for the Non-Calculus Physics Student: Projectile Motion, Circular Motion, Rotational Dynamics, and Statics.

ERIC Educational Resources Information Center

Mahoney, Joyce; And Others

1988-01-01

Evaluates 10 courseware packages covering topics for introductory physics. Discusses the price; sub-topics; program type; interaction; possible hardware; time; calculus required; graphics; and comments on each program. Recommends two packages in projectile and circular motion, and three packages in statics and rotational dynamics. (YP)

A TAPS Interactive Multimedia Package to Solve Engineering Dynamics Problem

ERIC Educational Resources Information Center

Sidhu, S. Manjit; Selvanathan, N.

2005-01-01

Purpose: To expose engineering students to using modern technologies, such as multimedia packages, to learn, visualize and solve engineering problems, such as in mechanics dynamics. Design/methodology/approach: A multimedia problem-solving prototype package is developed to help students solve an engineering problem in a step-by-step approach. A…

Real time flight simulation methodology

NASA Technical Reports Server (NTRS)

Parrish, E. A.; Cook, G.; Mcvey, E. S.

1977-01-01

Substitutional methods for digitization, input signal-dependent integrator approximations, and digital autopilot design were developed. The software framework of a simulator design package is described. Included are subroutines for iterative designs of simulation models and a rudimentary graphics package.

A MODFLOW Infiltration Device Package for Simulating Storm Water Infiltration.

PubMed

Jeppesen, Jan; Christensen, Steen

2015-01-01

This article describes a MODFLOW Infiltration Device (INFD) Package that can simulate infiltration devices and their two-way interaction with groundwater. The INFD Package relies on a water balance including inflow of storm water, leakage-like seepage through the device faces, overflow, and change in storage. The water balance for the device can be simulated in multiple INFD time steps within a single MODFLOW time step, and infiltration from the device can be routed through the unsaturated zone to the groundwater table. A benchmark test shows that the INFD Package's analytical solution for stage computes exact results for transient behavior. To achieve similar accuracy by the numerical solution of the MODFLOW Surface-Water Routing (SWR1) Process requires many small time steps. Furthermore, the INFD Package includes an improved representation of flow through the INFD sides that results in lower infiltration rates than simulated by SWR1. The INFD Package is also demonstrated in a transient simulation of a hypothetical catchment where two devices interact differently with groundwater. This simulation demonstrates that device and groundwater interaction depends on the thickness of the unsaturated zone because a shallow groundwater table (a likely result from storm water infiltration itself) may occupy retention volume, whereas a thick unsaturated zone may cause a phase shift and a change of amplitude in groundwater table response to a change of infiltration. We thus find that the INFD Package accommodates the simulation of infiltration devices and groundwater in an integrated manner on small as well as large spatial and temporal scales. © 2014, National Ground Water Association.

Fast Auroral Snapshot performance using a multi-body dynamic simulation

NASA Technical Reports Server (NTRS)

Zimbelman, Darrell; Walker, Mary

1993-01-01

This paper examines the complex dynamic interaction between two 2.6 m long stacer booms, four 30 m long flexible wire booms and the attitude control system of the Fast Auroral SnapshoT (FAST) spacecraft. The FAST vehicle will nominally operate as a negative orbit spinner, positioned in a 83 deg inclination, 350 x 4200 km orbit. For this study, a three-axis, non-linear, seven body dynamic simulation is developed using the TREETOPS software package. The significance of this approach is the ability to model each component of the FAST spacecraft as an individual member and connect them together in order to better understand the dynamic coupling between structures and the control system. Both the wire and stacer booms are modeled as separate bodies attached to a rigid central body. The wire booms are oriented perpendicular to the spin axis at right angles relative to each other, whereas the stacer booms are aligned with the spin axis. The analysis consists of a comparison between the simulated in-plane and out-of-plane boom motions with theoretically derived frequencies, and an examination of the dynamic coupling between the control system and boom oscillations. Results show that boom oscillations of up to 0.36 deg are acceptable in order to meet the performance requirements. The dynamic motion is well behaved when the precession coil is operating, however, activation of the spin coil produces an erratic trend in the spin rate which approaches the spin rate requirement.

Molecular modelling of protein-protein/protein-solvent interactions

NASA Astrophysics Data System (ADS)

Luchko, Tyler

The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule destabilization. No conformational change was observed but a nucleotide dependent 'softening' of the interaction was found instead, suggesting that an entropic force in a microtubule configuration could be the mechanism of microtubule collapse. Finally, to overcome much of the computational costs associated with explicit soIvent calculations, a new combination of molecular dynamics with the 3D-reference interaction site model (3D-RISM) of solvation was integrated into the Amber molecular dynamics package. Our implementation of 3D-RISM shows excellent agreement with explicit solvent free energy calculations. Several optimisation techniques, including a new multiple time step method, provide a nearly 100 fold performance increase, giving similar computational performance to explicit solvent.

Direct NOE simulation from long MD trajectories.

PubMed

Chalmers, G; Glushka, J N; Foley, B L; Woods, R J; Prestegard, J H

2016-04-01

A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected. Copyright © 2016 Elsevier Inc. All rights reserved.

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

NASA Astrophysics Data System (ADS)

Butterworth, J. M.; Butterworth, S.

2003-06-01

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.

Development and Verification of the Soil-Pile Interaction Extension for SubDyn

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

Damiani, Rick R; Wendt, Fabian F

SubDyn is the substructure structural-dynamics module for the aero-hydro-servo-elastic tool FAST v8. SubDyn uses a finite-element model (FEM) to simulate complex multimember lattice structures connected to conventional turbines and towers, and it can make use of the Craig-Bampton model reduction. Here we describe the newly added capability to handle soil-pile stiffness and compare results for monopile and jacket-based offshore wind turbines as obtained with FAST v8, SACS, and EDP (the latter two are modeling software packages commonly used in the offshore oil and gas industry). The level of agreement in terms of modal properties and loads for the entire offshoremore » wind turbine components is excellent, thus allowing SubDyn and FAST v8 to accurately simulate offshore wind turbines on fixed-bottom structures and accounting for the effect of soil dynamics, thus reducing risk to the project.« less

Simulation tools for particle-based reaction-diffusion dynamics in continuous space

PubMed Central

2014-01-01

Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Certain systems however, require these investments to be modeled adequately. Here we present a review on the current field of particle-based reaction-diffusion software packages operating on continuous space. Four nested levels of modeling detail are identified that capture incrementing amount of detail. Their applicability to different biological questions is discussed, arching from straight diffusion simulations to sophisticated and expensive models that bridge towards coarse grained molecular dynamics. PMID:25737778

Multinuclear NMR of CaSiO(3) glass: simulation from first-principles.

PubMed

Pedone, Alfonso; Charpentier, Thibault; Menziani, Maria Cristina

2010-06-21

An integrated computational method which couples classical molecular dynamics simulations with density functional theory calculations is used to simulate the solid-state NMR spectra of amorphous CaSiO(3). Two CaSiO(3) glass models are obtained by shell-model molecular dynamics simulations, successively relaxed at the GGA-PBE level of theory. The calculation of the NMR parameters (chemical shielding and quadrupolar parameters), which are then used to simulate solid-state 1D and 2D-NMR spectra of silicon-29, oxygen-17 and calcium-43, is achieved by the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods. It is shown that the limitations due to the finite size of the MD models can be overcome using a Kernel Estimation Density (KDE) approach to simulate the spectra since it better accounts for the disorder effects on the NMR parameter distribution. KDE allows reconstructing a smoothed NMR parameter distribution from the MD/GIPAW data. Simulated NMR spectra calculated with the present approach are found to be in excellent agreement with the experimental data. This further validates the CaSiO(3) structural model obtained by MD simulations allowing the inference of relationships between structural data and NMR response. The methods used to simulate 1D and 2D-NMR spectra from MD GIPAW data have been integrated in a package (called fpNMR) freely available on request.

ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

PubMed

Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

2018-05-08

Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

GillesPy: A Python Package for Stochastic Model Building and Simulation.

PubMed

Abel, John H; Drawert, Brian; Hellander, Andreas; Petzold, Linda R

2016-09-01

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community.

GillesPy: A Python Package for Stochastic Model Building and Simulation

PubMed Central

Abel, John H.; Drawert, Brian; Hellander, Andreas; Petzold, Linda R.

2017-01-01

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community. PMID:28630888

Modeling Nitrogen Dynamics in a Waste Stabilization Pond System Using Flexible Modeling Environment with MCMC

PubMed Central

Mukhtar, Hussnain; Lin, Yu-Pin; Shipin, Oleg V.; Petway, Joy R.

2017-01-01

This study presents an approach for obtaining realization sets of parameters for nitrogen removal in a pilot-scale waste stabilization pond (WSP) system. The proposed approach was designed for optimal parameterization, local sensitivity analysis, and global uncertainty analysis of a dynamic simulation model for the WSP by using the R software package Flexible Modeling Environment (R-FME) with the Markov chain Monte Carlo (MCMC) method. Additionally, generalized likelihood uncertainty estimation (GLUE) was integrated into the FME to evaluate the major parameters that affect the simulation outputs in the study WSP. Comprehensive modeling analysis was used to simulate and assess nine parameters and concentrations of ON-N, NH3-N and NO3-N. Results indicate that the integrated FME-GLUE-based model, with good Nash–Sutcliffe coefficients (0.53–0.69) and correlation coefficients (0.76–0.83), successfully simulates the concentrations of ON-N, NH3-N and NO3-N. Moreover, the Arrhenius constant was the only parameter sensitive to model performances of ON-N and NH3-N simulations. However, Nitrosomonas growth rate, the denitrification constant, and the maximum growth rate at 20 °C were sensitive to ON-N and NO3-N simulation, which was measured using global sensitivity. PMID:28704958

Three-Dimensional Muscle Architecture and Comprehensive Dynamic Properties of Rabbit Gastrocnemius, Plantaris and Soleus: Input for Simulation Studies

PubMed Central

Siebert, Tobias; Leichsenring, Kay; Rode, Christian; Wick, Carolin; Stutzig, Norman; Schubert, Harald; Blickhan, Reinhard; Böl, Markus

2015-01-01

The vastly increasing number of neuro-muscular simulation studies (with increasing numbers of muscles used per simulation) is in sharp contrast to a narrow database of necessary muscle parameters. Simulation results depend heavily on rough parameter estimates often obtained by scaling of one muscle parameter set. However, in vivo muscles differ in their individual properties and architecture. Here we provide a comprehensive dataset of dynamic (n = 6 per muscle) and geometric (three-dimensional architecture, n = 3 per muscle) muscle properties of the rabbit calf muscles gastrocnemius, plantaris, and soleus. For completeness we provide the dynamic muscle properties for further important shank muscles (flexor digitorum longus, extensor digitorum longus, and tibialis anterior; n = 1 per muscle). Maximum shortening velocity (normalized to optimal fiber length) of the gastrocnemius is about twice that of soleus, while plantaris showed an intermediate value. The force-velocity relation is similar for gastrocnemius and plantaris but is much more bent for the soleus. Although the muscles vary greatly in their three-dimensional architecture their mean pennation angle and normalized force-length relationships are almost similar. Forces of the muscles were enhanced in the isometric phase following stretching and were depressed following shortening compared to the corresponding isometric forces. While the enhancement was independent of the ramp velocity, the depression was inversely related to the ramp velocity. The lowest effect strength for soleus supports the idea that these effects adapt to muscle function. The careful acquisition of typical dynamical parameters (e.g. force-length and force-velocity relations, force elongation relations of passive components), enhancement and depression effects, and 3D muscle architecture of calf muscles provides valuable comprehensive datasets for e.g. simulations with neuro-muscular models, development of more realistic muscle models, or simulation of muscle packages. PMID:26114955

Application of the Finite Elemental Analysis to Modeling Temperature Change of the Vaccine in an Insulated Packaging Container during Transport.

PubMed

Ge, Changfeng; Cheng, Yujie; Shen, Yan

2013-01-01

This study demonstrated an attempt to predict temperatures of a perishable product such as vaccine inside an insulated packaging container during transport through finite element analysis (FEA) modeling. In order to use the standard FEA software for simulation, an equivalent heat conduction coefficient is proposed and calculated to describe the heat transfer of the air trapped inside the insulated packaging container. The three-dimensional, insulated packaging container is regarded as a combination of six panels, and the heat flow at each side panel is a one-dimension diffusion process. The transit-thermal analysis was applied to simulate the heat transition process from ambient environment to inside the container. Field measurements were carried out to collect the temperature during transport, and the collected data were compared to the FEA simulation results. Insulated packaging containers are used to transport temperature-sensitive products such as vaccine and other pharmaceutical products. The container is usually made of an extruded polystyrene foam filled with gel packs. World Health Organization guidelines recommend that all vaccines except oral polio vaccine be distributed in an environment where the temperature ranges between +2 to +8 °C. The primary areas of concern in designing the packaging for vaccine are how much of the foam thickness and gel packs should be used in order to keep the temperature in a desired range, and how to prevent the vaccine from exposure to freezing temperatures. This study uses numerical simulation to predict temperature change within an insulated packaging container in vaccine cold chain. It is our hope that this simulation will provide the vaccine industries with an alternative engineering tool to validate vaccine packaging and project thermal equilibrium within the insulated packaging container.

The effect of a simulation training package on skill acquisition for duplex arterial stenosis detection.

PubMed

Jaffer, Usman; Normahani, Pasha; Singh, Prashant; Aslam, Mohammed; Standfield, Nigel J

2015-01-01

In vascular surgery, duplex ultrasonography is a valuable diagnostic tool in patients with peripheral vascular disease, and there is increasing demand for vascular surgeons to be able to perform duplex scanning. This study evaluates the role of a novel simulation training package on vascular ultrasound (US) skill acquisition. A total of 19 novices measured predefined stenosis in a simulated pulsatile vessel using both peak systolic velocity ratio (PSVR) and diameter reduction (DR) methods before and after a short period of training using a simulated training package. The training package consisted of a simulated pulsatile vessel phantom, a set of instructional videos, duplex ultrasound objective structured assessment of technical skills (DUOSATS) tool, and a portable US scanner. Quantitative metrics (procedure time, percentage error using PSVR and DR methods, DUOSAT scores, and global rating scores) before and after training were compared. Subjects spent a median time of 144 mins (IQR: 60-195) training using the simulation package. Subjects exhibited statistically significant improvements when comparing pretraining and posttraining DUOSAT scores (pretraining = 17 [16-19.3] vs posttraining = 30 [27.8-31.8]; p < 0.01), global rating score (pretraining = 1 [1-2] vs posttraining = 4 [3.8-4]; p < 0.01), percentage error using both the DR (pretraining = 12.6% [9-29.6] vs posttraining = 10.3% [8.9-11.1]; p = 0.03) and PSVR (pretraining = 60% [40-60] vs posttraining = 20% [6.7-20]; p < 0.01) methods. In this study, subjects with no previous practical US experience developed the ability to both acquire and interpret arterial duplex images in a pulsatile simulated phantom following a short period of goal direct training using a simulation training package. A simulation training package may be a valuable tool for integration into a vascular training program. However, further work is needed to explore whether these newly attained skills are translated into clinical assessment. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

Predict the glass transition temperature of glycerol-water binary cryoprotectant by molecular dynamic simulation.

PubMed

Li, Dai-Xi; Liu, Bao-Lin; Liu, Yi-shu; Chen, Cheng-lung

2008-04-01

Vitrification is proposed to be the best way for the cryopreservation of organs. The glass transition temperature (T(g)) of vitrification solutions is a critical parameter of fundamental importance for cryopreservation by vitrification. The instruments that can detect the thermodynamic, mechanical and dielectric changes of a substance may be used to determine the glass transition temperature. T(g) is usually measured by using differential scanning calorimetry (DSC). In this study, the T(g) of the glycerol-aqueous solution (60%, wt/%) was determined by isothermal-isobaric molecular dynamic simulation (NPT-MD). The software package Discover in Material Studio with the Polymer Consortium Force Field (PCFF) was used for the simulation. The state parameters of heat capacity at constant pressure (C(p)), density (rho), amorphous cell volume (V(cell)) and specific volume (V(specific)) and radial distribution function (rdf) were obtained by NPT-MD in the temperature range of 90-270K. These parameters showed a discontinuity at a specific temperature in the plot of state parameter versus temperature. The temperature at the discontinuity is taken as the simulated T(g) value for glycerol-water binary solution. The T(g) values determined by simulation method were compared with the values in the literatures. The simulation values of T(g) (160.06-167.51K) agree well with the DSC results (163.60-167.10K) and the DMA results (159.00K). We drew the conclusion that molecular dynamic simulation (MDS) is a potential method for investigating the glass transition temperature (T(g)) of glycerol-water binary cryoprotectants and may be used for other vitrification solutions.

MDplot: Visualise Molecular Dynamics

PubMed Central

Margreitter, Christian; Oostenbrink, Chris

2017-01-01

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package′s functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. Availability The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project′s GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license. PMID:28845302

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks.

PubMed

Müssel, Christoph; Hopfensitz, Martin; Kestler, Hans A

2010-05-15

As the study of information processing in living cells moves from individual pathways to complex regulatory networks, mathematical models and simulation become indispensable tools for analyzing the complex behavior of such networks and can provide deep insights into the functioning of cells. The dynamics of gene expression, for example, can be modeled with Boolean networks (BNs). These are mathematical models of low complexity, but have the advantage of being able to capture essential properties of gene-regulatory networks. However, current implementations of BNs only focus on different sub-aspects of this model and do not allow for a seamless integration into existing preprocessing pipelines. BoolNet efficiently integrates methods for synchronous, asynchronous and probabilistic BNs. This includes reconstructing networks from time series, generating random networks, robustness analysis via perturbation, Markov chain simulations, and identification and visualization of attractors. The package BoolNet is freely available from the R project at http://cran.r-project.org/ or http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/boolnet/ under Artistic License 2.0. hans.kestler@uni-ulm.de Supplementary data are available at Bioinformatics online.

Implementation of EAM and FS potentials in HOOMD-blue

NASA Astrophysics Data System (ADS)

Yang, Lin; Zhang, Feng; Travesset, Alex; Wang, Caizhuang; Ho, Kaiming

HOOMD-blue is a general-purpose software to perform classical molecular dynamics simulations entirely on GPUs. We provide full support for EAM and FS type potentials in HOOMD-blue, and report accuracy and efficiency benchmarks, including comparisons with the LAMMPS GPU package. Two problems were selected to test the accuracy: the determination of the glass transition temperature of Cu64.5Zr35.5 alloy using an FS potential and the calculation of pair distribution functions of Ni3Al using an EAM potential. In both cases, the results using HOOMD-blue are indistinguishable from those obtained by the GPU package in LAMMPS within statistical uncertainties. As tests for time efficiency, we benchmark time-steps per second using LAMMPS GPU and HOOMD-blue on one NVIDIA Tesla GPU. Compared to our typical LAMMPS simulations on one CPU cluster node which has 16 CPUs, LAMMPS GPU can be 3-3.5 times faster, and HOOMD-blue can be 4-5.5 times faster. We acknowledge the support from Laboratory Directed Research and Development (LDRD) of Ames Laboratory.

Validation of thermal effects of LED package by using Elmer finite element simulation method

NASA Astrophysics Data System (ADS)

Leng, Lai Siang; Retnasamy, Vithyacharan; Mohamad Shahimin, Mukhzeer; Sauli, Zaliman; Taniselass, Steven; Bin Ab Aziz, Muhamad Hafiz; Vairavan, Rajendaran; Kirtsaeng, Supap

2017-02-01

The overall performance of the Light-emitting diode, LED package is critically affected by the heat attribution. In this study, open source software - Elmer FEM has been utilized to study the thermal analysis of the LED package. In order to perform a complete simulation study, both Salome software and ParaView software were introduced as Pre and Postprocessor. The thermal effect of the LED package was evaluated by this software. The result has been validated with commercially licensed software based on previous work. The percentage difference from both simulation results is less than 5% which is tolerable and comparable.

Mapping the Damping Dynamics of Mega-Ampere Electron Pulses Inside a Solid

NASA Astrophysics Data System (ADS)

Shaikh, Moniruzzaman; Lad, Amit D.; Birindelli, Gabriele; Pepitone, Kevin; Jha, Jagannath; Sarkar, Deep; Tata, Sheroy; Chatterjee, Gourab; Dey, Indranuj; Jana, Kamalesh; Singh, Prashant K.; Tikhonchuk, Vladimir T.; Rajeev, P. P.; Kumar, G. Ravindra

2018-02-01

We report the lifetime of intense-laser (2 ×1019 W /cm2 ) generated relativistic electron pulses in solids by measuring the time evolution of their Cherenkov emission. Using a picosecond resolution optical Kerr gating technique, we demonstrate that the electrons remain relativistic as long as 50 picoseconds—more than 1000 times longer than the incident light pulse. Numerical simulations of the propagation of relativistic electrons and the emitted Cherenkov radiation with Monte Carlo geant4 package reproduce the striking experimental findings.

Computer-aided-engineering system for modeling and analysis of ECLSS integration testing

NASA Technical Reports Server (NTRS)

Sepahban, Sonbol

1987-01-01

The accurate modeling and analysis of two-phase fluid networks found in environmental control and life support systems is presently undertaken by computer-aided engineering (CAE) techniques whose generalized fluid dynamics package can solve arbitrary flow networks. The CAE system for integrated test bed modeling and analysis will also furnish interfaces and subsystem/test-article mathematical models. Three-dimensional diagrams of the test bed are generated by the system after performing the requisite simulation and analysis.

NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data

PubMed Central

Rothman, Jason S.; Silver, R. Angus

2018-01-01

Acquisition, analysis and simulation of electrophysiological properties of the nervous system require multiple software packages. This makes it difficult to conserve experimental metadata and track the analysis performed. It also complicates certain experimental approaches such as online analysis. To address this, we developed NeuroMatic, an open-source software toolkit that performs data acquisition (episodic, continuous and triggered recordings), data analysis (spike rasters, spontaneous event detection, curve fitting, stationarity) and simulations (stochastic synaptic transmission, synaptic short-term plasticity, integrate-and-fire and Hodgkin-Huxley-like single-compartment models). The merging of a wide range of tools into a single package facilitates a more integrated style of research, from the development of online analysis functions during data acquisition, to the simulation of synaptic conductance trains during dynamic-clamp experiments. Moreover, NeuroMatic has the advantage of working within Igor Pro, a platform-independent environment that includes an extensive library of built-in functions, a history window for reviewing the user's workflow and the ability to produce publication-quality graphics. Since its original release, NeuroMatic has been used in a wide range of scientific studies and its user base has grown considerably. NeuroMatic version 3.0 can be found at http://www.neuromatic.thinkrandom.com and https://github.com/SilverLabUCL/NeuroMatic. PMID:29670519

MT3D-USGS version 1: A U.S. Geological Survey release of MT3DMS updated with new and expanded transport capabilities for use with MODFLOW

USGS Publications Warehouse

Bedekar, Vivek; Morway, Eric D.; Langevin, Christian D.; Tonkin, Matthew J.

2016-09-30

MT3D-USGS, a U.S. Geological Survey updated release of the groundwater solute transport code MT3DMS, includes new transport modeling capabilities to accommodate flow terms calculated by MODFLOW packages that were previously unsupported by MT3DMS and to provide greater flexibility in the simulation of solute transport and reactive solute transport. Unsaturated-zone transport and transport within streams and lakes, including solute exchange with connected groundwater, are among the new capabilities included in the MT3D-USGS code. MT3D-USGS also includes the capability to route a solute through dry cells that may occur in the Newton-Raphson formulation of MODFLOW (that is, MODFLOW-NWT). New chemical reaction Package options include the ability to simulate inter-species reactions and parent-daughter chain reactions. A new pump-and-treat recirculation package enables the simulation of dynamic recirculation with or without treatment for combinations of wells that are represented in the flow model, mimicking the above-ground treatment of extracted water. A reformulation of the treatment of transient mass storage improves conservation of mass and yields solutions for better agreement with analytical benchmarks. Several additional features of MT3D-USGS are (1) the separate specification of the partitioning coefficient (Kd) within mobile and immobile domains; (2) the capability to assign prescribed concentrations to the top-most active layer; (3) the change in mass storage owing to the change in water volume now appears as its own budget item in the global mass balance summary; (4) the ability to ignore cross-dispersion terms; (5) the definition of Hydrocarbon Spill-Source Package (HSS) mass loading zones using regular and irregular polygons, in addition to the currently supported circular zones; and (6) the ability to specify an absolute minimum thickness rather than the default percent minimum thickness in dry-cell circumstances.Benchmark problems that implement the new features and packages test the accuracy of new code through comparison to analytical benchmarks, as well as to solutions from other published codes. The input file structure for MT3D-USGS adheres to MT3DMS conventions for backward compatibility: the new capabilities and packages described herein are readily invoked by adding three-letter package name acronyms to the name file or by setting input flags as needed. Memory is managed in MT3D-USGS using FORTRAN modules in order to simplify code development and expansion.

Satellite Data Simulator Unit: A Multisensor, Multispectral Satellite Simulator Package

NASA Technical Reports Server (NTRS)

Masunaga, Hirohiko; Matsui, Toshihisa; Tao, Wei-Kuo; Hou, Arthur Y.; Kummerow, Christian D.; Nakajima, Teruyuki; Bauer, Peter; Olson, William S.; Sekiguchi, Miho; Nakajima, Teruyuki

2010-01-01

Several multisensor simulator packages are being developed by different research groups across the world. Such simulator packages [e.g., COSP , CRTM, ECSIM, RTTO, ISSARS (under development), and SDSU (this article), among others] share overall aims, although some are targeted more on particular satellite programs or specific applications (for research purposes or for operational use) than others. The SDSU or Satellite Data Simulator Unit is a general-purpose simulator composed of Fortran 90 codes and applicable to spaceborne microwave radiometer, radar, and visible/infrared imagers including, but not limited to, the sensors listed in a table. That shows satellite programs particularly suitable for multisensor data analysis: some are single satellite missions carrying two or more instruments, while others are constellations of satellites flying in formation. The TRMM and A-Train are ongoing satellite missions carrying diverse sensors that observe clouds and precipitation, and will be continued or augmented within the decade to come by future multisensor missions such as the GPM and Earth-CARE. The ultimate goals of these present and proposed satellite programs are not restricted to clouds and precipitation but are to better understand their interactions with atmospheric dynamics/chemistry and feedback to climate. The SDSU's applicability is not technically limited to hydrometeor measurements either, but may be extended to air temperature and humidity observations by tuning the SDSU to sounding channels. As such, the SDSU and other multisensor simulators would potentially contribute to a broad area of climate and atmospheric sciences. The SDSU is not optimized to any particular orbital geometry of satellites. The SDSU is applicable not only to low-Earth orbiting platforms as listed in Table 1, but also to geostationary meteorological satellites. Although no geosynchronous satellite carries microwave instruments at present or in the near future, the SDSU would be useful for future geostationary satellites with a microwave radiometer and/or a radar aboard, which could become more feasible as engineering challenges are met. In this short article, the SDSU algorithm architecture and potential applications are reviewed in brief.

FESetup: Automating Setup for Alchemical Free Energy Simulations.

PubMed

Loeffler, Hannes H; Michel, Julien; Woods, Christopher

2015-12-28

FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

Documentation of a computer program to simulate aquifer-system compaction using the modular finite-difference ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Prudic, David E.

1988-01-01

The process of permanent compaction is not routinely included in simulations of groundwater flow. To simulate storage changes from both elastic and inelastic compaction, a computer program was written for use with the U. S. Geological Survey modular finite-difference groundwater flow model. The new program is called the Interbed-Storage Package. In the Interbed-Storage Package, elastic compaction or expansion is assumed to be proportional to change in head. The constant of proportionality is the product of skeletal component of elastic specific storage and thickness of the sediments. Similarly, inelastic compaction is assumed to be proportional to decline in head. The constant of proportionality is the product of the skeletal component of inelastic specific storage and the thickness of the sediments. Storage changes are incorporated into the groundwater flow model by adding an additional term to the flow equation. Within a model time step, the package appropriately apportions storage changes between elastic and inelastic components on the basis of the relation of simulated head to the previous minimum head. Another package that allows for a time-varying specified-head boundary is also documented. This package was written to reduce the data requirements for test simulations of the Interbed-Storage Package. (USGS)

A user's guide to the ssWavelets package

Treesearch

J.H. ​Gove

2017-01-01

ssWavelets is an R package that is meant to be used in conjunction with the sampSurf package (Gove, 2012) to perform wavelet decomposition on the results of a sampling surface simulation. In general, the wavelet filter decomposes the sampSurf simulation results by scale (distance), with each scale corresponding to a different level of the...

Simulating the Effects of Financial Aid Packages on College Student Stopout, Reenrollment Spells, and Graduation Chances

ERIC Educational Resources Information Center

DesJardins, Stephen L.; McCall, Brian P.

2010-01-01

This study investigates the impact that different financial aid packages have on student stopout, reenrollment, and graduation probabilities. The authors simulate how various financial aid packaging regimes affect the occurrence and timing of these events. Their findings indicate that the number and duration of enrollment and stopout spells affect…

Synergia: an accelerator modeling tool with 3-D space charge

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

Amundson, James F.; Spentzouris, P.; /Fermilab

2004-07-01

High precision modeling of space-charge effects, together with accurate treatment of single-particle dynamics, is essential for designing future accelerators as well as optimizing the performance of existing machines. We describe Synergia, a high-fidelity parallel beam dynamics simulation package with fully three dimensional space-charge capabilities and a higher order optics implementation. We describe the computational techniques, the advanced human interface, and the parallel performance obtained using large numbers of macroparticles. We also perform code benchmarks comparing to semi-analytic results and other codes. Finally, we present initial results on particle tune spread, beam halo creation, and emittance growth in the Fermilab boostermore » accelerator.« less

Migration and sorption phenomena in packaged foods.

PubMed

Gnanasekharan, V; Floros, J D

1997-10-01

Rapidly developing analytical capabilities and continuously evolving stringent regulations have made food/package interactions a subject of intense research. This article focuses on: (1) the migration of package components such as oligomers and monomers, processing aids, additives, and residual reactants in to packaged foods, and (2) sorption of food components such as flavors, lipids, and moisture into packages. Principles of diffusion and thermodynamics are utilized to describe the mathematics of migration and sorption. Mathematical models are developed from first principles, and their applicability is illustrated using numerical simulations and published data. Simulations indicate that available models are system (polymer-penetrant) specific. Furthermore, some models best describe the early stages of migration/sorption, whereas others should be used for the late stages of these phenomena. Migration- and/or sorption-related problems with respect to glass, metal, paper-based and polymeric packaging materials are discussed, and their importance is illustrated using published examples. The effects of migrating and absorbed components on food safety, quality, and the environment are presented for various foods and packaging materials. The impact of currently popular packaging techniques such as microwavable, ovenable, and retortable packaging on migration and sorption are discussed with examples. Analytical techniques for investigating migration and sorption phenomena in food packaging are critically reviewed, with special emphasis on the use and characteristics of food-simulating liquids (FSLs). Finally, domestic and international regulations concerning migration in packaged foods, and their impact on food packaging is briefly presented.

A User-Friendly Software Package for HIFU Simulation

NASA Astrophysics Data System (ADS)

Soneson, Joshua E.

2009-04-01

A freely-distributed, MATLAB (The Mathworks, Inc., Natick, MA)-based software package for simulating axisymmetric high-intensity focused ultrasound (HIFU) beams and their heating effects is discussed. The package (HIFU_Simulator) consists of a propagation module which solves the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation and a heating module which solves Pennes' bioheat transfer (BHT) equation. The pressure, intensity, heating rate, temperature, and thermal dose fields are computed, plotted, the output is released to the MATLAB workspace for further user analysis or postprocessing.

spMC: an R-package for 3D lithological reconstructions based on spatial Markov chains

NASA Astrophysics Data System (ADS)

Sartore, Luca; Fabbri, Paolo; Gaetan, Carlo

2016-09-01

The paper presents the spatial Markov Chains (spMC) R-package and a case study of subsoil simulation/prediction located in a plain site of Northeastern Italy. spMC is a quite complete collection of advanced methods for data inspection, besides spMC implements Markov Chain models to estimate experimental transition probabilities of categorical lithological data. Furthermore, simulation methods based on most known prediction methods (as indicator Kriging and CoKriging) were implemented in spMC package. Moreover, other more advanced methods are available for simulations, e.g. path methods and Bayesian procedures, that exploit the maximum entropy. Since the spMC package was developed for intensive geostatistical computations, part of the code is implemented for parallel computations via the OpenMP constructs. A final analysis of this computational efficiency compares the simulation/prediction algorithms by using different numbers of CPU cores, and considering the example data set of the case study included in the package.

Numerical simulation of ion transport in an atmosphere-to-vacuum interface taking into account gas dynamics and space charge.

PubMed

Skoblin, Michael G; Chudinov, Alexey V; Sulimenkov, Ilia V; Brusov, Vladimir S; Makarov, Alexander A; Wouters, Eloy R; Kozlovskiy, Viacheslav I

2017-08-01

A two-step approach was developed for the study of ion transport in an atmospheric pressure interface. In the first step, the flow in the interface was numerically simulated using the standard gas dynamic package ANSYS CFX 15.0. In the second step, the calculated fields of pressure, temperature, and velocity were imported into a custom-built software application for simulation of ion motion under the influence of both gas dynamic and electrostatic forces. To account for space charge effects in axially symmetric interfaces an analytical expression was used for the Coulomb force. For all other types of interfaces, an iterative approach for the Coulomb force computation was developed. The simulations show that the influence of the space charge is the main contributor to the loss of ion current in the heated capillary. In addition, the maximum ion current which can be transmitted through the heated capillary (0.58 mm inner diameter and 58.5 mm length) is limited to ∼6 nA for ions with m/z = 508 Da and with reduced ion mobility 1.05 cm 2 V -1 s -1 . This limit remains practically constant and independent of the ion current at the entrance of the capillary. For a particular ion type, this limit depends on its m/z ratio and ion mobility.

Discrete stochastic simulation methods for chemically reacting systems.

PubMed

Cao, Yang; Samuels, David C

2009-01-01

Discrete stochastic chemical kinetics describe the time evolution of a chemically reacting system by taking into account the fact that, in reality, chemical species are present with integer populations and exhibit some degree of randomness in their dynamical behavior. In recent years, with the development of new techniques to study biochemistry dynamics in a single cell, there are increasing studies using this approach to chemical kinetics in cellular systems, where the small copy number of some reactant species in the cell may lead to deviations from the predictions of the deterministic differential equations of classical chemical kinetics. This chapter reviews the fundamental theory related to stochastic chemical kinetics and several simulation methods based on that theory. We focus on nonstiff biochemical systems and the two most important discrete stochastic simulation methods: Gillespie's stochastic simulation algorithm (SSA) and the tau-leaping method. Different implementation strategies of these two methods are discussed. Then we recommend a relatively simple and efficient strategy that combines the strengths of the two methods: the hybrid SSA/tau-leaping method. The implementation details of the hybrid strategy are given here and a related software package is introduced. Finally, the hybrid method is applied to simple biochemical systems as a demonstration of its application.

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.

Structural evolution of Colloidal Gels under Flow

NASA Astrophysics Data System (ADS)

Boromand, Arman; Maia, Joao; Jamali, Safa

Colloidal suspensions are ubiquitous in different industrial applications ranging from cosmetic and food industries to soft robotics and aerospace. Owing to the fact that mechanical properties of colloidal gels are controlled by its microstructure and network topology, we trace the particles in the networks formed under different attraction potentials and try to find a universal behavior in yielding of colloidal gels. Many authors have implemented different simulation techniques such as molecular dynamics (MD) and Brownian dynamics (BD) to capture better picture during phase separation and yielding mechanism in colloidal system with short-ranged attractive force. However, BD neglects multi-body hydrodynamic interactions (HI) which are believed to be responsible for the second yielding of colloidal gels. We envision using dissipative particle dynamics (DPD) with modified depletion potential and hydrodynamic interactions, as a coarse-grain model, can provide a robust simulation package to address the gel formation process and yielding in short ranged-attractive colloidal systems. The behavior of colloidal gels with different attraction potentials under flow is examined and structural fingerprints of yielding in these systems will be discussed.

Chemical vapor deposition fluid flow simulation modelling tool

NASA Technical Reports Server (NTRS)

Bullister, Edward T.

1992-01-01

Accurate numerical simulation of chemical vapor deposition (CVD) processes requires a general purpose computational fluid dynamics package combined with specialized capabilities for high temperature chemistry. In this report, we describe the implementation of these specialized capabilities in the spectral element code NEKTON. The thermal expansion of the gases involved is shown to be accurately approximated by the low Mach number perturbation expansion of the incompressible Navier-Stokes equations. The radiative heat transfer between multiple interacting radiating surfaces is shown to be tractable using the method of Gebhart. The disparate rates of reaction and diffusion in CVD processes are calculated via a point-implicit time integration scheme. We demonstrate the use above capabilities on prototypical CVD applications.

Consistent multiphysics simulation of a central tower CSP plant as applied to ISTORE

NASA Astrophysics Data System (ADS)

Votyakov, Evgeny V.; Papanicolas, Costas N.

2017-06-01

We present a unified consistent multiphysics approach to model a central tower CSP plant. The framework for the model includes Monte Carlo ray tracing (RT) and computational fluid dynamics (CFD) components utilizing the OpenFOAM C++ software library. The RT part works effectively with complex surfaces of engineering design given in CAD formats. The CFD simulation, which is based on 3D Navier-Stokes equations, takes into account all possible heat transfer mechanisms: radiation, conduction, and convection. Utilizing this package, the solar field of the experimental Platform for Research, Observation, and TEchnological Applications in Solar Energy (PROTEAS) and the Integrated STOrage and Receiver (ISTORE), developed at the Cyprus Institute, are being examined.

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

DOE PAGES

Mones, Letif; Jones, Andrew; Götz, Andreas W.; ...

2015-02-03

We present the implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis usingmore » various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.« less

Reduced-order modeling of piezoelectric energy harvesters with nonlinear circuits under complex conditions

NASA Astrophysics Data System (ADS)

Xiang, Hong-Jun; Zhang, Zhi-Wei; Shi, Zhi-Fei; Li, Hong

2018-04-01

A fully coupled modeling approach is developed for piezoelectric energy harvesters in this work based on the use of available robust finite element packages and efficient reducing order modeling techniques. At first, the harvester is modeled using finite element packages. The dynamic equilibrium equations of harvesters are rebuilt by extracting system matrices from the finite element model using built-in commands without any additional tools. A Krylov subspace-based scheme is then applied to obtain a reduced-order model for improving simulation efficiency but preserving the key features of harvesters. Co-simulation of the reduced-order model with nonlinear energy harvesting circuits is achieved in a system level. Several examples in both cases of harmonic response and transient response analysis are conducted to validate the present approach. The proposed approach allows to improve the simulation efficiency by several orders of magnitude. Moreover, the parameters used in the equivalent circuit model can be conveniently obtained by the proposed eigenvector-based model order reduction technique. More importantly, this work establishes a methodology for modeling of piezoelectric energy harvesters with any complicated mechanical geometries and nonlinear circuits. The input load may be more complex also. The method can be employed by harvester designers to optimal mechanical structures or by circuit designers to develop novel energy harvesting circuits.

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

PubMed Central

Mones, Letif; Jones, Andrew; Götz, Andreas W; Laino, Teodoro; Walker, Ross C; Leimkuhler, Ben; Csányi, Gábor; Bernstein, Noam

2015-01-01

The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25649827

ICEG2D (v2.0) - An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils With Ice Accretion

NASA Technical Reports Server (NTRS)

Thompson David S.; Soni, Bharat K.

2001-01-01

An integrated geometry/grid/simulation software package, ICEG2D, is being developed to automate computational fluid dynamics (CFD) simulations for single- and multi-element airfoils with ice accretions. The current version, ICEG213 (v2.0), was designed to automatically perform four primary functions: (1) generate a grid-ready surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generate high-quality structured and generalized grids starting from a defined surface definition, (3) generate the input and restart files needed to run the structured grid CFD solver NPARC or the generalized grid CFD solver HYBFL2D, and (4) using the flow solutions, generate solution-adaptive grids. ICEG2D (v2.0) can be operated in either a batch mode using a script file or in an interactive mode by entering directives from a command line within a Unix shell. This report summarizes activities completed in the first two years of a three-year research and development program to address automation issues related to CFD simulations for airfoils with ice accretions. As well as describing the technology employed in the software, this document serves as a users manual providing installation and operating instructions. An evaluation of the software is also presented.

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

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

Mones, Letif; Jones, Andrew; Götz, Andreas W.

We present the implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis usingmore » various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.« less

Determination of the effects of water adsorption on the sensitivity and detonation performance of the explosive JOB-9003 by molecular dynamics simulation.

PubMed

Hang, GuiYun; Yu, WenLi; Wang, Tao; Li, Zhen

2016-11-01

In order to determine the adsorption mechanism of water on the crystal surfaces of the explosive JOB-9003 and the effect of this adsorption on the sensitivity and detonation performance of this explosive, a model of the crystal of JOB-9003 was created in the software package Materials Studio (MS). The adsorption process was simulated, and molecular dynamics simulation was performed with the COMPASS force field in the NPT ensemble to calculate the sensitivity and detonation performance of the explosive. The results show that the maximum trigger bond length decreases whereas the interaction energy of the trigger bond and the cohesive energy density increase after adsorption, indicating that the sensitivity of JOB-9003 decreases. The results for the detonation performance show that the detonation pressure, detonation velocity, and detonation heat decrease upon the adsorption of water, thus illustrating that the detonation performance of JOB-9003 is degraded. In summary, the adsorption of water has a positive effect on the sensitivity and safety of the explosive JOB-9003 but a negative effect on its detonation performance.

Reviews

NASA Astrophysics Data System (ADS)

2006-11-01

WE RECOMMEND Critical mass Philip Ball explores the idea of the physics of society. Eurekas and Euphorias A humorous yet insightful collection of scientific anecdotes. Wind turbine Low-cost wind turbine produces excellent results. Science Center Nemo Hands-on science centre has some great displays for teenagers. Crocodile Physics There’s something for everyone in this lesson software package. Wireless Dynamics Sensor System A fun way to measure and record altitude and acceleration. WORTH A LOOK Climate Change Begins at Home This well researched book tackles the issue of saving our planet. The Little Doctor Datalogger Datalogger has lots of facilities but needs some manual processing. HANDLE WITH CARE The Physics of Basketball Only of interest to budding physicists obsessed with basketball. Virtual Physics This package offers nice simulations but not a lot else. WEB WATCH An eclectic mix of nuclear- and general-physics websites.

Gro2mat: a package to efficiently read gromacs output in MATLAB.

PubMed

Dien, Hung; Deane, Charlotte M; Knapp, Bernhard

2014-07-30

Molecular dynamics (MD) simulations are a state-of-the-art computational method used to investigate molecular interactions at atomic scale. Interaction processes out of experimental reach can be monitored using MD software, such as Gromacs. Here, we present the gro2mat package that allows fast and easy access to Gromacs output files from Matlab. Gro2mat enables direct parsing of the most common Gromacs output formats including the binary xtc-format. No openly available Matlab parser currently exists for this format. The xtc reader is orders of magnitudes faster than other available pdb/ascii workarounds. Gro2mat is especially useful for scientists with an interest in quick prototyping of new mathematical and statistical approaches for Gromacs trajectory analyses. © 2014 Wiley Periodicals, Inc. Copyright © 2014 Wiley Periodicals, Inc.

Package analysis of 3D-printed piezoresistive strain gauge sensors

NASA Astrophysics Data System (ADS)

Das, Sumit Kumar; Baptist, Joshua R.; Sahasrabuddhe, Ritvij; Lee, Woo H.; Popa, Dan O.

2016-05-01

Poly(3,4-ethyle- nedioxythiophene)-poly(styrenesulfonate) or PEDOT:PSS is a flexible polymer which exhibits piezo-resistive properties when subjected to structural deformation. PEDOT:PSS has a high conductivity and thermal stability which makes it an ideal candidate for use as a pressure sensor. Applications of this technology includes whole body robot skin that can increase the safety and physical collaboration of robots in close proximity to humans. In this paper, we present a finite element model of strain gauge touch sensors which have been 3D-printed onto Kapton and silicone substrates using Electro-Hydro-Dynamic ink-jetting. Simulations of the piezoresistive and structural model for the entire packaged sensor was carried out using COMSOLR , and compared with experimental results for validation. The model will be useful in designing future robot skin with predictable performances.

Ohmic Heating of an Electrically Conductive Food Package.

PubMed

Kanogchaipramot, Kanyawee; Tongkhao, Kullanart; Sajjaanantakul, Tanaboon; Kamonpatana, Pitiya

2016-12-01

Ohmic heating through an electrically conductive food package is a new approach to heat the food and its package as a whole after packing to avoid post-process contamination and to serve consumer needs for convenience. This process has been successfully completed using polymer film integrated with an electrically conductive film to form a conductive package. Orange juice packed in the conductive package surrounded with a conductive medium was pasteurized in an ohmic heater. A mathematical model was developed to simulate the temperature distribution within the package and its surroundings. A 3-D thermal-electric model showed heating uniformity inside the food package while the hot zone appeared in the orange juice adjacent to the conductive film. The accuracy of the model was determined by comparing the experimental results with the simulated temperature and current drawn; the model showed good agreement between the actual and simulated results. An inoculated pack study using Escherichia coli O157:H7 indicated negative growth of viable microorganisms at the target and over target lethal process temperatures, whereas the microorganism was present in the under target temperature treatment. Consequently, our developed ohmic heating system with conductive packaging offers potential for producing safe food. © 2016 Institute of Food Technologists®.

Differential maneuvering simulator data reduction and analysis software

NASA Technical Reports Server (NTRS)

Beasley, G. P.; Sigman, R. S.

1972-01-01

A multielement data reduction and analysis software package has been developed for use with the Langley differential maneuvering simulator (DMS). This package, which has several independent elements, was developed to support all phases of DMS aircraft simulation studies with a variety of both graphical and tabular information. The overall software package is considered unique because of the number, diversity, and sophistication of the element programs available for use in a single study. The purpose of this paper is to discuss the overall DMS data reduction and analysis package by reviewing the development of the various elements of the software, showing typical results that can be obtained, and discussing how each element can be used.

Documentation of a computer program to simulate transient leakage from confining units using the modular finite-difference, ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Leahy, P.P.; Navoy, A.S.

1994-01-01

Transient leakage into or out of a compressible fine-grained confining unit results from ground- water storage changes within the unit. The computer program described in this report provides a new method of simulating transient leakage using the U.S. Geological Survey modular finite- difference ground-water flow model (MODFLOW). The new program is referred to as the Transient- Leakage Package. The Transient-Leakage Package solves integrodifferential equations that describe flow across the upper and lower boundaries of confining units. For each confining unit, vertical hydraulic conductivity, thickness, and specific storage are specified in input arrays. These properties can vary from cell to cell and the confining unit need not be present at all locations in the grid; however, the confining units must be bounded above and below by model layers in which head is calculated or specified. The package was used in an example problem to simulate drawdown around a pumping well in a system with two aquifers separated by a confining unit. For drawdown values in excess of 1 centimeter, the solution using the new package closely matched an exact analytical solution. The problem also was simulated without the new package by using a separate model layer to represent the confining unit. That simulation was refined by using two model layers to represent the confining unit. The simulation using the Transient-Leakage Package was faster and more accurate than either of the simulations using model layers to represent the confining unit.

Physical and digital simulations for IVA robotics

NASA Technical Reports Server (NTRS)

Hinman, Elaine; Workman, Gary L.

1992-01-01

Space based materials processing experiments can be enhanced through the use of IVA robotic systems. A program to determine requirements for the implementation of robotic systems in a microgravity environment and to develop some preliminary concepts for acceleration control of small, lightweight arms has been initiated with the development of physical and digital simulation capabilities. The physical simulation facilities incorporate a robotic workcell containing a Zymark Zymate II robot instrumented for acceleration measurements, which is able to perform materials transfer functions while flying on NASA's KC-135 aircraft during parabolic manuevers to simulate reduced gravity. Measurements of accelerations occurring during the reduced gravity periods will be used to characterize impacts of robotic accelerations in a microgravity environment in space. Digital simulations are being performed with TREETOPS, a NASA developed software package which is used for the dynamic analysis of systems with a tree topology. Extensive use of both simulation tools will enable the design of robotic systems with enhanced acceleration control for use in the space manufacturing environment.

Microcomputer based software for biodynamic simulation

NASA Technical Reports Server (NTRS)

Rangarajan, N.; Shams, T.

1993-01-01

This paper presents a description of a microcomputer based software package, called DYNAMAN, which has been developed to allow an analyst to simulate the dynamics of a system consisting of a number of mass segments linked by joints. One primary application is in predicting the motion of a human occupant in a vehicle under the influence of a variety of external forces, specially those generated during a crash event. Extensive use of a graphical user interface has been made to aid the user in setting up the input data for the simulation and in viewing the results from the simulation. Among its many applications, it has been successfully used in the prototype design of a moving seat that aids in occupant protection during a crash, by aircraft designers in evaluating occupant injury in airplane crashes, and by users in accident reconstruction for reconstructing the motion of the occupant and correlating the impacts with observed injuries.

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.

Shipboard communications center modernization network simulation report

DOT National Transportation Integrated Search

1995-08-01

Commercially available simulation packages were investigated to determine their suitability for modeling the USCG Cutter Communications Center (CCC). The suitability of a candidate package was based upon it meeting the operational goals and hardware ...

Effectiveness of Simulation in a Hybrid and Online Networking Course.

ERIC Educational Resources Information Center

Cameron, Brian H.

2003-01-01

Reports on a study that compares the performance of students enrolled in two sections of a Web-based computer networking course: one utilizing a simulation package and the second utilizing a static, graphical software package. Analysis shows statistically significant improvements in performance in the simulation group compared to the…

MDWiZ: a platform for the automated translation of molecular dynamics simulations.

PubMed

Rusu, Victor H; Horta, Vitor A C; Horta, Bruno A C; Lins, Roberto D; Baron, Riccardo

2014-03-01

A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

User's guide to the Variably Saturated Flow (VSF) process to MODFLOW

USGS Publications Warehouse

Thoms, R. Brad; Johnson, Richard L.; Healy, Richard W.

2006-01-01

A new process for simulating three-dimensional (3-D) variably saturated flow (VSF) using Richards' equation has been added to the 3-D modular finite-difference ground-water model MODFLOW. Five new packages are presented here as part of the VSF Process--the Richards' Equation Flow (REF1) Package, the Seepage Face (SPF1) Package, the Surface Ponding (PND1) Package, the Surface Evaporation (SEV1) Package, and the Root Zone Evapotranspiration (RZE1) Package. Additionally, a new Adaptive Time-Stepping (ATS1) Package is presented for use by both the Ground-Water Flow (GWF) Process and VSF. The VSF Process allows simulation of flow in unsaturated media above the ground-water zone and facilitates modeling of ground-water/surface-water interactions. Model performance is evaluated by comparison to an analytical solution for one-dimensional (1-D) constant-head infiltration (Dirichlet boundary condition), field experimental data for a 1-D constant-head infiltration, laboratory experimental data for two-dimensional (2-D) constant-flux infiltration (Neumann boundary condition), laboratory experimental data for 2-D transient drainage through a seepage face, and numerical model results (VS2DT) of a 2-D flow-path simulation using realistic surface boundary conditions. A hypothetical 3-D example case also is presented to demonstrate the new capability using periodic boundary conditions (for example, daily precipitation) and varied surface topography over a larger spatial scale (0.133 square kilometer). The new model capabilities retain the modular structure of the MODFLOW code and preserve MODFLOW's existing capabilities as well as compatibility with commercial pre-/post-processors. The overall success of the VSF Process in simulating mixed boundary conditions and variable soil types demonstrates its utility for future hydrologic investigations. This report presents a new flow package implementing the governing equations for variably saturated ground-water flow, four new boundary condition packages unique to unsaturated flow, the Adaptive Time-Stepping Package for use with both the GWF Process and the new VSF Process, detailed descriptions of the input and output files for each package, and six simulation examples verifying model performance.

A Global, Multi-Waveband Model for the Zodiacal Cloud

NASA Technical Reports Server (NTRS)

Grogan, Keith; Dermott, Stanley F.; Kehoe, Thomas J. J.

2003-01-01

This recently completed three-year project was undertaken by the PI at the University of Florida, NASA Goddard and JPL, and by the Co-I and Collaborator at the University of Florida. The funding was used to support a continuation of research conducted at the University of Florida over the last decade which focuses on the dynamics of dust particles in the interplanetary environment. The main objectives of this proposal were: To produce improved dynamical models of the zodiacal cloud by performing numerical simulations of the orbital evolution of asteroidal and cometary dust particles. To provide visualizations of the results using our visualization software package, SIMUL, simulating the viewing geometries of IRAS and COBE and comparing the model results with archived data. To use the results to provide a more accurate model of the brightness distribution of the zodiacal cloud than existing empirical models. In addition, our dynamical approach can provide insight into fundamental properties of the cloud, including but not limited to the total mass and surface area of dust, the size-frequency distribution of dust, and the relative contributions of asteroidal and cometary material. The model can also be used to provide constraints on trace signals from other sources, such as dust associated with the "Plutinos" , objects captured in the 2:3 resonance with Neptune.

Virtual surgery for patients with nasal obstruction: Use of computational fluid dynamics (MeComLand®, Digbody® & Noseland®) to document objective flow parameters and optimise surgical results.

PubMed

Burgos, Manuel A; Sevilla García, Maria Agustina; Sanmiguel Rojas, Enrique; Del Pino, Carlos; Fernández Velez, Carlos; Piqueras, Francisco; Esteban Ortega, Francisco

Computational fluid dynamics (CFD) is a mathematical tool to analyse airflow. We present a novel CFD software package to improve results following nasal surgery for obstruction. A group of engineers in collaboration with otolaryngologists have developed a very intuitive CFD software package called MeComLand®, which uses the patient's cross-sectional (tomographic) images, thus showing in detail results originated by CFD such as airflow distributions, velocity profiles, pressure, or wall shear stress. NOSELAND® helps medical evaluation with dynamic reports by using a 3D endoscopic view. Using this CFD-based software a patient underwent virtual surgery (septoplasty, turbinoplasty, spreader grafts, lateral crural J-flap and combinations) to choose the best improvement in nasal flow. To present a novel software package to improve nasal surgery results. To apply the software on CT slices from a patient affected by septal deviation. To evaluate several surgical procedures (septoplasty, turbinectomy, spreader-grafts, J-flap and combination among them) to find the best alternative with less morbidity. The combination of all the procedures does not provide the best nasal flow improvement. Septoplasty plus turbinoplasty obtained the best results. Turbinoplasty alone rendered almost similar results to septoplasty in our simulation. CFD provides useful complementary information to cover diagnosis, prognosis, and follow-up of nasal pathologies based on quantitative magnitudes linked to fluid flow. MeComLand®, DigBody® and NoseLand® represent a non-invasive, low-cost alternative for the functional study of patients with nasal obstruction. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Otorrinolaringología y Cirugía de Cabeza y Cuello. All rights reserved.

Halley's Comet and Beyond.

ERIC Educational Resources Information Center

Sneider, Cary; DeVore, Edna

1986-01-01

Reviews software packages under these headings: (1) simulations of experiments; (2) space flight simulators; (3) planetariums; (4) space adventure games; and (5) drill and practice packages (designed for testing purposes or for helping students learn basic astronomy vocabulary). (JN)

Reconstruction of an Immune Dynamic Model to Simulate the Contrasting Role of Auxin and Cytokinin in Plant Immunity.

PubMed

Kaltdorf, Martin; Dandekar, Thomas; Naseem, Muhammad

2017-01-01

In order to increase our understanding of biological dependencies in plant immune signaling pathways, the known interactions involved in plant immune networks are modeled. This allows computational analysis to predict the functions of growth related hormones in plant-pathogen interaction. The SQUAD (Standardized Qualitative Dynamical Systems) algorithm first determines stable system states in the network and then use them to compute continuous dynamical system states. Our reconstructed Boolean model encompassing hormone immune networks of Arabidopsis thaliana (Arabidopsis) and pathogenicity factors injected by model pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) can be exploited to determine the impact of growth hormones in plant immunity. We describe a detailed working protocol how to use the modified SQUAD-package by exemplifying the contrasting effects of auxin and cytokinins in shaping plant-pathogen interaction.

MODFLOW-2000 Ground-Water Model?User Guide to the Subsidence and Aquifer-System Compaction (SUB) Package

USGS Publications Warehouse

Hoffmann, Jörn; Leake, S.A.; Galloway, D.L.; Wilson, Alicia M.

2003-01-01

This report documents a computer program, the Subsidence and Aquifer-System Compaction (SUB) Package, to simulate aquifer-system compaction and land subsidence using the U.S. Geological Survey modular finite-difference ground-water flow model, MODFLOW-2000. The SUB Package simulates elastic (recoverable) compaction and expansion, and inelastic (permanent) compaction of compressible fine-grained beds (interbeds) within the aquifers. The deformation of the interbeds is caused by head or pore-pressure changes, and thus by changes in effective stress, within the interbeds. If the stress is less than the preconsolidation stress of the sediments, the deformation is elastic; if the stress is greater than the preconsolidation stress, the deformation is inelastic. The propagation of head changes within the interbeds is defined by a transient, one-dimensional (vertical) diffusion equation. This equation accounts for delayed release of water from storage or uptake of water into storage in the interbeds. Properties that control the timing of the storage changes are vertical hydraulic diffusivity and interbed thickness. The SUB Package supersedes the Interbed Storage Package (IBS1) for MODFLOW, which assumes that water is released from or taken into storage with changes in head in the aquifer within a single model time step and, therefore, can be reasonably used to simulate only thin interbeds. The SUB Package relaxes this assumption and can be used to simulate time-dependent drainage and compaction of thick interbeds and confining units. The time-dependent drainage can be turned off, in which case the SUB Package gives results identical to those from IBS1. Three sample problems illustrate the usefulness of the SUB Package. One sample problem verifies that the package works correctly. This sample problem simulates the drainage of a thick interbed in response to a step change in head in the adjacent aquifer and closely matches the analytical solution. A second sample problem illustrates the effects of seasonally varying discharge and recharge to an aquifer system with a thick interbed. A third sample problem simulates a multilayered regional ground-water basin. Model input files for the third sample problem are included in the appendix.

An Evaluative Review of Simulated Dynamic Smart 3d Objects

NASA Astrophysics Data System (ADS)

Romeijn, H.; Sheth, F.; Pettit, C. J.

2012-07-01

Three-dimensional (3D) modelling of plants can be an asset for creating agricultural based visualisation products. The continuum of 3D plants models ranges from static to dynamic objects, also known as smart 3D objects. There is an increasing requirement for smarter simulated 3D objects that are attributed mathematically and/or from biological inputs. A systematic approach to plant simulation offers significant advantages to applications in agricultural research, particularly in simulating plant behaviour and the influences of external environmental factors. This approach of 3D plant object visualisation is primarily evident from the visualisation of plants using photographed billboarded images, to more advanced procedural models that come closer to simulating realistic virtual plants. However, few programs model physical reactions of plants to external factors and even fewer are able to grow plants based on mathematical and/or biological parameters. In this paper, we undertake an evaluation of plant-based object simulation programs currently available, with a focus upon the components and techniques involved in producing these objects. Through an analytical review process we consider the strengths and weaknesses of several program packages, the features and use of these programs and the possible opportunities in deploying these for creating smart 3D plant-based objects to support agricultural research and natural resource management. In creating smart 3D objects the model needs to be informed by both plant physiology and phenology. Expert knowledge will frame the parameters and procedures that will attribute the object and allow the simulation of dynamic virtual plants. Ultimately, biologically smart 3D virtual plants that react to changes within an environment could be an effective medium to visually represent landscapes and communicate land management scenarios and practices to planners and decision-makers.

The dynamic and steady state behavior of a PEM fuel cell as an electric energy source

NASA Astrophysics Data System (ADS)

Costa, R. A.; Camacho, J. R.

The main objective of this work is to extract information on the internal behavior of three small polymer electrolyte membrane fuel cells under static and dynamic load conditions. A computational model was developed using Scilab [SCILAB 4, Scilab-a free scientific software package, http://www.scilab.org/, INRIA, France, December, 2005] to simulate the static and dynamic performance [J.M. Correa, A.F. Farret, L.N. Canha, An analysis of the dynamic performance of proton exchange membrane fuel cells using an electrochemical model, in: 27th Annual Conference of IEEE Industrial Electronics Society, 2001, pp. 141-146] of this particular type of fuel cell. This dynamic model is based on electrochemical equations and takes into consideration most of the chemical and physical characteristics of the device in order to generate electric power. The model takes into consideration the operating, design parameters and physical material properties. The results show the internal losses and concentration effects behavior, which are of interest for power engineers and researchers.

A Symbolic and Graphical Computer Representation of Dynamical Systems

NASA Astrophysics Data System (ADS)

Gould, Laurence I.

2005-04-01

AUTONO is a Macsyma/Maxima program, designed at the University of Hartford, for solving autonomous systems of differential equations as well as for relating Lagrangians and Hamiltonians to their associated dynamical equations. AUTONO can be used in a number of fields to decipher a variety of complex dynamical systems with ease, producing their Lagrangian and Hamiltonian equations in seconds. These equations can then be incorporated into VisSim, a modeling and simulation program, which yields graphical representations of motion in a given system through easily chosen input parameters. The program, along with the VisSim differential-equations graphical package, allows for resolution and easy understanding of complex problems in a relatively short time; thus enabling quicker and more advanced computing of dynamical systems on any number of platforms---from a network of sensors on a space probe, to the behavior of neural networks, to the effects of an electromagnetic field on components in a dynamical system. A flowchart of AUTONO, along with some simple applications and VisSim output, will be shown.

Detecting subnetwork-level dynamic correlations.

PubMed

Yan, Yan; Qiu, Shangzhao; Jin, Zhuxuan; Gong, Sihong; Bai, Yun; Lu, Jianwei; Yu, Tianwei

2017-01-15

The biological regulatory system is highly dynamic. The correlations between many functionally related genes change over different biological conditions. Finding dynamic relations on the existing biological network may reveal important regulatory mechanisms. Currently no method is available to detect subnetwork-level dynamic correlations systematically on the genome-scale network. Two major issues hampered the development. The first is gene expression profiling data usually do not contain time course measurements to facilitate the analysis of dynamic relations, which can be partially addressed by using certain genes as indicators of biological conditions. Secondly, it is unclear how to effectively delineate subnetworks, and define dynamic relations between them. Here we propose a new method named LANDD (Liquid Association for Network Dynamics Detection) to find subnetworks that show substantial dynamic correlations, as defined by subnetwork A is concentrated with Liquid Association scouting genes for subnetwork B. The method produces easily interpretable results because of its focus on subnetworks that tend to comprise functionally related genes. Also, the collective behaviour of genes in a subnetwork is a much more reliable indicator of underlying biological conditions compared to using single genes as indicators. We conducted extensive simulations to validate the method's ability to detect subnetwork-level dynamic correlations. Using a real gene expression dataset and the human protein-protein interaction network, we demonstrate the method links subnetworks of distinct biological processes, with both confirmed relations and plausible new functional implications. We also found signal transduction pathways tend to show extensive dynamic relations with other functional groups. The R package is available at https://cran.r-project.org/web/packages/LANDD CONTACTS: yunba@pcom.edu, jwlu33@hotmail.com or tianwei.yu@emory.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Literacity: A multimedia adult literacy package combining NASA technology, recursive ID theory, and authentic instruction theory

NASA Technical Reports Server (NTRS)

Willis, Jerry; Willis, Dee Anna; Walsh, Clare; Stephens, Elizabeth; Murphy, Timothy; Price, Jerry; Stevens, William; Jackson, Kevin; Villareal, James A.; Way, Bob

1994-01-01

An important part of NASA's mission involves the secondary application of its technologies in the public and private sectors. One current application under development is LiteraCity, a simulation-based instructional package for adults who do not have functional reading skills. Using fuzzy logic routines and other technologies developed by NASA's Information Systems Directorate and hypermedia sound, graphics, and animation technologies the project attempts to overcome the limited impact of adult literacy assessment and instruction by involving the adult in an interactive simulation of real-life literacy activities. The project uses a recursive instructional development model and authentic instruction theory. This paper describes one component of a project to design, develop, and produce a series of computer-based, multimedia instructional packages. The packages are being developed for use in adult literacy programs, particularly in correctional education centers. They use the concepts of authentic instruction and authentic assessment to guide development. All the packages to be developed are instructional simulations. The first is a simulation of 'finding a friend a job.'

Three-Dimensional (3D) Nanometrology Based on Scanning Electron Microscope (SEM) Stereophotogrammetry.

PubMed

Tondare, Vipin N; Villarrubia, John S; Vlada R, András E

2017-10-01

Three-dimensional (3D) reconstruction of a sample surface from scanning electron microscope (SEM) images taken at two perspectives has been known for decades. Nowadays, there exist several commercially available stereophotogrammetry software packages. For testing these software packages, in this study we used Monte Carlo simulated SEM images of virtual samples. A virtual sample is a model in a computer, and its true dimensions are known exactly, which is impossible for real SEM samples due to measurement uncertainty. The simulated SEM images can be used for algorithm testing, development, and validation. We tested two stereophotogrammetry software packages and compared their reconstructed 3D models with the known geometry of the virtual samples used to create the simulated SEM images. Both packages performed relatively well with simulated SEM images of a sample with a rough surface. However, in a sample containing nearly uniform and therefore low-contrast zones, the height reconstruction error was ≈46%. The present stereophotogrammetry software packages need further improvement before they can be used reliably with SEM images with uniform zones.

Gala: A Python package for galactic dynamics

NASA Astrophysics Data System (ADS)

Price-Whelan, Adrian M.

2017-10-01

Gala is an Astropy-affiliated Python package for galactic dynamics. Python enables wrapping low-level languages (e.g., C) for speed without losing flexibility or ease-of-use in the user-interface. The API for Gala was designed to provide a class-based and user-friendly interface to fast (C or Cython-optimized) implementations of common operations such as gravitational potential and force evaluation, orbit integration, dynamical transformations, and chaos indicators for nonlinear dynamics. Gala also relies heavily on and interfaces well with the implementations of physical units and astronomical coordinate systems in the Astropy package (astropy.units and astropy.coordinates). Gala was designed to be used by both astronomical researchers and by students in courses on gravitational dynamics or astronomy. It has already been used in a number of scientific publications and has also been used in graduate courses on Galactic dynamics to, e.g., provide interactive visualizations of textbook material.

C++QEDv2: The multi-array concept and compile-time algorithms in the definition of composite quantum systems

NASA Astrophysics Data System (ADS)

Vukics, András

2012-06-01

C++QED is a versatile framework for simulating open quantum dynamics. It allows to build arbitrarily complex quantum systems from elementary free subsystems and interactions, and simulate their time evolution with the available time-evolution drivers. Through this framework, we introduce a design which should be generic for high-level representations of composite quantum systems. It relies heavily on the object-oriented and generic programming paradigms on one hand, and on the other hand, compile-time algorithms, in particular C++ template-metaprogramming techniques. The core of the design is the data structure which represents the state vectors of composite quantum systems. This data structure models the multi-array concept. The use of template metaprogramming is not only crucial to the design, but with its use all computations pertaining to the layout of the simulated system can be shifted to compile time, hence cutting on runtime. Program summaryProgram title: C++QED Catalogue identifier: AELU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:http://cpc.cs.qub.ac.uk/licence/aelu_v1_0.html. The C++QED package contains other software packages, Blitz, Boost and FLENS, all of which may be distributed freely but have individual license requirements. Please see individual packages for license conditions. No. of lines in distributed program, including test data, etc.: 597 974 No. of bytes in distributed program, including test data, etc.: 4 874 839 Distribution format: tar.gz Programming language: C++ Computer: i386-i686, x86_64 Operating system: In principle cross-platform, as yet tested only on UNIX-like systems (including Mac OS X). RAM: The framework itself takes about 60 MB, which is fully shared. The additional memory taken by the program which defines the actual physical system (script) is typically less than 1 MB. The memory storing the actual data scales with the system dimension for state-vector manipulations, and the square of the dimension for density-operator manipulations. This might easily be GBs, and often the memory of the machine limits the size of the simulated system. Classification: 4.3, 4.13, 6.2, 20 External routines: Boost C++ libraries (http://www.boost.org/), GNU Scientific Library (http://www.gnu.org/software/gsl/), Blitz++ (http://www.oonumerics.org/blitz/), Linear Algebra Package - Flexible Library for Efficient Numerical Solutions (http://flens.sourceforge.net/). Nature of problem: Definition of (open) composite quantum systems out of elementary building blocks [1]. Manipulation of such systems, with emphasis on dynamical simulations such as Master-equation evolution [2] and Monte Carlo wave-function simulation [3]. Solution method: Master equation, Monte Carlo wave-function method. Restrictions: Total dimensionality of the system. Master equation - few thousands. Monte Carlo wave-function trajectory - several millions. Unusual features: Because of the heavy use of compile-time algorithms, compilation of programs written in the framework may take a long time and much memory (up to several GBs). Additional comments: The framework is not a program, but provides and implements an application-programming interface for developing simulations in the indicated problem domain. Supplementary information: http://cppqed.sourceforge.net/. Running time: Depending on the magnitude of the problem, can vary from a few seconds to weeks.

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

PubMed

Salomon-Ferrer, Romelia; Götz, Andreas W; Poole, Duncan; Le Grand, Scott; Walker, Ross C

2013-09-10

We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mechanical ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the technical details of the approach as it extends beyond previously reported work [Götz et al., J. Chem. Theory Comput. 2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm. 2013, DOI: 10.1016/j.cpc.2012.09.022].We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.

Flight simulation software at NASA Dryden Flight Research Center

NASA Technical Reports Server (NTRS)

Norlin, Ken A.

1995-01-01

The NASA Dryden Flight Research Center has developed a versatile simulation software package that is applicable to a broad range of fixed-wing aircraft. This package has evolved in support of a variety of flight research programs. The structure is designed to be flexible enough for use in batch-mode, real-time pilot-in-the-loop, and flight hardware-in-the-loop simulation. Current simulations operate on UNIX-based platforms and are coded with a FORTRAN shell and C support routines. This paper discusses the features of the simulation software design and some basic model development techniques. The key capabilities that have been included in the simulation are described. The NASA Dryden simulation software is in use at other NASA centers, within industry, and at several universities. The straightforward but flexible design of this well-validated package makes it especially useful in an engineering environment.

Evolutionary Design and Simulation of a Tube Crawling Inspection Robot

NASA Technical Reports Server (NTRS)

Craft, Michael; Howsman, Tom; ONeil, Daniel; Howell, Joe T. (Technical Monitor)

2002-01-01

The Space Robotics Assembly Team Simulation (SpaceRATS) is an expansive concept that will hopefully lead to a space flight demonstration of a robotic team cooperatively assembling a system from its constitutive parts. A primary objective of the SpaceRATS project is to develop a generalized evolutionary design approach for multiple classes of robots. The portion of the overall SpaceRats program associated with the evolutionary design and simulation of an inspection robot's morphology is the subject of this paper. The vast majority of this effort has concentrated on the use and modification of Darwin2K, a robotic design and simulation software package, to analyze the design of a tube crawling robot. This robot is designed for carrying out inspection duties in relatively inaccessible locations within a liquid rocket engine similar to the SSME. A preliminary design of the tube crawler robot was completed, and the mechanical dynamics of the system were simulated. An evolutionary approach to optimizing a few parameters of the system was utilized, resulting in a more optimum design.

Space life support engineering program

NASA Technical Reports Server (NTRS)

Seagrave, Richard C.

1991-01-01

This report covers the first six months of work performed under the NASA University Grant awarded to Iowa State University to perform research on two topics relating to the development of closed-loop long-term life support systems. A comprehensive study to develop software to simulate the dynamic operation of water reclamation systems in long-term closed-loop life support systems is being carried out as part of an overall program for the design of systems for a Mars voyage. This project is being done in parallel with a similar effort in the Department of Chemistry to develop durable accurate low-cost sensors for monitoring of trace chemical and biological species in recycled water supplies. Aspen-Plus software is being used on a group of high-performance workstations to develop the steady state descriptions for a number of existing technologies. Following completion, a dynamic simulation package will be developed for determining the response of such systems to changes in the metabolic needs of the crew and to upsets in system hardware performance.

Direct-coupled microcomputer-based building emulator for building energy management and control systems

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

Lam, H.N.

1999-07-01

In this paper, the development and implementation of a direct-coupled building emulator for a building energy management and control system (EMCS) is presented. The building emulator consists of a microcomputer and a computer model of an air-conditioning system implemented in a modular dynamic simulation software package for direct-coupling to an EMCS, without using analog-to-digital and digital-to-analog converters. The building emulator can be used to simulate in real time the behavior of the air-conditioning system under a given operating environment and subject to a given usage pattern. Software modules for data communication, graphical display, dynamic data exchange, and synchronization of simulationmore » outputs with real time have been developed to achieve direct digital data transfer between the building emulator and a commercial EMCS. Based on the tests conducted, the validity of the building emulator has been established and the proportional-plus-integral control function of the EMCS assessed.« less

Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

PubMed

Thomas, Philipp; Matuschek, Hannes; Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen's system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA's performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license.

Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion

PubMed Central

Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen’s system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA’s performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license. PMID:22723865

Detonation Propagation through Nitromethane Embedded Metal Foam

NASA Astrophysics Data System (ADS)

Lieberthal, Brandon; Maines, Warren R.; Stewart, D. Scott

2015-11-01

There is considerable interest in developing a better understanding of dynamic behaviors of multicomponent systems. We report results of Eulerian hydrodynamic simulations of shock waves propagating through metal foam at approximately 20% relative density and various porosities using a reactive flow model in the ALE3D software package. We investigate the applied pressure and energy of the shock wave and its effects on the fluid and the inert material interface. By varying pore sizes, as well as metal impedance, we predict the overall effects of heterogeneous material systems at the mesoscale. In addition, we observe a radially expanding blast front in these heterogeneous models and apply the theory of Detonation Shock Dynamics to the convergence behavior of the lead shock.

cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.

PubMed

Petkevičiūtė, D; Pasi, M; Gonzalez, O; Maddocks, J H

2014-11-10

cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model, (b) time-averaged atomistic molecular dynamics (or MD) simulations, and (c) NMR or X-ray experimental observation, for (i) the Dickerson-Drew dodecamer and (ii) three oligomers containing A-tracts. The cgDNA predictions are rather close to those of the MD simulations, but many orders of magnitude faster to compute. Both the cgDNA and MD predictions are in reasonable agreement with the available experimental data. Our conclusion is that cgDNA can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Modeling and analysis of equipment managers in manufacturing execution systems for semiconductor packaging.

PubMed

Cheng, F T; Yang, H C; Luo, T L; Feng, C; Jeng, M

2000-01-01

Equipment Managers (EMs) play a major role in a Manufacturing Execution System (MES). They serve as the communication bridge between the components of an MES and the equipment. The purpose of this paper is to propose a novel methodology for developing analytical and simulation models for the EM such that the validity and performance of the EM can be evaluated. Domain knowledge and requirements are collected from a real semiconductor packaging factory. By using IDEFO and state diagrams, a static functional model and a dynamic state model of the EM are built. Next, these two models are translated into a Petri net model. This allows qualitative and quantitative analyses of the system. The EM net model is then expanded into the MES net model. Therefore, the performance of an EM in the MES environment can be evaluated. These evaluation results are good references for design and decision making.

Mars Aerocapture Systems Study

NASA Technical Reports Server (NTRS)

Wright, Henry S.; Oh, David Y.; Westhelle, Carlos H.; Fisher, Jody L.; Dyke, R. Eric; Edquist, Karl T.; Brown, James L.; Justh, Hilary L.; Munk, Michelle M.

2006-01-01

Mars Aerocapture Systems Study (MASS) is a detailed study of the application of aerocapture to a large Mars robotic orbiter to assess and identify key technology gaps. This study addressed use of an Opposition class return segment for use in the Mars Sample Return architecture. Study addressed mission architecture issues as well as system design. Key trade studies focused on design of aerocapture aeroshell, spacecraft design and packaging, guidance, navigation and control with simulation, computational fluid dynamics, and thermal protection system sizing. Detailed master equipment lists are included as well as a cursory cost assessment.

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

Hart, David; Klise, Katherine A.

The PyEPANET package is a set of commands for the Python programming language that are built to wrap the EPANET toolkit library commands, without requiring the end user to program using the ctypes package. This package does not contain the EPANET code, nor does it implement the functions within the EPANET software, and it requires the separately downloaded or compiled EPANET2 toolkit dynamic library (epanet.dll, libepanent.so, or epanet.dylib) and/or the EPANET-MSX dynamic library in order to function.

Extreme scale multi-physics simulations of the tsunamigenic 2004 Sumatra megathrust earthquake

NASA Astrophysics Data System (ADS)

Ulrich, T.; Gabriel, A. A.; Madden, E. H.; Wollherr, S.; Uphoff, C.; Rettenberger, S.; Bader, M.

2017-12-01

SeisSol (www.seissol.org) is an open-source software package based on an arbitrary high-order derivative Discontinuous Galerkin method (ADER-DG). It solves spontaneous dynamic rupture propagation on pre-existing fault interfaces according to non-linear friction laws, coupled to seismic wave propagation with high-order accuracy in space and time (minimal dispersion errors). SeisSol exploits unstructured meshes to account for complex geometries, e.g. high resolution topography and bathymetry, 3D subsurface structure, and fault networks. We present the up-to-date largest (1500 km of faults) and longest (500 s) dynamic rupture simulation modeling the 2004 Sumatra-Andaman earthquake. We demonstrate the need for end-to-end-optimization and petascale performance of scientific software to realize realistic simulations on the extreme scales of subduction zone earthquakes: Considering the full complexity of subduction zone geometries leads inevitably to huge differences in element sizes. The main code improvements include a cache-aware wave propagation scheme and optimizations of the dynamic rupture kernels using code generation. In addition, a novel clustered local-time-stepping scheme for dynamic rupture has been established. Finally, asynchronous output has been implemented to overlap I/O and compute time. We resolve the frictional sliding process on the curved mega-thrust and a system of splay faults, as well as the seismic wave field and seafloor displacement with frequency content up to 2.2 Hz. We validate the scenario by geodetic, seismological and tsunami observations. The resulting rupture dynamics shed new light on the activation and importance of splay faults.

The Cloud Feedback Model Intercomparison Project Observational Simulator Package: Version 2

NASA Astrophysics Data System (ADS)

Swales, Dustin J.; Pincus, Robert; Bodas-Salcedo, Alejandro

2018-01-01

The Cloud Feedback Model Intercomparison Project Observational Simulator Package (COSP) gathers together a collection of observation proxies or satellite simulators that translate model-simulated cloud properties to synthetic observations as would be obtained by a range of satellite observing systems. This paper introduces COSP2, an evolution focusing on more explicit and consistent separation between host model, coupling infrastructure, and individual observing proxies. Revisions also enhance flexibility by allowing for model-specific representation of sub-grid-scale cloudiness, provide greater clarity by clearly separating tasks, support greater use of shared code and data including shared inputs across simulators, and follow more uniform software standards to simplify implementation across a wide range of platforms. The complete package including a testing suite is freely available.

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

PubMed Central

2012-01-01

We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs). We discuss the algorithms that are used to exploit the processing power of the GPUs and show the performance that can be achieved in comparison to simulations on conventional CPU clusters. The implementation supports three different precision models in which the contributions to the forces are calculated in single precision floating point arithmetic but accumulated in double precision (SPDP), or everything is computed in single precision (SPSP) or double precision (DPDP). In addition to performance, we have focused on understanding the implications of the different precision models on the outcome of implicit solvent MD simulations. We show results for a range of tests including the accuracy of single point force evaluations and energy conservation as well as structural properties pertainining to protein dynamics. The numerical noise due to rounding errors within the SPSP precision model is sufficiently large to lead to an accumulation of errors which can result in unphysical trajectories for long time scale simulations. We recommend the use of the mixed-precision SPDP model since the numerical results obtained are comparable with those of the full double precision DPDP model and the reference double precision CPU implementation but at significantly reduced computational cost. Our implementation provides performance for GB simulations on a single desktop that is on par with, and in some cases exceeds, that of traditional supercomputers. PMID:22582031

ATTIRE (analytical tools for thermal infrared engineering): A sensor simulation and modeling package

NASA Astrophysics Data System (ADS)

Jaggi, S.

1993-02-01

The Advanced Sensor Development Laboratory (ASDL) at the Stennis Space Center develops, maintains and calibrates remote sensing instruments for the National Aeronautics & Space Administration (NASA). To perform system design trade-offs, analysis, and establish system parameters, ASDL has developed a software package for analytical simulation of sensor systems. This package called 'Analytical Tools for Thermal InfraRed Engineering' - ATTIRE, simulates the various components of a sensor system. The software allows each subsystem of the sensor to be analyzed independently for its performance. These performance parameters are then integrated to obtain system level information such as Signal-to-Noise Ratio (SNR), Noise Equivalent Radiance (NER), Noise Equivalent Temperature Difference (NETD) etc. This paper describes the uses of the package and the physics that were used to derive the performance parameters.

XCAT/DRASIM: a realistic CT/human-model simulation package

NASA Astrophysics Data System (ADS)

Fung, George S. K.; Stierstorfer, Karl; Segars, W. Paul; Taguchi, Katsuyuki; Flohr, Thomas G.; Tsui, Benjamin M. W.

2011-03-01

The aim of this research is to develop a complete CT/human-model simulation package by integrating the 4D eXtended CArdiac-Torso (XCAT) phantom, a computer generated NURBS surface based phantom that provides a realistic model of human anatomy and respiratory and cardiac motions, and the DRASIM (Siemens Healthcare) CT-data simulation program. Unlike other CT simulation tools which are based on simple mathematical primitives or voxelized phantoms, this new simulation package has the advantages of utilizing a realistic model of human anatomy and physiological motions without voxelization and with accurate modeling of the characteristics of clinical Siemens CT systems. First, we incorporated the 4D XCAT anatomy and motion models into DRASIM by implementing a new library which consists of functions to read-in the NURBS surfaces of anatomical objects and their overlapping order and material properties in the XCAT phantom. Second, we incorporated an efficient ray-tracing algorithm for line integral calculation in DRASIM by computing the intersection points of the rays cast from the x-ray source to the detector elements through the NURBS surfaces of the multiple XCAT anatomical objects along the ray paths. Third, we evaluated the integrated simulation package by performing a number of sample simulations of multiple x-ray projections from different views followed by image reconstruction. The initial simulation results were found to be promising by qualitative evaluation. In conclusion, we have developed a unique CT/human-model simulation package which has great potential as a tool in the design and optimization of CT scanners, and the development of scanning protocols and image reconstruction methods for improving CT image quality and reducing radiation dose.

Air-cooling characteristics of simulated grape packages

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

Frederick, R.L.; Comunian, F.

Experimental simulation of the external forced convection on the outside of grape packages was performed. Average heat transfer coefficients for air flow around such containers were found to range from 8 to 13.4 W/(m[sup 2]K). A physical description of the convective process was formulated on the basis of data obtained in three types of experiment. Expressions for the average heat transfer coefficient from single packages in air flow were proposed.

A Tutorial on RxODE: Simulating Differential Equation Pharmacometric Models in R.

PubMed

Wang, W; Hallow, K M; James, D A

2016-01-01

This tutorial presents the application of an R package, RxODE, that facilitates quick, efficient simulations of ordinary differential equation models completely within R. Its application is illustrated through simulation of design decision effects on an adaptive dosing regimen. The package provides an efficient, versatile way to specify dosing scenarios and to perform simulation with variability with minimal custom coding. Models can be directly translated to Rshiny applications to facilitate interactive, real-time evaluation/iteration on simulation scenarios.

Molecular dynamics simulation: a tool for exploration and discovery using simple models

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

2014-12-01

Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome is not always a foregone conclusion. The present survey focuses on several simple model systems that exhibit surprisingly rich emergent behavior, all studied by molecular dynamics (MD) simulation. The examples are taken from the disparate fields of fluid dynamics, granular matter and supramolecular self-assembly. In studies of fluids modeled at the detailed microscopic level using discrete particles, the simulations demonstrate that complex hydrodynamic phenomena in rotating and convecting fluids—the Taylor-Couette and Rayleigh-Bénard instabilities—can not only be observed within the limited length and time scales accessible to MD, but even allow quantitative agreement to be achieved. Simulation of highly counter-intuitive segregation phenomena in granular mixtures, again using MD methods, but now augmented by forces producing damping and friction, leads to results that resemble experimentally observed axial and radial segregation in the case of a rotating cylinder and to a novel form of horizontal segregation in a vertically vibrated layer. Finally, when modeling self-assembly processes analogous to the formation of the polyhedral shells that package spherical viruses, simulation of suitably shaped particles reveals the ability to produce complete, error-free assembly and leads to the important general observation that reversible growth steps contribute to the high yield. While there are limitations to the MD approach, both computational and conceptual, the results offer a tantalizing hint of the kinds of phenomena that can be explored and what might be discovered when sufficient resources are brought to bear on a problem.

Performance of a reconfigured atmospheric general circulation model at low resolution

NASA Astrophysics Data System (ADS)

Wen, Xinyu; Zhou, Tianjun; Wang, Shaowu; Wang, Bin; Wan, Hui; Li, Jian

2007-07-01

Paleoclimate simulations usually require model runs over a very long time. The fast integration version of a state-of-the-art general circulation model (GCM), which shares the same physical and dynamical processes but with reduced horizontal resolution and increased time step, is usually developed. In this study, we configure a fast version of an atmospheric GCM (AGCM), the Grid Atmospheric Model of IAP/LASG (Institute of Atmospheric Physics/State Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics), at low resolution (GAMIL-L, hereafter), and compare the simulation results with the NCEP/NCAR reanalysis and other data to examine its performance. GAMIL-L, which is derived from the original GAMIL, is a finite difference AGCM with 72×40 grids in longitude and latitude and 26 vertical levels. To validate the simulated climatology and variability, two runs were achieved. One was a 60-year control run with fixed climatological monthly sea surface temperature (SST) forcing, and the other was a 50-yr (1950 2000) integration with observational time-varying monthly SST forcing. Comparisons between these two cases and the reanalysis, including intra-seasonal and inter-annual variability are also presented. In addition, the differences between GAMIL-L and the original version of GAMIL are also investigated. The results show that GAMIL-L can capture most of the large-scale dynamical features of the atmosphere, especially in the tropics and mid latitudes, although a few deficiencies exist, such as the underestimated Hadley cell and thereby the weak strength of the Asia summer monsoon. However, the simulated mean states over high latitudes, especially over the polar regions, are not acceptable. Apart from dynamics, the thermodynamic features mainly depend upon the physical parameterization schemes. Since the physical package of GAMIL-L is exactly the same as the original high-resolution version of GAMIL, in which the NCAR Community Atmosphere Model (CAM2) physical package was used, there are only small differences between them in the precipitation and temperature fields. Because our goal is to develop a fast-running AGCM and employ it in the coupled climate system model of IAP/LASG for paleoclimate studies such as ENSO and Australia-Asia monsoon, particular attention has been paid to the model performances in the tropics. More model validations, such as those ran for the Southern Oscillation and South Asia monsoon, indicate that GAMIL-L is reasonably competent and valuable in this regard.

Guidelines for the analysis of free energy calculations

PubMed Central

Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.

2015-01-01

Free energy calculations based on molecular dynamics (MD) simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical–analysis.py, freely available on GitHub at https://github.com/choderalab/pymbar–examples, that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope these tools and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134

A Python tool to set up relative free energy calculations in GROMACS

PubMed Central

Klimovich, Pavel V.; Mobley, David L.

2015-01-01

Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper [14], recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge [16]. Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations. PMID:26487189

A Geant4 simulation of the depth dose percentage in brain tumors treatments using protons and carbon ions

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

Diaz, José A. M., E-mail: joadiazme@unal.edu.co; Torres, D. A., E-mail: datorresg@unal.edu.co

2016-07-07

The deposited energy and dose distribution of beams of protons and carbon over a head are simulated using the free tool package Geant4 and the data analysis package ROOT-C++. The present work shows a methodology to understand the microscopical process occurring in a session of hadron-therapy using advance simulation tools.

Increasing the Number of Replications in Item Response Theory Simulations: Automation through SAS and Disk Operating System

ERIC Educational Resources Information Center

Gagne, Phill; Furlow, Carolyn; Ross, Terris

2009-01-01

In item response theory (IRT) simulation research, it is often necessary to use one software package for data generation and a second software package to conduct the IRT analysis. Because this can substantially slow down the simulation process, it is sometimes offered as a justification for using very few replications. This article provides…

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

PubMed

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-07-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

Dynamic contrast-enhanced MRI: Study of inter-software accuracy and reproducibility using simulated and clinical data.

PubMed

Beuzit, Luc; Eliat, Pierre-Antoine; Brun, Vanessa; Ferré, Jean-Christophe; Gandon, Yves; Bannier, Elise; Saint-Jalmes, Hervé

2016-06-01

To test the reproducibility and accuracy of pharmacokinetic parameter measurements on five analysis software packages (SPs) for dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), using simulated and clinical data. This retrospective study was Institutional Review Board-approved. Simulated tissues consisted of pixel clusters of calculated dynamic signal changes for combinations of Tofts model pharmacokinetic parameters (volume transfer constant [K(trans) ], extravascular extracellular volume fraction [ve ]), longitudinal relaxation time (T1 ). The clinical group comprised 27 patients treated for rectal cancer, with 36 3T DCE-MR scans performed between November 2012 and February 2014, including dual-flip-angle T1 mapping and a dynamic postcontrast T1 -weighted, 3D spoiled gradient-echo sequence. The clinical and simulated images were postprocessed with five SPs to measure K(trans) , ve , and the initial area under the gadolinium curve (iAUGC). Modified Bland-Altman analysis was conducted, intraclass correlation coefficients (ICCs) and within-subject coefficients of variation were calculated. Thirty-one examinations from 23 patients were of sufficient technical quality and postprocessed. Measurement errors were observed on the simulated data for all the pharmacokinetic parameters and SPs, with a bias ranging from -0.19 min(-1) to 0.09 min(-1) for K(trans) , -0.15 to 0.01 for ve , and -0.65 to 1.66 mmol.L(-1) .min for iAUGC. The ICC between SPs revealed moderate agreement for the simulated data (K(trans) : 0.50; ve : 0.67; iAUGC: 0.77) and very poor agreement for the clinical data (K(trans) : 0.10; ve : 0.16; iAUGC: 0.21). Significant errors were found in the calculated DCE-MRI pharmacokinetic parameters for the perfusion analysis SPs, resulting in poor inter-software reproducibility. J. Magn. Reson. Imaging 2016;43:1288-1300. © 2015 Wiley Periodicals, Inc.

Dynamics of beta-amyloid peptide in cholesterol superlattice domain

NASA Astrophysics Data System (ADS)

Smirnov, Anton; Zhu, Qing; Vaughn, Mark; Khare, Rajesh; Cheng, K.

2006-10-01

Presence of beta-amyloid peptide (beta-A) plagues in membranes of neuron cells is a clinical signature of Alzheimer disease. The onset of beta-A peptide aggregation occurs via a conformational transition from an alpha-helix state to a beta-sheet state. A gradual build-up of beta-A content in the neuronal extracellular space is another characteristic of the beta-A plague formation. Hypothetically, both the pathological conformation and the predominant localization of the beta-A can be a result of specific dynamic characteristics of the interphase between cellular membrane and extracellular milieu. In this study, the beta-A interphase problem has been investigated using a virtual membrane model implemented on the base of GROMACS molecular dynamics simulation package. The detailed folding pattern of beta-A has been examined using a novice interphase model comprised of a cholesterol supperlattice membrane and two water layers.

On Fitting Generalized Linear Mixed-effects Models for Binary Responses using Different Statistical Packages

PubMed Central

Zhang, Hui; Lu, Naiji; Feng, Changyong; Thurston, Sally W.; Xia, Yinglin; Tu, Xin M.

2011-01-01

Summary The generalized linear mixed-effects model (GLMM) is a popular paradigm to extend models for cross-sectional data to a longitudinal setting. When applied to modeling binary responses, different software packages and even different procedures within a package may give quite different results. In this report, we describe the statistical approaches that underlie these different procedures and discuss their strengths and weaknesses when applied to fit correlated binary responses. We then illustrate these considerations by applying these procedures implemented in some popular software packages to simulated and real study data. Our simulation results indicate a lack of reliability for most of the procedures considered, which carries significant implications for applying such popular software packages in practice. PMID:21671252

Advances in HYDRA and its application to simulations of Inertial Confinement Fusion targets

NASA Astrophysics Data System (ADS)

Marinak, M. M.; Kerbel, G. D.; Koning, J. M.; Patel, M. V.; Sepke, S. M.; Brown, P. N.; Chang, B.; Procassini, R.; Veitzer, S. A.

2008-11-01

We will outline new capabilities added to the HYDRA 2D/3D multiphysics ICF simulation code. These include a new SN multigroup radiation transport package (1D), constitutive models for elastic-plastic (strength) effects, and a mix model. A Monte Carlo burn package is being incorporated to model diagnostic signatures of neutrons, gamma rays and charged particles. A 3D MHD package that treats resistive MHD is available. Improvements to HYDRA's implicit Monte Carlo photonics package, including the addition of angular biasing, now enable integrated hohlraum simulations to complete in substantially shorter time. The heavy ion beam deposition package now includes a new model for ion stopping power developed by the Tech-X Corporation, with improved accuracy below the Bragg peak. Examples will illustrate HYDRA's enhanced capabilities to simulate various aspects of inertial confinement fusion targets.This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344. The work of Tech-X personnel was funded by the Department of Energy under Small Business Innovation Research Contract No. DE-FG02-03ER83797.

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

PubMed Central

2016-01-01

Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date, the discovery of allosteric binding sites and lead compounds has been mostly serendipitous, achieved through high-throughput screening. Over the past decade, structural data has become more readily available for larger protein systems and more membrane protein classes (e.g., GPCRs and ion channels), which are common allosteric drug targets. In parallel, improved simulation methods now provide better atomistic understanding of the protein dynamics and cooperative motions that are critical to allosteric mechanisms. As a result of these advances, the field of predictive allosteric drug development is now on the cusp of a new era of rational structure-based computational methods. Here, we review algorithms that predict allosteric sites based on sequence data and molecular dynamics simulations, describe tools that assess the druggability of these pockets, and discuss how Markov state models and topology analyses provide insight into the relationship between protein dynamics and allosteric drug binding. In each section, we first provide an overview of the various method classes before describing relevant algorithms and software packages. PMID:27074285

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.

PubMed

Wagner, Jeffrey R; Lee, Christopher T; Durrant, Jacob D; Malmstrom, Robert D; Feher, Victoria A; Amaro, Rommie E

2016-06-08

Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date, the discovery of allosteric binding sites and lead compounds has been mostly serendipitous, achieved through high-throughput screening. Over the past decade, structural data has become more readily available for larger protein systems and more membrane protein classes (e.g., GPCRs and ion channels), which are common allosteric drug targets. In parallel, improved simulation methods now provide better atomistic understanding of the protein dynamics and cooperative motions that are critical to allosteric mechanisms. As a result of these advances, the field of predictive allosteric drug development is now on the cusp of a new era of rational structure-based computational methods. Here, we review algorithms that predict allosteric sites based on sequence data and molecular dynamics simulations, describe tools that assess the druggability of these pockets, and discuss how Markov state models and topology analyses provide insight into the relationship between protein dynamics and allosteric drug binding. In each section, we first provide an overview of the various method classes before describing relevant algorithms and software packages.

Implementation of interconnect simulation tools in spice

NASA Technical Reports Server (NTRS)

Satsangi, H.; Schutt-Aine, J. E.

1993-01-01

Accurate computer simulation of high speed digital computer circuits and communication circuits requires a multimode approach to simulate both the devices and the interconnects between devices. Classical circuit analysis algorithms (lumped parameter) are needed for circuit devices and the network formed by the interconnected devices. The interconnects, however, have to be modeled as transmission lines which incorporate electromagnetic field analysis. An approach to writing a multimode simulator is to take an existing software package which performs either lumped parameter analysis or field analysis and add the missing type of analysis routines to the package. In this work a traditionally lumped parameter simulator, SPICE, is modified so that it will perform lossy transmission line analysis using a different model approach. Modifying SPICE3E2 or any other large software package is not a trivial task. An understanding of the programming conventions used, simulation software, and simulation algorithms is required. This thesis was written to clarify the procedure for installing a device into SPICE3E2. The installation of three devices is documented and the installations of the first two provide a foundation for installation of the lossy line which is the third device. The details of discussions are specific to SPICE, but the concepts will be helpful when performing installations into other circuit analysis packages.

Regional demand forecasting and simulation model: user's manual. Task 4, final report

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

Parhizgari, A M

1978-09-25

The Department of Energy's Regional Demand Forecasting Model (RDFOR) is an econometric and simulation system designed to estimate annual fuel-sector-region specific consumption of energy for the US. Its purposes are to (1) provide the demand side of the Project Independence Evaluation System (PIES), (2) enhance our empirical insights into the structure of US energy demand, and (3) assist policymakers in their decisions on and formulations of various energy policies and/or scenarios. This report provides a self-contained user's manual for interpreting, utilizing, and implementing RDFOR simulation software packages. Chapters I and II present the theoretical structure and the simulation of RDFOR,more » respectively. Chapter III describes several potential scenarios which are (or have been) utilized in the RDFOR simulations. Chapter IV presents an overview of the complete software package utilized in simulation. Chapter V provides the detailed explanation and documentation of this package. The last chapter describes step-by-step implementation of the simulation package using the two scenarios detailed in Chapter III. The RDFOR model contains 14 fuels: gasoline, electricity, natural gas, distillate and residual fuels, liquid gases, jet fuel, coal, oil, petroleum products, asphalt, petroleum coke, metallurgical coal, and total fuels, spread over residential, commercial, industrial, and transportation sectors.« less

Implementation and use of direct-flow connections in a coupled ground-water and surface-water model

USGS Publications Warehouse

Swain, Eric D.

1994-01-01

The U.S. Geological Survey's MODFLOW finite-difference ground-water flow model has been coupled with three surface-water packages - the MODBRANCH, River, and Stream packages - to simulate surface water and its interaction with ground water. Prior to the development of the coupling packages, the only interaction between these modeling packages was that leakage values could be passed between MODFLOW and the three surface-water packages. To facilitate wider and more flexible uses of the models, a computer program was developed and added to MODFLOW to allow direct flows or stages to be passed between any of the packages and MODFLOW. The flows or stages calculated in one package can be set as boundary discharges or stages to be used in another package. Several modeling packages can be used in the same simulation depending upon the level of sophistication needed in the various reaches being modeled. This computer program is especially useful when any of the River, Stream, or MODBRANCH packages are used to model a river flowing directly into or out of wetlands in direct connection with the aquifer and represented in the model as an aquifer block. A field case study is shown to illustrate an application.

Estimating the impact of enterprise resource planning project management decisions on post-implementation maintenance costs: a case study using simulation modelling

NASA Astrophysics Data System (ADS)

Fryling, Meg

2010-11-01

Organisations often make implementation decisions with little consideration for the maintenance phase of an enterprise resource planning (ERP) system, resulting in significant recurring maintenance costs. Poor cost estimations are likely related to the lack of an appropriate framework for enterprise-wide pre-packaged software maintenance, which requires an ongoing relationship with the software vendor (Markus, M.L., Tanis, C., and Fenema, P.C., 2000. Multisite ERP implementation. CACM, 43 (4), 42-46). The end result is that critical project decisions are made with little empirical data, resulting in substantial long-term cost impacts. The product of this research is a formal dynamic simulation model that enables theory testing, scenario exploration and policy analysis. The simulation model ERPMAINT1 was developed by combining and extending existing frameworks in several research domains, and by incorporating quantitative and qualitative case study data. The ERPMAINT1 model evaluates tradeoffs between different ERP project management decisions and their impact on post-implementation total cost of ownership (TCO). Through model simulations a variety of dynamic insights were revealed that could assist ERP project managers. Major findings from the simulation show that upfront investments in mentoring and system exposure translate to long-term cost savings. The findings also indicate that in addition to customisations, add-ons have a significant impact on TCO.

Molecular docking and dynamics simulations of A.niger RNase from Aspergillus niger ATCC26550: for potential prevention of human cancer.

PubMed

Kumar, Gundampati Ravi; Chikati, Rajasekhar; Pandrangi, Santhi Latha; Kandapal, Manoj; Sonkar, Kirti; Gupta, Neeraj; Mulakayala, Chaitanya; Jagannadham, Medicherla V; Kumar, Chitta Suresh; Saxena, Sunita; Das, Mira Debnath

2013-02-01

The aim of the present research was to study the anticancer effects of Aspergillus niger (A.niger) RNase. We found that RNase (A.niger RNase) significantly and dose dependently inhibited invasiveness of breast cancer cell line MDA MB 231 by 55 % (P<0.01) at 1 μM concentration. At a concentration of 2 μM, the anti invasive effect of the enzyme increased to 90 % (P<0.002). Keeping the aim to determine molecular level interactions (molecular simulations and protein docking) of human actin with A.niger RNase we extended our work in-vitro to in-silico studies. To gain better relaxation and accurate arrangement of atoms, refinement was done on the human actin and A.niger RNase by energy minimization (EM) and molecular dynamics (MD) simulations using 43A(2) force field of Gromacs96 implemented in the Gromacs 4.0.5 package, finally the interaction energies were calculated by protein-protein docking using the HEX. These in vitro and in-silico structural studies prove the effective inhibition of actin activity by A.niger RNase in neoplastic cells and thereby provide new insights for the development of novel anti cancer drugs.

Molecular Dynamics Simulations of Hydration Effects on Solvation, Diffusivity, and Permeability in Chitosan/Chitin Films.

PubMed

McDonnell, Marshall T; Greeley, Duncan A; Kit, Kevin M; Keffer, David J

2016-09-01

The effects of hydration on the solvation, diffusivity, solubility, and permeability of oxygen molecules in sustainable, biodegradable chitosan/chitin food packaging films were studied via molecular dynamics and confined random walk simulations. With increasing hydration, the membrane has a more homogeneous water distribution with the polymer chains being fully solvated. The diffusivity increased by a factor of 4 for oxygen molecules and by an order of magnitude for water with increasing the humidity. To calculate the Henry's constant and solubility of oxygen in the membranes with changing hydration, the excess chemical potential was calculated via free energy perturbation, thermodynamic integration and direct particle deletion methods. The simulations predicted a higher solubility and permeability for the lower humidity, in contradiction to experimental results. All three methods for calculating the solubility were in good agreement. It was found that the Coulombic interactions in the potential caused the oxygen to bind too strongly to the protonated amine group. Insight from this work will help guide molecular modeling of chitosan/chitin membranes, specifically permeability measurements for small solute molecules. Efforts to chemically tailor chitosan/chitin membranes to favor discrete as opposed to continuous aqueous domains could reduce oxygen permeability.

Simulating the Dynamics of Earth's Core: Using NCCS Supercomputers Speeds Calculations

NASA Technical Reports Server (NTRS)

2002-01-01

If one wanted to study Earth's core directly, one would have to drill through about 1,800 miles of solid rock to reach liquid core-keeping the tunnel from collapsing under pressures that are more than 1 million atmospheres and then sink an instrument package to the bottom that could operate at 8,000 F with 10,000 tons of force crushing every square inch of its surface. Even then, several of these tunnels would probably be needed to obtain enough data. Faced with difficult or impossible tasks such as these, scientists use other available sources of information - such as seismology, mineralogy, geomagnetism, geodesy, and, above all, physical principles - to derive a model of the core and, study it by running computer simulations. One NASA researcher is doing just that on NCCS computers. Physicist and applied mathematician Weijia Kuang, of the Space Geodesy Branch, and his collaborators at Goddard have what he calls the,"second - ever" working, usable, self-consistent, fully dynamic, three-dimensional geodynamic model (see "The Geodynamic Theory"). Kuang runs his model simulations on the supercomputers at the NCCS. He and Jeremy Bloxham, of Harvard University, developed the original version, written in Fortran 77, in 1996.

Software package for modeling spin-orbit motion in storage rings

NASA Astrophysics Data System (ADS)

Zyuzin, D. V.

2015-12-01

A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 106-109 particles in a beam during 109 turns in an accelerator (about 1012-1015 integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin-orbit dynamics.

An order (n) algorithm for the dynamics simulation of robotic systems

NASA Technical Reports Server (NTRS)

Chun, H. M.; Turner, J. D.; Frisch, Harold P.

1989-01-01

The formulation of an Order (n) algorithm for DISCOS (Dynamics Interaction Simulation of Controls and Structures), which is an industry-standard software package for simulation and analysis of flexible multibody systems is presented. For systems involving many bodies, the new Order (n) version of DISCOS is much faster than the current version. Results of the experimental validation of the dynamics software are also presented. The experiment is carried out on a seven-joint robot arm at NASA's Goddard Space Flight Center. The algorithm used in the current version of DISCOS requires the inverse of a matrix whose dimension is equal to the number of constraints in the system. Generally, the number of constraints in a system is roughly proportional to the number of bodies in the system, and matrix inversion requires O(p exp 3) operations, where p is the dimension of the matrix. The current version of DISCOS is therefore considered an Order (n exp 3) algorithm. In contrast, the Order (n) algorithm requires inversion of matrices which are small, and the number of matrices to be inverted increases only linearly with the number of bodies. The newly-developed Order (n) DISCOS is currently capable of handling chain and tree topologies as well as multiple closed loops. Continuing development will extend the capability of the software to deal with typical robotics applications such as put-and-place, multi-arm hand-off and surface sliding.

An electron-beam dose deposition experiment: TIGER 1-D simulation code versus thermoluminescent dosimetry

NASA Astrophysics Data System (ADS)

Murrill, Steven R.; Tipton, Charles W.; Self, Charles T.

1991-03-01

The dose absorbed in an integrated circuit (IC) die exposed to a pulse of low-energy electrons is a strong function of both electron energy and surrounding packaging materials. This report describes an experiment designed to measure how well the Integrated TIGER Series one-dimensional (1-D) electron transport simulation program predicts dose correction factors for a state-of-the-art IC package and package/printed circuit board (PCB) combination. These derived factors are compared with data obtained experimentally using thermoluminescent dosimeters (TLD's) and the FX-45 flash x-ray machine (operated in electron-beam (e-beam) mode). The results of this experiment show that the TIGER 1-D simulation code can be used to accurately predict FX-45 e-beam dose deposition correction factors for reasonably complex IC packaging configurations.

Documentation of a computer program to simulate aquifer-system compaction using the modular finite-difference ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Prudic, David E.

1991-01-01

Removal of ground water by pumping from aquifers may result in compaction of compressible fine-grained beds that are within or adjacent to the aquifers. Compaction of the sediments and resulting land subsidence may be permanent if the head declines result in vertical stresses beyond the previous maximum stress. The process of permanent compaction is not routinely included in simulations of ground-water flow. To simulate storage changes from both elastic and inelastic compaction, a computer program was written for use with the U.S. Geological Survey modular finite-difference ground- water flow model. The new program, the Interbed-Storage Package, is designed to be incorporated into this model. In the Interbed-Storage Package, elastic compaction or expansion is assumed to be proportional to change in head. The constant of proportionality is the product of the skeletal component of elastic specific storage and the thickness of the sediments. Similarly, inelastic compaction is assumed to be proportional to decline in head. The constant of proportionality is the product of the skeletal component of inelastic specific storage and the thickness of the sediments. Storage changes are incorporated into the ground-water flow model by adding an additional term to the right-hand side of the flow equation. Within a model time step, the package appropriately apportions storage changes between elastic and inelastic components on the basis of the relation of simulated head to the previous minimum (preconsolidation) head. Two tests were performed to verify that the package works correctly. The first test compared model-calculated storage and compaction changes to hand-calculated values for a three-dimensional simulation. Model and hand-calculated values were essentially equal. The second test was performed to compare the results of the Interbed-Storage Package with results of the one-dimensional Helm compaction model. This test problem simulated compaction in doubly draining confining beds stressed by head changes in adjacent aquifers. The Interbed-Storage Package and the Helm model computed essentially equal values of compaction. Documentation of the Interbed-Storage Package includes data input instructions, flow charts, narratives, and listings for each of the five modules included in the package. The documentation also includes an appendix describing input instructions and a listing of a computer program for time-variant specified-head boundaries. That package was developed to reduce the amount of data input and output associated with one of the Interbed-Storage Package test problems.

Using GPU parallelization to perform realistic simulations of the LPCTrap experiments

NASA Astrophysics Data System (ADS)

Fabian, X.; Mauger, F.; Quéméner, G.; Velten, Ph.; Ban, G.; Couratin, C.; Delahaye, P.; Durand, D.; Fabre, B.; Finlay, P.; Fléchard, X.; Liénard, E.; Méry, A.; Naviliat-Cuncic, O.; Pons, B.; Porobic, T.; Severijns, N.; Thomas, J. C.

2015-11-01

The LPCTrap setup is a sensitive tool to measure the β - ν angular correlation coefficient, a β ν , which can yield the mixing ratio ρ of a β decay transition. The latter enables the extraction of the Cabibbo-Kobayashi-Maskawa (CKM) matrix element V u d . In such a measurement, the most relevant observable is the energy distribution of the recoiling daughter nuclei following the nuclear β decay, which is obtained using a time-of-flight technique. In order to maximize the precision, one can reduce the systematic errors through a thorough simulation of the whole set-up, especially with a correct model of the trapped ion cloud. This paper presents such a simulation package and focuses on the ion cloud features; particular attention is therefore paid to realistic descriptions of trapping field dynamics, buffer gas cooling and the N-body space charge effects.

LB3D: A parallel implementation of the Lattice-Boltzmann method for simulation of interacting amphiphilic fluids

NASA Astrophysics Data System (ADS)

Schmieschek, S.; Shamardin, L.; Frijters, S.; Krüger, T.; Schiller, U. D.; Harting, J.; Coveney, P. V.

2017-08-01

We introduce the lattice-Boltzmann code LB3D, version 7.1. Building on a parallel program and supporting tools which have enabled research utilising high performance computing resources for nearly two decades, LB3D version 7 provides a subset of the research code functionality as an open source project. Here, we describe the theoretical basis of the algorithm as well as computational aspects of the implementation. The software package is validated against simulations of meso-phases resulting from self-assembly in ternary fluid mixtures comprising immiscible and amphiphilic components such as water-oil-surfactant systems. The impact of the surfactant species on the dynamics of spinodal decomposition are tested and quantitative measurement of the permeability of a body centred cubic (BCC) model porous medium for a simple binary mixture is described. Single-core performance and scaling behaviour of the code are reported for simulations on current supercomputer architectures.

Robust design of an inkjet-printed capacitive sensor for position tracking of a MOEMS-mirror in a Michelson interferometer setup

NASA Astrophysics Data System (ADS)

Faller, Lisa-Marie; Zangl, Hubert

2017-05-01

To guarantee high performance of Micro Optical Electro Mechanical Systems (MOEMS), precise position feedback is crucial. To overcome drawbacks of widely used optical feedback, we propose an inkjet-printed capacitive position sensor as smart packaging solution. Printing processes suffer from tolerances in excess of those from standard processes. Thus, FEM simulations covering assumed tolerances of the system are adopted. These simulations are structured following a Design Of Computer Experiments (DOCE) and are then employed to determine a optimal sensor design. Based on the simulation results, statistical models are adopted for the dynamic system. These models are to be used together with specifically designed hardware, considered to cope with challenging requirements of ≍50nm position accuracy at 10MS/s with 1000μm measurement range. Noise analysis is performed considering the influence of uncertainties to assess resolution and bandwidth capabilities.

Numerical simulation of transient temperature profiles for canned apple puree in semi-rigid aluminum based packaging during pasteurization.

PubMed

Shafiekhani, Soraya; Zamindar, Nafiseh; Hojatoleslami, Mohammad; Toghraie, Davood

2016-06-01

Pasteurization of canned apple puree was simulated for a 3-D geometry in a semi-rigid aluminum based container which was heated from all sides at 378 K. The computational fluid dynamics code Ansys Fluent 14.0 was used and the governing equations for energy, momentum, and continuity were computed using a finite volume method. The food model was assumed to have temperature-dependent properties. To validate the simulation, the apple puree was pasteurized in a water cascading retort. The effect of the mesh structures was studied for the temperature profiles during thermal processing. The experimental temperature in the slowest heating zone in the container was compared with the temperature predicted by the model and the difference was not significant. The study also investigated the impact of head space (water-vapor) on heat transfer.

Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Pandey, Ras; Farmer, Barry

Ebola virus matrix protein VP40 (consisting of 326 residues) plays a critical role in viral assembly and its functions such as regulation of viral transcription, packaging, and budding of mature virions into the plasma membrane of infected cells. How does the protein VP40 go through structural evolution during the viral life cycle remains an open question? Using a coarse-grained Monte Carlo simulation we investigate the structural evolution of VP40 as a function of temperature with the input of a knowledge-based residue-residue interaction. A number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) are analyzed with our large-scale simulations. Our preliminary data show that the structure of the protein evolves through different state with well-defined morphologies which can be identified and quantified via a detailed analysis of structure factor.

Isentropic Compression up to 200 KBars for LX 04, Numerical Simulations and Comparison with Experiments

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

Lefrancois, A.; Hare, D.; L'Eplattenier, P.

2006-02-13

Isentropic compression experiments and numerical simulations on LX-04 (HMX / Viton 85/15) were performed respectively at Z accelerator facility from Sandia National Laboratory and at Lawrence Livermore National Laboratory in order to study the isentrope and associated Hugoniot of this HE. 2D and 3D configurations have been calculated here to test the new beta version of the electromagnetism package coupled with the dynamics in Ls-Dyna and compared with the ICE Z shot 1067 on LX 04. The electromagnetism module is being developed in the general-purpose explicit and implicit finite element program LS-DYNA{reg_sign} in order to perform coupled mechanical/thermal/electromagnetism simulations. Themore » Maxwell equations are solved using a Finite Element Method (FEM) for the solid conductors coupled with a Boundary Element Method (BEM) for the surrounding air (or vacuum). More details can be read in the references.« less

Gaussian Accelerated Molecular Dynamics in NAMD

PubMed Central

2016-01-01

Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that provides efficient free energy calculations of biomolecules. Like the previous accelerated molecular dynamics (aMD), GaMD allows for “unconstrained” enhanced sampling without the need to set predefined collective variables and so is useful for studying complex biomolecular conformational changes such as protein folding and ligand binding. Furthermore, because the boost potential is constructed using a harmonic function that follows Gaussian distribution in GaMD, cumulant expansion to the second order can be applied to recover the original free energy profiles of proteins and other large biomolecules, which solves a long-standing energetic reweighting problem of the previous aMD method. Taken together, GaMD offers major advantages for both unconstrained enhanced sampling and free energy calculations of large biomolecules. Here, we have implemented GaMD in the NAMD package on top of the existing aMD feature and validated it on three model systems: alanine dipeptide, the chignolin fast-folding protein, and the M3 muscarinic G protein-coupled receptor (GPCR). For alanine dipeptide, while conventional molecular dynamics (cMD) simulations performed for 30 ns are poorly converged, GaMD simulations of the same length yield free energy profiles that agree quantitatively with those of 1000 ns cMD simulation. Further GaMD simulations have captured folding of the chignolin and binding of the acetylcholine (ACh) endogenous agonist to the M3 muscarinic receptor. The reweighted free energy profiles are used to characterize the protein folding and ligand binding pathways quantitatively. GaMD implemented in the scalable NAMD is widely applicable to enhanced sampling and free energy calculations of large biomolecules. PMID:28034310

Gaussian Accelerated Molecular Dynamics in NAMD.

PubMed

Pang, Yui Tik; Miao, Yinglong; Wang, Yi; McCammon, J Andrew

2017-01-10

Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that provides efficient free energy calculations of biomolecules. Like the previous accelerated molecular dynamics (aMD), GaMD allows for "unconstrained" enhanced sampling without the need to set predefined collective variables and so is useful for studying complex biomolecular conformational changes such as protein folding and ligand binding. Furthermore, because the boost potential is constructed using a harmonic function that follows Gaussian distribution in GaMD, cumulant expansion to the second order can be applied to recover the original free energy profiles of proteins and other large biomolecules, which solves a long-standing energetic reweighting problem of the previous aMD method. Taken together, GaMD offers major advantages for both unconstrained enhanced sampling and free energy calculations of large biomolecules. Here, we have implemented GaMD in the NAMD package on top of the existing aMD feature and validated it on three model systems: alanine dipeptide, the chignolin fast-folding protein, and the M 3 muscarinic G protein-coupled receptor (GPCR). For alanine dipeptide, while conventional molecular dynamics (cMD) simulations performed for 30 ns are poorly converged, GaMD simulations of the same length yield free energy profiles that agree quantitatively with those of 1000 ns cMD simulation. Further GaMD simulations have captured folding of the chignolin and binding of the acetylcholine (ACh) endogenous agonist to the M 3 muscarinic receptor. The reweighted free energy profiles are used to characterize the protein folding and ligand binding pathways quantitatively. GaMD implemented in the scalable NAMD is widely applicable to enhanced sampling and free energy calculations of large biomolecules.

Application of the ADAMS program to deployable space truss structures

NASA Technical Reports Server (NTRS)

Calleson, R. E.

1985-01-01

The need for a computer program to perform kinematic and dynamic analyses of large truss structures while deploying from a packaged configuration in space led to the evaluation of several existing programs. ADAMS (automatic dynamic analysis of mechanical systems), a generalized program from performing the dynamic simulation of mechanical systems undergoing large displacements, is applied to two concepts of deployable space antenna units. One concept is a one cube folding unit of Martin Marietta's Box Truss Antenna and the other is a tetrahedral truss unit of a Tetrahedral Truss Antenna. Adequate evaluation of dynamic forces during member latch-up into the deployed configuration is not yet available from the present version of ADAMS since it is limited to the assembly of rigid bodies. Included is a method for estimating the maximum bending stress in a surface member at latch-up. Results include member displacement and velocity responses during extension and an example of member bending stresses at latch-up.

Smooth time-dependent receiver operating characteristic curve estimators.

PubMed

Martínez-Camblor, Pablo; Pardo-Fernández, Juan Carlos

2018-03-01

The receiver operating characteristic curve is a popular graphical method often used to study the diagnostic capacity of continuous (bio)markers. When the considered outcome is a time-dependent variable, two main extensions have been proposed: the cumulative/dynamic receiver operating characteristic curve and the incident/dynamic receiver operating characteristic curve. In both cases, the main problem for developing appropriate estimators is the estimation of the joint distribution of the variables time-to-event and marker. As usual, different approximations lead to different estimators. In this article, the authors explore the use of a bivariate kernel density estimator which accounts for censored observations in the sample and produces smooth estimators of the time-dependent receiver operating characteristic curves. The performance of the resulting cumulative/dynamic and incident/dynamic receiver operating characteristic curves is studied by means of Monte Carlo simulations. Additionally, the influence of the choice of the required smoothing parameters is explored. Finally, two real-applications are considered. An R package is also provided as a complement to this article.

Design of object-oriented distributed simulation classes

NASA Technical Reports Server (NTRS)

Schoeffler, James D. (Principal Investigator)

1995-01-01

Distributed simulation of aircraft engines as part of a computer aided design package is being developed by NASA Lewis Research Center for the aircraft industry. The project is called NPSS, an acronym for 'Numerical Propulsion Simulation System'. NPSS is a flexible object-oriented simulation of aircraft engines requiring high computing speed. It is desirable to run the simulation on a distributed computer system with multiple processors executing portions of the simulation in parallel. The purpose of this research was to investigate object-oriented structures such that individual objects could be distributed. The set of classes used in the simulation must be designed to facilitate parallel computation. Since the portions of the simulation carried out in parallel are not independent of one another, there is the need for communication among the parallel executing processors which in turn implies need for their synchronization. Communication and synchronization can lead to decreased throughput as parallel processors wait for data or synchronization signals from other processors. As a result of this research, the following have been accomplished. The design and implementation of a set of simulation classes which result in a distributed simulation control program have been completed. The design is based upon MIT 'Actor' model of a concurrent object and uses 'connectors' to structure dynamic connections between simulation components. Connectors may be dynamically created according to the distribution of objects among machines at execution time without any programming changes. Measurements of the basic performance have been carried out with the result that communication overhead of the distributed design is swamped by the computation time of modules unless modules have very short execution times per iteration or time step. An analytical performance model based upon queuing network theory has been designed and implemented. Its application to realistic configurations has not been carried out.

Design of Object-Oriented Distributed Simulation Classes

NASA Technical Reports Server (NTRS)

Schoeffler, James D.

1995-01-01

Distributed simulation of aircraft engines as part of a computer aided design package being developed by NASA Lewis Research Center for the aircraft industry. The project is called NPSS, an acronym for "Numerical Propulsion Simulation System". NPSS is a flexible object-oriented simulation of aircraft engines requiring high computing speed. It is desirable to run the simulation on a distributed computer system with multiple processors executing portions of the simulation in parallel. The purpose of this research was to investigate object-oriented structures such that individual objects could be distributed. The set of classes used in the simulation must be designed to facilitate parallel computation. Since the portions of the simulation carried out in parallel are not independent of one another, there is the need for communication among the parallel executing processors which in turn implies need for their synchronization. Communication and synchronization can lead to decreased throughput as parallel processors wait for data or synchronization signals from other processors. As a result of this research, the following have been accomplished. The design and implementation of a set of simulation classes which result in a distributed simulation control program have been completed. The design is based upon MIT "Actor" model of a concurrent object and uses "connectors" to structure dynamic connections between simulation components. Connectors may be dynamically created according to the distribution of objects among machines at execution time without any programming changes. Measurements of the basic performance have been carried out with the result that communication overhead of the distributed design is swamped by the computation time of modules unless modules have very short execution times per iteration or time step. An analytical performance model based upon queuing network theory has been designed and implemented. Its application to realistic configurations has not been carried out.

Software Integration in Multi-scale Simulations: the PUPIL System

NASA Astrophysics Data System (ADS)

Torras, J.; Deumens, E.; Trickey, S. B.

2006-10-01

The state of the art for computational tools in both computational chemistry and computational materials physics includes many algorithms and functionalities which are implemented again and again. Several projects aim to reduce, eliminate, or avoid this problem. Most such efforts seem to be focused within a particular specialty, either quantum chemistry or materials physics. Multi-scale simulations, by their very nature however, cannot respect that specialization. In simulation of fracture, for example, the energy gradients that drive the molecular dynamics (MD) come from a quantum mechanical treatment that most often derives from quantum chemistry. That “QM” region is linked to a surrounding “CM” region in which potentials yield the forces. The approach therefore requires the integration or at least inter-operation of quantum chemistry and materials physics algorithms. The same problem occurs in “QM/MM” simulations in computational biology. The challenge grows if pattern recognition or other analysis codes of some kind must be used as well. The most common mode of inter-operation is user intervention: codes are modified as needed and data files are managed “by hand” by the user (interactively and via shell scripts). User intervention is however inefficient by nature, difficult to transfer to the community, and prone to error. Some progress (e.g Sethna’s work at Cornell [C.R. Myers et al., Mat. Res. Soc. Symp. Proc., 538(1999) 509, C.-S. Chen et al., Poster presented at the Material Research Society Meeting (2000)]) has been made on using Python scripts to achieve a more efficient level of interoperation. In this communication we present an alternative approach to merging current working packages without the necessity of major recoding and with only a relatively light wrapper interface. The scheme supports communication among the different components required for a given multi-scale calculation and access to the functionalities of those components for the potential user. A general main program allows the management of every package with a special communication protocol between their interfaces following the directives introduced by the user which are stored in an XML structured file. The initial prototype of the PUPIL (Program for User Packages Interfacing and Linking) system has been done using Java as a fast, easy prototyping object oriented (OO) language. In order to test it, we have applied this prototype to a previously studied problem, the fracture of a silica nanorod. We did so joining two different packages to do a QM/MD calculation. The results show the potential for this software system to do different kind of simulations and its simplicity of maintenance.

Teaching Science and Mathematics Subjects Using the Excel Spreadsheet Package

ERIC Educational Resources Information Center

Ibrahim, Dogan

2009-01-01

The teaching of scientific subjects usually require laboratories where students can put the theory they have learned into practice. Traditionally, electronic programmable calculators, dedicated software, or expensive software simulation packages, such as MATLAB have been used to simulate scientific experiments. Recently, spreadsheet programs have…

PLATSIM: A Simulation and Analysis Package for Large-Order Flexible Systems. Version 2.0

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Kenny, Sean P.; Giesy, Daniel P.

1997-01-01

The software package PLATSIM provides efficient time and frequency domain analysis of large-order generic space platforms. PLATSIM can perform open-loop analysis or closed-loop analysis with linear or nonlinear control system models. PLATSIM exploits the particular form of sparsity of the plant matrices for very efficient linear and nonlinear time domain analysis, as well as frequency domain analysis. A new, original algorithm for the efficient computation of open-loop and closed-loop frequency response functions for large-order systems has been developed and is implemented within the package. Furthermore, a novel and efficient jitter analysis routine which determines jitter and stability values from time simulations in a very efficient manner has been developed and is incorporated in the PLATSIM package. In the time domain analysis, PLATSIM simulates the response of the space platform to disturbances and calculates the jitter and stability values from the response time histories. In the frequency domain analysis, PLATSIM calculates frequency response function matrices and provides the corresponding Bode plots. The PLATSIM software package is written in MATLAB script language. A graphical user interface is developed in the package to provide convenient access to its various features.

Structural and thermodynamic principles of viral packaging.

PubMed

Petrov, Anton S; Harvey, Stephen C

2007-01-01

Packaging of genetic material inside a capsid is one of the major processes in the lifecycle of bacteriophages. To establish the basic principles of packing double-stranded DNA into a phage, we present a low-resolution model of bacteriophage varphi29 and report simulations of DNA packaging. The simulations show excellent agreement with available experimental data, including the forces of packaging and the average structures seen in cryo-electron microscopy. The conformation of DNA inside the bacteriophage is primarily determined by the shape of the capsid and the elastic properties of DNA, but the energetics of packaging are dominated by electrostatic repulsions and the large entropic penalty associated with DNA confinement. In this slightly elongated capsid, the DNA assumes a folded toroidal conformation, rather than a coaxial spool. The model can be used to study packaging of other bacteriophages with different shapes under a range of environmental conditions.

Extended shortest path selection for package routing of complex networks

NASA Astrophysics Data System (ADS)

Ye, Fan; Zhang, Lei; Wang, Bing-Hong; Liu, Lu; Zhang, Xing-Yi

The routing strategy plays a very important role in complex networks such as Internet system and Peer-to-Peer networks. However, most of the previous work concentrates only on the path selection, e.g. Flooding and Random Walk, or finding the shortest path (SP) and rarely considering the local load information such as SP and Distance Vector Routing. Flow-based Routing mainly considers load balance and still cannot achieve best optimization. Thus, in this paper, we propose a novel dynamic routing strategy on complex network by incorporating the local load information into SP algorithm to enhance the traffic flow routing optimization. It was found that the flow in a network is greatly affected by the waiting time of the network, so we should not consider only choosing optimized path for package transformation but also consider node congestion. As a result, the packages should be transmitted with a global optimized path with smaller congestion and relatively short distance. Analysis work and simulation experiments show that the proposed algorithm can largely enhance the network flow with the maximum throughput within an acceptable calculating time. The detailed analysis of the algorithm will also be provided for explaining the efficiency.

Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite

DOE PAGES

Pogorelov, N.V.; Borovikov, S. N.; Bedford, M. C.; ...

2013-04-01

Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS) is a package of numerical codes capable of performing adaptive mesh refinement simulations of complex plasma flows in the presence of discontinuities and charge exchange between ions and neutral atoms. The flow of the ionized component is described with the ideal MHD equations, while the transport of atoms is governed either by the Boltzmann equation or multiple Euler gas dynamics equations. We have enhanced the code with additional physical treatments for the transport of turbulence and acceleration of pickup ions in the interplanetary space and at the termination shock. In this article, we present themore » results of our numerical simulation of the solar wind (SW) interaction with the local interstellar medium (LISM) in different time-dependent and stationary formulations. Numerical results are compared with the Ulysses, Voyager, and OMNI observations. Finally, the SW boundary conditions are derived from in-situ spacecraft measurements and remote observations.« less

Simulation and Analyses of Stage Separation Two-Stage Reusable Launch Vehicles

NASA Technical Reports Server (NTRS)

Pamadi, Bandu N.; Neirynck, Thomas A.; Hotchko, Nathaniel J.; Tartabini, Paul V.; Scallion, William I.; Murphy, Kelly J.; Covell, Peter F.

2005-01-01

NASA has initiated the development of methodologies, techniques and tools needed for analysis and simulation of stage separation of next generation reusable launch vehicles. As a part of this activity, ConSep simulation tool is being developed which is a MATLAB-based front-and-back-end to the commercially available ADAMS(registered Trademark) solver, an industry standard package for solving multi-body dynamic problems. This paper discusses the application of ConSep to the simulation and analysis of staging maneuvers of two-stage-to-orbit (TSTO) Bimese reusable launch vehicles, one staging at Mach 3 and the other at Mach 6. The proximity and isolated aerodynamic database were assembled using the data from wind tunnel tests conducted at NASA Langley Research Center. The effects of parametric variations in mass, inertia, flight path angle, altitude from their nominal values at staging were evaluated. Monte Carlo runs were performed for Mach 3 staging to evaluate the sensitivity to uncertainties in aerodynamic coefficients.

Simulation and Analyses of Stage Separation of Two-Stage Reusable Launch Vehicles

NASA Technical Reports Server (NTRS)

Pamadi, Bandu N.; Neirynck, Thomas A.; Hotchko, Nathaniel J.; Tartabini, Paul V.; Scallion, William I.; Murphy, K. J.; Covell, Peter F.

2007-01-01

NASA has initiated the development of methodologies, techniques and tools needed for analysis and simulation of stage separation of next generation reusable launch vehicles. As a part of this activity, ConSep simulation tool is being developed which is a MATLAB-based front-and-back-end to the commercially available ADAMS(Registerd TradeMark) solver, an industry standard package for solving multi-body dynamic problems. This paper discusses the application of ConSep to the simulation and analysis of staging maneuvers of two-stage-to-orbit (TSTO) Bimese reusable launch vehicles, one staging at Mach 3 and the other at Mach 6. The proximity and isolated aerodynamic database were assembled using the data from wind tunnel tests conducted at NASA Langley Research Center. The effects of parametric variations in mass, inertia, flight path angle, altitude from their nominal values at staging were evaluated. Monte Carlo runs were performed for Mach 3 staging to evaluate the sensitivity to uncertainties in aerodynamic coefficients.

An infectious way to teach students about outbreaks.

PubMed

Cremin, Íde; Watson, Oliver; Heffernan, Alastair; Imai, Natsuko; Ahmed, Norin; Bivegete, Sandra; Kimani, Teresia; Kyriacou, Demetris; Mahadevan, Preveina; Mustafa, Rima; Pagoni, Panagiota; Sophiea, Marisa; Whittaker, Charlie; Beacroft, Leo; Riley, Steven; Fisher, Matthew C

2018-06-01

The study of infectious disease outbreaks is required to train today's epidemiologists. A typical way to introduce and explain key epidemiological concepts is through the analysis of a historical outbreak. There are, however, few training options that explicitly utilise real-time simulated stochastic outbreaks where the participants themselves comprise the dataset they subsequently analyse. In this paper, we present a teaching exercise in which an infectious disease outbreak is simulated over a five-day period and subsequently analysed. We iteratively developed the teaching exercise to offer additional insight into analysing an outbreak. An R package for visualisation, analysis and simulation of the outbreak data was developed to accompany the practical to reinforce learning outcomes. Computer simulations of the outbreak revealed deviations from observed dynamics, highlighting how simplifying assumptions conventionally made in mathematical models often differ from reality. Here we provide a pedagogical tool for others to use and adapt in their own settings. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

NASA Astrophysics Data System (ADS)

Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

2010-09-01

The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full documentation is provided in the distribution file. This includes an INSTALL file giving details of how to build the package. A set of test runs is provided in the examples directory. The distribution file for this program is over 90 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or ab-initio molecular dynamics simulation on hundreds of atoms.

Simulation-based Bayesian inference for latent traits of item response models: Introduction to the ltbayes package for R.

PubMed

Johnson, Timothy R; Kuhn, Kristine M

2015-12-01

This paper introduces the ltbayes package for R. This package includes a suite of functions for investigating the posterior distribution of latent traits of item response models. These include functions for simulating realizations from the posterior distribution, profiling the posterior density or likelihood function, calculation of posterior modes or means, Fisher information functions and observed information, and profile likelihood confidence intervals. Inferences can be based on individual response patterns or sets of response patterns such as sum scores. Functions are included for several common binary and polytomous item response models, but the package can also be used with user-specified models. This paper introduces some background and motivation for the package, and includes several detailed examples of its use.

Thick photosensitive polyimide film side wall angle variability and scum improvement for IC packaging stress control

NASA Astrophysics Data System (ADS)

Mehta, Sohan Singh; Yeung, Marco; Mirza, Fahad; Raman, Thiagarajan; Longenbach, Travis; Morgan, Justin; Duggan, Mark; Soedibyo, Rio A.; Reidy, Sean; Rabie, Mohamed; Cho, Jae Kyu; Premachandran, C. S.; Faruqui, Danish

2018-03-01

In this paper, we demonstrate photosensitive polyimide (PSPI) profile optimization to effectively reduce stress concentrations and enable PSPI as protection package-induced stress. Through detailed package simulation, we demonstrate 45% reduction in stress as the sidewall angle (SWA) of PSPI is increased from 45 to 80 degrees in Cu pillar package types. Through modulation of coating and develop multi-step baking temperature and time, as well as dose energy and post litho surface treatments, we demonstrate a method for reliably obtaining PSPI sidewall angle >75 degree. Additionally, we experimentally validate the simulation findings that PSPI sidewall angle impacts chip package interaction (CPI). Finally, we conclude this paper with PSPI material and tool qualification requirements for future technology node based on current challenges.

On fitting generalized linear mixed-effects models for binary responses using different statistical packages.

PubMed

Zhang, Hui; Lu, Naiji; Feng, Changyong; Thurston, Sally W; Xia, Yinglin; Zhu, Liang; Tu, Xin M

2011-09-10

The generalized linear mixed-effects model (GLMM) is a popular paradigm to extend models for cross-sectional data to a longitudinal setting. When applied to modeling binary responses, different software packages and even different procedures within a package may give quite different results. In this report, we describe the statistical approaches that underlie these different procedures and discuss their strengths and weaknesses when applied to fit correlated binary responses. We then illustrate these considerations by applying these procedures implemented in some popular software packages to simulated and real study data. Our simulation results indicate a lack of reliability for most of the procedures considered, which carries significant implications for applying such popular software packages in practice. Copyright © 2011 John Wiley & Sons, Ltd.

A Generic Simulation Framework for Non-Entangled based Experimental Quantum Cryptography and Communication: Quantum Cryptography and Communication Simulator (QuCCs)

NASA Astrophysics Data System (ADS)

Buhari, Abudhahir; Zukarnain, Zuriati Ahmad; Khalid, Roszelinda; Zakir Dato', Wira Jaafar Ahmad

2016-11-01

The applications of quantum information science move towards bigger and better heights for the next generation technology. Especially, in the field of quantum cryptography and quantum computation, the world already witnessed various ground-breaking tangible product and promising results. Quantum cryptography is one of the mature field from quantum mechanics and already available in the markets. The current state of quantum cryptography is still under various researches in order to reach the heights of digital cryptography. The complexity of quantum cryptography is higher due to combination of hardware and software. The lack of effective simulation tool to design and analyze the quantum cryptography experiments delays the reaching distance of the success. In this paper, we propose a framework to achieve an effective non-entanglement based quantum cryptography simulation tool. We applied hybrid simulation technique i.e. discrete event, continuous event and system dynamics. We also highlight the limitations of a commercial photonic simulation tool based experiments. Finally, we discuss ideas for achieving one-stop simulation package for quantum based secure key distribution experiments. All the modules of simulation framework are viewed from the computer science perspective.

SLiM 2: Flexible, Interactive Forward Genetic Simulations.

PubMed

Haller, Benjamin C; Messer, Philipp W

2017-01-01

Modern population genomic datasets hold immense promise for revealing the evolutionary processes operating in natural populations, but a crucial prerequisite for this goal is the ability to model realistic evolutionary scenarios and predict their expected patterns in genomic data. To that end, we present SLiM 2: an evolutionary simulation framework that combines a powerful, fast engine for forward population genetic simulations with the capability of modeling a wide variety of complex evolutionary scenarios. SLiM achieves this flexibility through scriptability, which provides control over most aspects of the simulated evolutionary scenarios with a simple R-like scripting language called Eidos. An example SLiM simulation is presented to illustrate the power of this approach. SLiM 2 also includes a graphical user interface for simulation construction, interactive runtime control, and dynamic visualization of simulation output, facilitating easy and fast model development with quick prototyping and visual debugging. We conclude with a performance comparison between SLiM and two other popular forward genetic simulation packages. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Browndye: A software package for Brownian dynamics

NASA Astrophysics Data System (ADS)

Huber, Gary A.; McCammon, J. Andrew

2010-11-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. Program summaryProgram title: Browndye Catalogue identifier: AEGT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license, included in distribution No. of lines in distributed program, including test data, etc.: 143 618 No. of bytes in distributed program, including test data, etc.: 1 067 861 Distribution format: tar.gz Programming language: C++, OCaml ( http://caml.inria.fr/) Computer: PC, Workstation, Cluster Operating system: Linux Has the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreads RAM: Depends linearly on size of physical system Classification: 3 External routines: uses the output of APBS [1] ( http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained and installed separately. Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne Twister. These are included in the Browndye distribution. Nature of problem: Exploration and determination of rate constants of bimolecular interactions involving large biological molecules. Solution method: Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces. Running time: Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.

A Turbine Based Combined Cycle Engine Inlet Model and Mode Transition Simulation Based on HiTECC Tool

NASA Technical Reports Server (NTRS)

Csank, Jeffrey; Stueber, Thomas

2012-01-01

An inlet system is being tested to evaluate methodologies for a turbine based combined cycle propulsion system to perform a controlled inlet mode transition. Prior to wind tunnel based hardware testing of controlled mode transitions, simulation models are used to test, debug, and validate potential control algorithms. One candidate simulation package for this purpose is the High Mach Transient Engine Cycle Code (HiTECC). The HiTECC simulation package models the inlet system, propulsion systems, thermal energy, geometry, nozzle, and fuel systems. This paper discusses the modification and redesign of the simulation package and control system to represent the NASA large-scale inlet model for Combined Cycle Engine mode transition studies, mounted in NASA Glenn s 10-foot by 10-foot Supersonic Wind Tunnel. This model will be used for designing and testing candidate control algorithms before implementation.

A Turbine Based Combined Cycle Engine Inlet Model and Mode Transition Simulation Based on HiTECC Tool

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Stueber, Thomas J.

2012-01-01

An inlet system is being tested to evaluate methodologies for a turbine based combined cycle propulsion system to perform a controlled inlet mode transition. Prior to wind tunnel based hardware testing of controlled mode transitions, simulation models are used to test, debug, and validate potential control algorithms. One candidate simulation package for this purpose is the High Mach Transient Engine Cycle Code (HiTECC). The HiTECC simulation package models the inlet system, propulsion systems, thermal energy, geometry, nozzle, and fuel systems. This paper discusses the modification and redesign of the simulation package and control system to represent the NASA large-scale inlet model for Combined Cycle Engine mode transition studies, mounted in NASA Glenn s 10- by 10-Foot Supersonic Wind Tunnel. This model will be used for designing and testing candidate control algorithms before implementation.

Some aspects of robotics calibration, design and control

NASA Technical Reports Server (NTRS)

Tawfik, Hazem

1990-01-01

The main objective is to introduce techniques in the areas of testing and calibration, design, and control of robotic systems. A statistical technique is described that analyzes a robot's performance and provides quantitative three-dimensional evaluation of its repeatability, accuracy, and linearity. Based on this analysis, a corrective action should be taken to compensate for any existing errors and enhance the robot's overall accuracy and performance. A comparison between robotics simulation software packages that were commercially available (SILMA, IGRIP) and that of Kennedy Space Center (ROBSIM) is also included. These computer codes simulate the kinematics and dynamics patterns of various robot arm geometries to help the design engineer in sizing and building the robot manipulator and control system. A brief discussion on an adaptive control algorithm is provided.

SIMWEST - A simulation model for wind energy storage systems

NASA Technical Reports Server (NTRS)

Edsinger, R. W.; Warren, A. W.; Gordon, L. H.; Chang, G. C.

1978-01-01

This paper describes a comprehensive and efficient computer program for the modeling of wind energy systems with storage. The level of detail of SIMWEST (SImulation Model for Wind Energy STorage) is consistent with evaluating the economic feasibility as well as the general performance of wind energy systems with energy storage options. The software package consists of two basic programs and a library of system, environmental, and control components. The first program is a precompiler which allows the library components to be put together in building block form. The second program performs the technoeconomic system analysis with the required input/output, and the integration of system dynamics. An example of the application of the SIMWEST program to a current 100 kW wind energy storage system is given.

Numerical simulation of flows around deformed aircraft model in a wind tunnel

NASA Astrophysics Data System (ADS)

Lysenkov, A. V.; Bosnyakov, S. M.; Glazkov, S. A.; Gorbushin, A. R.; Kuzmina, S. I.; Kursakov, I. A.; Matyash, S. V.; Ishmuratov, F. Z.

2016-10-01

To obtain accurate data of calculation method error requires detailed simulation of the experiment in wind tunnel with keeping all features of the model, installation and gas flow. Two examples of such detailed data comparison are described in this paper. The experimental characteristics of NASA CRM model obtained in the ETW wind tunnel (Cologne, Germany), and CFD characteristics of this model obtained with the use of EWT-TsAGI application package are compared. Following comparison is carried out for an airplane model in the T-128 wind tunnel (TsAGI, Russia). It is seen that deformation influence on integral characteristics grows with increasing Re number and, accordingly, the dynamic pressure. CFD methods application for problems of experimental research in the wind tunnel allows to separate viscosity and elasticity effects.

High Performance Computing Modeling Advances Accelerator Science for High-Energy Physics

DOE PAGES

Amundson, James; Macridin, Alexandru; Spentzouris, Panagiotis

2014-07-28

The development and optimization of particle accelerators are essential for advancing our understanding of the properties of matter, energy, space, and time. Particle accelerators are complex devices whose behavior involves many physical effects on multiple scales. Therefore, advanced computational tools utilizing high-performance computing are essential for accurately modeling them. In the past decade, the US Department of Energy's SciDAC program has produced accelerator-modeling tools that have been employed to tackle some of the most difficult accelerator science problems. The authors discuss the Synergia framework and its applications to high-intensity particle accelerator physics. Synergia is an accelerator simulation package capable ofmore » handling the entire spectrum of beam dynamics simulations. Our authors present Synergia's design principles and its performance on HPC platforms.« less

Multi-dimensional simulation package for ultrashort pulse laser-matter interactions

NASA Astrophysics Data System (ADS)

Suslova, Anastassiya; Hassanein, Ahmed

2017-10-01

Advanced simulation models recently became a popular tool of investigation of ultrashort pulse lasers (USPLs) to enhance understanding of the physics and allow minimizing the experimental costs for optimization of laser and target parameters for various applications. Our research interest is focused on developing multi-dimensional simulation package FEMTO-2D to investigate the USPL-matter interactions and laser induced effects. The package is based on solution of two heat conduction equations for electron and lattice sub-systems - enhanced two temperature model (TTM). We have implemented theoretical approach based on the collision theory to define the thermal dependence of target material optical properties and thermodynamic parameters. Our approach allowed elimination of fitted parameters commonly used in TTM based simulations. FEMTO-2D is used to simulated the light absorption and interactions for several metallic targets as a function of wavelength and pulse duration for wide range of laser intensity. The package has capability to consider different angles of incidence and polarization. It has also been used to investigate the damage threshold of the gold coated optical components with the focus on the role of the film thickness and substrate heat sink effect. This work was supported by the NSF, PIRE project.

Dynamic simulation of train-truck collision at level crossings

NASA Astrophysics Data System (ADS)

Ling, Liang; Guan, Qinghua; Dhanasekar, Manicka; Thambiratnam, David P.

2017-01-01

Trains crashing onto heavy road vehicles stuck across rail tracks are more likely occurrences at level crossings due to ongoing increase in the registration of heavy vehicles and these long heavy vehicles getting caught in traffic after partly crossing the boom gate; these incidents lead to significant financial losses and societal costs. This paper presents an investigation of the dynamic responses of trains under frontal collision on road trucks obliquely stuck on rail tracks at level crossings. This study builds a nonlinear three-dimensional multi-body dynamic model of a passenger train colliding with an obliquely stuck road truck on a ballasted track. The model is first benchmarked against several train dynamics packages and its predictions of the dynamic response and derailment potential are shown rational. A geometry-based derailment assessment criterion is applied to evaluate the derailment behaviour of the frontal obliquely impacted trains under different conditions. Sensitivities of several key influencing parameters, such as the train impact speed, the truck mass, the friction at truck tyres, the train-truck impact angle, the contact friction at the collision zone, the wheel/rail friction and the train suspension are reported.

AirSTAR: A UAV Platform for Flight Dynamics and Control System Testing

NASA Technical Reports Server (NTRS)

Jordan, Thomas L.; Foster, John V.; Bailey, Roger M.; Belcastro, Christine M.

2006-01-01

As part of the NASA Aviation Safety Program at Langley Research Center, a dynamically scaled unmanned aerial vehicle (UAV) and associated ground based control system are being developed to investigate dynamics modeling and control of large transport vehicles in upset conditions. The UAV is a 5.5% (seven foot wingspan), twin turbine, generic transport aircraft with a sophisticated instrumentation and telemetry package. A ground based, real-time control system is located inside an operations vehicle for the research pilot and associated support personnel. The telemetry system supports over 70 channels of data plus video for the downlink and 30 channels for the control uplink. Data rates are in excess of 200 Hz. Dynamic scaling of the UAV, which includes dimensional, weight, inertial, actuation, and control system scaling, is required so that the sub-scale vehicle will realistically simulate the flight characteristics of the full-scale aircraft. This testbed will be utilized to validate modeling methods, flight dynamics characteristics, and control system designs for large transport aircraft, with the end goal being the development of technologies to reduce the fatal accident rate due to loss-of-control.

A novel methodology to model the cooling processes of packed horticultural produce using 3D shape models

NASA Astrophysics Data System (ADS)

Gruyters, Willem; Verboven, Pieter; Rogge, Seppe; Vanmaercke, Simon; Ramon, Herman; Nicolai, Bart

2017-10-01

Freshly harvested horticultural produce require a proper temperature management to maintain their high economic value. Towards this end, low temperature storage is of crucial importance to maintain a high product quality. Optimizing both the package design of packed produce and the different steps in the postharvest cold chain can be achieved by numerical modelling of the relevant transport phenomena. This work presents a novel methodology to accurately model both the random filling of produce in a package and the subsequent cooling process. First, a cultivar-specific database of more than 100 realistic CAD models of apple and pear fruit is built with a validated geometrical 3D shape model generator. To have an accurate representation of a realistic picking season, the model generator also takes into account the biological variability of the produce shape. Next, a discrete element model (DEM) randomly chooses surface meshed bodies from the database to simulate the gravitational filling process of produce in a box or bin, using actual mechanical properties of the fruit. A computational fluid dynamics (CFD) model is then developed with the final stacking arrangement of the produce to study the cooling efficiency of packages under several conditions and configurations. Here, a typical precooling operation is simulated to demonstrate the large differences between using actual 3D shapes of the fruit and an equivalent spheres approach that simplifies the problem drastically. From this study, it is concluded that using a simplified representation of the actual fruit shape may lead to a severe overestimation of the cooling behaviour.

Coarse-graining to the meso and continuum scales with molecular-dynamics-like models

NASA Astrophysics Data System (ADS)

Plimpton, Steve

Many engineering-scale problems that industry or the national labs try to address with particle-based simulations occur at length and time scales well beyond the most optimistic hopes of traditional coarse-graining methods for molecular dynamics (MD), which typically start at the atomic scale and build upward. However classical MD can be viewed as an engine for simulating particles at literally any length or time scale, depending on the models used for individual particles and their interactions. To illustrate I'll highlight several coarse-grained (CG) materials models, some of which are likely familiar to molecular-scale modelers, but others probably not. These include models for water droplet freezing on surfaces, dissipative particle dynamics (DPD) models of explosives where particles have internal state, CG models of nano or colloidal particles in solution, models for aspherical particles, Peridynamics models for fracture, and models of granular materials at the scale of industrial processing. All of these can be implemented as MD-style models for either soft or hard materials; in fact they are all part of our LAMMPS MD package, added either by our group or contributed by collaborators. Unlike most all-atom MD simulations, CG simulations at these scales often involve highly non-uniform particle densities. So I'll also discuss a load-balancing method we've implemented for these kinds of models, which can improve parallel efficiencies. From the physics point-of-view, these models may be viewed as non-traditional or ad hoc. But because they are MD-style simulations, there's an opportunity for physicists to add statistical mechanics rigor to individual models. Or, in keeping with a theme of this session, to devise methods that more accurately bridge models from one scale to the next.

FUN3D Manual: 12.9

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.;

FUN3D Manual: 13.2

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.;

FUN3D Manual: 12.6

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.;

FUN3D Manual: 12.7

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.;

FUN3D Manual: 12.5

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.;

FUN3D Manual: 12.8

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.;

FUN3D Manual: 12.4

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.;

FUN3D Manual: 13.1

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.;

FUN3D Manual: 13.0

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bill; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.;

The SPORT-NMR Software: A Tool for Determining Relaxation Times in Unresolved NMR Spectra

NASA Astrophysics Data System (ADS)

Geppi, Marco; Forte, Claudia

1999-03-01

A software package which allows the correct determination of individual relaxation times for all the nonequivalent nuclei in poorly resolved NMR spectra is described. The procedure used, based on the fitting of each spectrum in the series recorded in the relaxation experiment, should improve the analysis of relaxation data in terms of quantitative dynamic information, especially in anisotropic phases. Tests on simulated data and experimental examples concerning1H and13CT1ρmeasurement in a solid copolymer and2HT1ZandT1Qmeasurement in a liquid crystal are shown and discussed.

FUN3D Manual: 13.3

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.;

A standard format and a graphical user interface for spin system specification.

PubMed

Biternas, A G; Charnock, G T P; Kuprov, Ilya

2014-03-01

We introduce a simple and general XML format for spin system description that is the result of extensive consultations within Magnetic Resonance community and unifies under one roof all major existing spin interaction specification conventions. The format is human-readable, easy to edit and easy to parse using standard XML libraries. We also describe a graphical user interface that was designed to facilitate construction and visualization of complicated spin systems. The interface is capable of generating input files for several popular spin dynamics simulation packages. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Unmanned Air Vehicle -Version 1.0

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

Fred Oppel, SNL 06134

2013-04-17

This package contains modules that model the mobility of systems such as helicopters and fixed wing flying in the air. This package currently models first order physics - basically a velocity integrator. UAV mobility uses an internal clock to maintain stable, high-fidelity simulations over large time steps This package depends on interface that reside in the Mobility package.

Parachute Dynamics Investigations Using a Sensor Package Airdropped from a Small-Scale Airplane

NASA Technical Reports Server (NTRS)

Dooley, Jessica; Lorenz, Ralph D.

2005-01-01

We explore the utility of various sensors by recovering parachute-probe dynamics information from a package released from a small-scale, remote-controlled airplane. The airdrops aid in the development of datasets for the exploration of planetary probe trajectory recovery algorithms, supplementing data collected from instrumented, full-scale tests and computer models.

Establishing conditions for simulating hydrophobic solutes in electric fields by molecular dynamics: effects of the long-range van der Waals treatment on the apparent particle mobility.

PubMed

Miličević, Zoran; Marrink, Siewert J; Smith, Ana-Sunčana; Smith, David M

2014-08-01

Despite considerable effort over the last decade, the interactions between solutes and solvents in the presence of electric fields have not yet been fully understood. A very useful manner in which to study these systems is through the application of molecular dynamics (MD) simulations. However, a number of MD studies have shown a tremendous sensitivity of the migration rate of a hydrophobic solute to the treatment of the long range part of the van der Waals interactions. While the origin of this sensitivity was never explained, the mobility is currently regarded as an artifact of an improper simulation setup. We explain the spread in observed mobilites by performing extensive molecular dynamics simulations using the GROMACS software package on a system consisting of a model hydrophobic object (Lennard-Jones particle) immersed in water both in the presence and absence of a static electric field. We retrieve a unidirectional field-induced mobility of the hydrophobic object when the forces are simply truncated. Careful analysis of the data shows that, only in the specific case of truncated forces, a non-zero van der Waals force acts, on average, on the Lennard-Jones particle. Using the Stokes law we demonstrate that this force yields quantitative agreement with the field-induced mobility found within this setup. In contrast, when the treatment of forces is continuous, no net force is observed. In this manner, we provide a simple explanation for the previously controversial reports.

Molecular dynamics simulation of three plastic additives' diffusion in polyethylene terephthalate.

PubMed

Li, Bo; Wang, Zhi-Wei; Lin, Qin-Bao; Hu, Chang-Ying

2017-06-01

Accurate diffusion coefficient data of additives in a polymer are of paramount importance for estimating the migration of the additives over time. This paper shows how this diffusion coefficient can be estimated for three plastic additives [2-(2'-hydroxy-5'-methylphenyl) (UV-P), 2,6-di-tert-butyl-4-methylphenol (BHT) and di-(2-ethylhexyl) phthalate (DEHP)] in polyethylene terephthalate (PET) using the molecular dynamics (MD) simulation method. MD simulations were performed at temperatures of 293-433 K. The diffusion coefficient was calculated through the Einstein relationship connecting the data of mean-square displacement at different times. Comparison of the diffusion coefficients simulated by the MD simulation technique, predicted by the Piringer model and experiments, showed that, except for a few samples, the MD-simulated values were in agreement with the experimental values within one order of magnitude. Furthermore, the diffusion process for additives is discussed in detail, and four factors - the interaction energy between additive molecules and PET, fractional free volume, molecular shape and size, and self-diffusion of the polymer - are proposed to illustrate the microscopic diffusion mechanism. The movement trajectories of additives in PET cell models suggested that the additive molecules oscillate slowly rather than hopping for a long time. Occasionally, when a sufficiently large hole was created adjacently, the molecule could undergo spatial motion by jumping into the free-volume hole and consequently start a continuous oscillation and hop. The results indicate that MD simulation is a useful approach for predicting the microstructure and diffusion coefficient of plastic additives, and help to estimate the migration level of additives from PET packaging.

"FluSpec": A Simulated Experiment in Fluorescence Spectroscopy

ERIC Educational Resources Information Center

Bigger, Stephen W.; Bigger, Andrew S.; Ghiggino, Kenneth P.

2014-01-01

The "FluSpec" educational software package is a fully contained tutorial on the technique of fluorescence spectroscopy as well as a simulator on which experiments can be performed. The procedure for each of the experiments is also contained within the package along with example analyses of results that are obtained using the software.

Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations

NASA Astrophysics Data System (ADS)

Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.

2016-10-01

In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

PubMed Central

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-01-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 PMID:26753008

Comparison of TAPS Packages for Engineering

ERIC Educational Resources Information Center

Sidhu, S. Manjit

2008-01-01

Purpose: This paper aims to present the development of technology-assisted problem solving (TAPS) packages at University Tenaga Nasional (UNITEN). The project is the further work of the development of interactive multimedia based packages targeted for students having problems in understanding the subject of engineering mechanics dynamics.…

Versatile Software Package For Near Real-Time Analysis of Experimental Data

NASA Technical Reports Server (NTRS)

Wieseman, Carol D.; Hoadley, Sherwood T.

1998-01-01

This paper provides an overview of a versatile software package developed for time- and frequency-domain analyses of experimental wind-tunnel data. This package, originally developed for analyzing data in the NASA Langley Transonic Dynamics Tunnel (TDT), is applicable for analyzing any time-domain data. A Matlab-based software package, TDT-analyzer, provides a compendium of commonly-required dynamic analysis functions in a user-friendly interactive and batch processing environment. TDT-analyzer has been used extensively to provide on-line near real-time and post-test examination and reduction of measured data acquired during wind tunnel tests of aeroelastically-scaled models of aircraft and rotorcraft as well as a flight test of the NASA High Alpha Research Vehicle (HARV) F-18. The package provides near real-time results in an informative and timely manner far exceeding prior methods of data reduction at the TDT.

Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.

PubMed

Mermelstein, Daniel J; Lin, Charles; Nelson, Gard; Kretsch, Rachael; McCammon, J Andrew; Walker, Ross C

2018-07-15

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD-based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

PubMed

Salis, Howard; Sotiropoulos, Vassilios; Kaznessis, Yiannis N

2006-02-24

Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations produce a more accurate picture of single cell dynamics, including interesting phenomena missed by deterministic methods, such as noise-induced oscillations and transitions between stable states. However, the computational cost of the original stochastic simulation algorithm can be high, motivating the use of hybrid stochastic methods. Hybrid stochastic methods partition the system into multiple subsets and describe each subset as a different representation, such as a jump Markov, Poisson, continuous Markov, or deterministic process. By applying valid approximations and self-consistently merging disparate descriptions, a method can be considerably faster, while retaining accuracy. In this paper, we describe Hy3S, a collection of multiscale simulation programs. Building on our previous work on developing novel hybrid stochastic algorithms, we have created the Hy3S software package to enable scientists and engineers to both study and design extremely large well-mixed biological systems with many thousands of reactions and chemical species. We have added adaptive stochastic numerical integrators to permit the robust simulation of dynamically stiff biological systems. In addition, Hy3S has many useful features, including embarrassingly parallelized simulations with MPI; special discrete events, such as transcriptional and translation elongation and cell division; mid-simulation perturbations in both the number of molecules of species and reaction kinetic parameters; combinatorial variation of both initial conditions and kinetic parameters to enable sensitivity analysis; use of NetCDF optimized binary format to quickly read and write large datasets; and a simple graphical user interface, written in Matlab, to help users create biological systems and analyze data. We demonstrate the accuracy and efficiency of Hy3S with examples, including a large-scale system benchmark and a complex bistable biochemical network with positive feedback. The software itself is open-sourced under the GPL license and is modular, allowing users to modify it for their own purposes. Hy3S is a powerful suite of simulation programs for simulating the stochastic dynamics of networks of biochemical reactions. Its first public version enables computational biologists to more efficiently investigate the dynamics of realistic biological systems.

Application of MODFLOW’s farm process to California’s Central Valley

USGS Publications Warehouse

Faunt, Claudia; Hanson, Randall T.; Schmid, Wolfgang; Belitz, Kenneth

2008-01-01

landscape processes. The FMP provides coupled simulation of the ground-water and surface-water components of the hydrologic cycle for irrigated and non-irrigated areas. A dynamic allocation of ground-water recharge and ground-water pumping is simulated on the basis of residual crop-water demand after surface-water deliveries and root uptake from shallow ground water. The FMP links with the Streamflow Routing Package SFR1) to facilitate the simulated conveyance of surface-water deliveries. Ground-water Pumpage through both single-aquifer and multi-node wells, irrigation return flow, and variable irrigation efficiencies also are simulated by the FMP. The simulated deliveries and ground-water pumpage in the updated model reflect climatic differences, differences among defined water-balance regions, and changes in the waterdelivery system, during the 1961–2003 simulation period. The model is designed to accept forecasts from Global Climate Models (GCMs) to simulate the potential effects on surface-water delivery, ground-water pumpage, and ground-water storage in response to climate change. The model provides a detailed transient analysis of changes in ground-water availability in relation to climatic variability, urbanization, and changes in irrigated agriculture.

SIMA: Python software for analysis of dynamic fluorescence imaging data.

PubMed

Kaifosh, Patrick; Zaremba, Jeffrey D; Danielson, Nathan B; Losonczy, Attila

2014-01-01

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

Software package for modeling spin–orbit motion in storage rings

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

Zyuzin, D. V., E-mail: d.zyuzin@fz-juelich.de

2015-12-15

A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 10{sup 6}–10{sup 9} particles in a beam during 10{supmore » 9} turns in an accelerator (about 10{sup 12}–10{sup 15} integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin–orbit dynamics.« less

Molecular dynamics simulations of DNA-polycation complexes

NASA Astrophysics Data System (ADS)

Ziebarth, Jesse; Wang, Yongmei

2008-03-01

A necessary step in the preparation of DNA for use in gene therapy is the packaging of DNA with a vector that can condense DNA and provide protection from degrading enzymes. Because of the immunoresponses caused by viral vectors, there has been interest in developing synthetic gene therapy vectors, with polycations emerging as promising candidates. Molecular dynamics simulations of the DNA duplex CGCGAATTCGCG in the presence of 20 monomer long sequences of the polycations, poly-L-lysine (PLL) and polyethyleneimine (PEI), with explicit counterions and TIP3P water, are performed to provide insight into the structure and formation of DNA polyplexes. After an initial separation of approximately 50 å, the DNA and polycation come together and form a stable complex within 10 ns. The DNA does not undergo any major structural changes upon complexation and remains in the B-form. In the formed complex, the charged amine groups of the polycation mainly interact with DNA phosphate groups, and rarely occupy electronegative sites in either the major or minor grooves. Differences between complexation with PEI and PLL will be discussed.

Sensitivity analysis of Repast computational ecology models with R/Repast.

PubMed

Prestes García, Antonio; Rodríguez-Patón, Alfonso

2016-12-01

Computational ecology is an emerging interdisciplinary discipline founded mainly on modeling and simulation methods for studying ecological systems. Among the existing modeling formalisms, the individual-based modeling is particularly well suited for capturing the complex temporal and spatial dynamics as well as the nonlinearities arising in ecosystems, communities, or populations due to individual variability. In addition, being a bottom-up approach, it is useful for providing new insights on the local mechanisms which are generating some observed global dynamics. Of course, no conclusions about model results could be taken seriously if they are based on a single model execution and they are not analyzed carefully. Therefore, a sound methodology should always be used for underpinning the interpretation of model results. The sensitivity analysis is a methodology for quantitatively assessing the effect of input uncertainty in the simulation output which should be incorporated compulsorily to every work based on in-silico experimental setup. In this article, we present R/Repast a GNU R package for running and analyzing Repast Simphony models accompanied by two worked examples on how to perform global sensitivity analysis and how to interpret the results.

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

PubMed

Fonner, John M; Schmidt, Christine E; Ren, Pengyu

2010-10-01

Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials.

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.

PubMed

Pasi, Marco; Lavery, Richard; Ceres, Nicoletta

2013-01-08

We present a coarse-grain protein model PaLaCe (Pasi-Lavery-Ceres) that has been developed principally to allow fast computational studies of protein mechanics and to clarify the links between mechanics and function. PaLaCe uses a two-tier protein representation with one to three pseudoatoms representing each amino acid for the main nonbonded interactions, combined with atomic-scale peptide groups and some side chain atoms to allow the explicit representation of backbone hydrogen bonds and to simplify the treatment of bonded interactions. The PaLaCe force field is composed of physics-based terms, parametrized using Boltzmann inversion of conformational probability distributions derived from a protein structure data set, and iteratively refined to reproduce the experimental distributions. PaLaCe has been implemented in the MMTK simulation package and can be used for energy minimization, normal mode calculations, and molecular or stochastic dynamics. We present simulations with PaLaCe that test its ability to maintain stable structures for folded proteins, reproduce their dynamic fluctuations, and correctly model large-scale, force-induced conformational changes.

GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations

NASA Astrophysics Data System (ADS)

Nguyen, Trung Dac

2017-03-01

The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.

Microwave heating causes rapid degradation of antioxidants in polypropylene packaging, leading to greatly increased specific migration to food simulants as shown by ESI-MS and GC-MS.

PubMed

Alin, Jonas; Hakkarainen, Minna

2011-05-25

Microwave heating of commercial microwavable polypropylene packaging in contact with fatty food simulants caused significant antioxidant degradation and increased specific migration as shown by electrospray ionization-mass spectrometry (ESI-MS) and gas chromatography-mass spectrometry (GC-MS). Degradation of the antioxidants Irgafos 168 and Irganox 1010 was not detected during conventional heating of polypropylene packaging at the same temperature. The migration into aqueous food simulants was primarily restricted by the water solubility of the migrants. Using isooctane as fatty food simulant caused significant swelling and greatly enhanced overall migration values compared to the other fatty food simulant, 99.9% ethanol, or the aqueous food simulants 10% ethanol, 3% acetic acid, or water. ESI-MS spectra clearly reflected the overall migration values, and the number and amount of compounds detected decreased as the hydrophilicity of the food simulant increased. ESI-MS was shown to be an excellent tool for the analysis of semivolatile migrants and a good complement to GC-MS analysis of volatile migrants.

Experimental Verification of the Use of Metal Filled Via Hole Fences for Crosstalk Control of Microstrip Lines in LTCC Packages

NASA Technical Reports Server (NTRS)

Ponchak, George E.; Chun, Donghoon; Katehi, Linda P. B.; Yook, Jong-Gwan

1999-01-01

Coupling between microstrip lines in dense RF packages is a common problem that degrades circuit performance. Prior 3D-FEM electromagnetic simulations have shown that metal filled via hole fences between two adjacent microstrip lines actually increases coupling between the lines; however, if the top of the via posts are connected by a metal Strip, coupling is reduced. In this paper, experimental verification of the 3D-FEM simulations Is demonstrated for commercially fabricated LTCC packages.

Stochastic simulation and analysis of biomolecular reaction networks

PubMed Central

Frazier, John M; Chushak, Yaroslav; Foy, Brent

2009-01-01

Background In recent years, several stochastic simulation algorithms have been developed to generate Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks. However, the effects of various stochastic simulation and data analysis conditions on the observed dynamics of complex biomolecular reaction networks have not recieved much attention. In order to investigate these issues, we employed a a software package developed in out group, called Biomolecular Network Simulator (BNS), to simulate and analyze the behavior of such systems. The behavior of a hypothetical two gene in vitro transcription-translation reaction network is investigated using the Gillespie exact stochastic algorithm to illustrate some of the factors that influence the analysis and interpretation of these data. Results Specific issues affecting the analysis and interpretation of simulation data are investigated, including: (1) the effect of time interval on data presentation and time-weighted averaging of molecule numbers, (2) effect of time averaging interval on reaction rate analysis, (3) effect of number of simulations on precision of model predictions, and (4) implications of stochastic simulations on optimization procedures. Conclusion The two main factors affecting the analysis of stochastic simulations are: (1) the selection of time intervals to compute or average state variables and (2) the number of simulations generated to evaluate the system behavior. PMID:19534796

An alternative to FASTSIM for tangential solution of the wheel-rail contact

NASA Astrophysics Data System (ADS)

Sichani, Matin Sh.; Enblom, Roger; Berg, Mats

2016-06-01

In most rail vehicle dynamics simulation packages, tangential solution of the wheel-rail contact is gained by means of Kalker's FASTSIM algorithm. While 5-25% error is expected for creep force estimation, the errors of shear stress distribution, needed for wheel-rail damage analysis, may rise above 30% due to the parabolic traction bound. Therefore, a novel algorithm named FaStrip is proposed as an alternative to FASTSIM. It is based on the strip theory which extends the two-dimensional rolling contact solution to three-dimensional contacts. To form FaStrip, the original strip theory is amended to obtain accurate estimations for any contact ellipse size and it is combined by a numerical algorithm to handle spin. The comparison between the two algorithms shows that using FaStrip improves the accuracy of the estimated shear stress distribution and the creep force estimation in all studied cases. In combined lateral creepage and spin cases, for instance, the error in force estimation reduces from 18% to less than 2%. The estimation of the slip velocities in the slip zone, needed for wear analysis, is also studied. Since FaStrip is as fast as FASTSIM, it can be an alternative for tangential solution of the wheel-rail contact in simulation packages.

Aqueous Molecular Dynamics Simulations of the M. tuberculosis Enoyl-ACP Reductase-NADH System and Its Complex with a Substrate Mimic or Diphenyl Ethers Inhibitors

PubMed Central

da Silva Lima, Camilo Henrique; de Alencastro, Ricardo Bicca; Kaiser, Carlos Roland; de Souza, Marcus Vinícius Nora; Rodrigues, Carlos Rangel; Albuquerque, Magaly Girão

2015-01-01

Molecular dynamics (MD) simulations of 12 aqueous systems of the NADH-dependent enoyl-ACP reductase from Mycobacterium tuberculosis (InhA) were carried out for up to 20–40 ns using the GROMACS 4.5 package. Simulations of the holoenzyme, holoenzyme-substrate, and 10 holoenzyme-inhibitor complexes were conducted in order to gain more insight about the secondary structure motifs of the InhA substrate-binding pocket. We monitored the lifetime of the main intermolecular interactions: hydrogen bonds and hydrophobic contacts. Our MD simulations demonstrate the importance of evaluating the conformational changes that occur close to the active site of the enzyme-cofactor complex before and after binding of the ligand and the influence of the water molecules. Moreover, the protein-inhibitor total steric (ELJ) and electrostatic (EC) interaction energies, related to Gly96 and Tyr158, are able to explain 80% of the biological response variance according to the best linear equation, pKi = 7.772 − 0.1885 × Gly96 + 0.0517 × Tyr158 (R2 = 0.80; n = 10), where interactions with Gly96, mainly electrostatic, increase the biological response, while those with Tyr158 decrease. These results will help to understand the structure-activity relationships and to design new and more potent anti-TB drugs. PMID:26457706

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

PubMed

Vermaas, Josh V; Hardy, David J; Stone, John E; Tajkhorshid, Emad; Kohlmeyer, Axel

2016-06-27

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.

Path selection system simulation and evaluation for a Martian roving vehicle

NASA Technical Reports Server (NTRS)

Boheim, S. L.; Prudon, W. C.

1972-01-01

The simulation and evaluation of proposed path selection systems for an autonomous Martian roving vehicle was developed. The package incorporates a number of realistic features, such as the simulation of random effects due to vehicle bounce and sensor-reading uncertainty, to increase the reliability of the results. Qualitative and quantitative evaluation criteria were established. The performance of three different path selection systems was evaluated to determine the effectiveness of the simulation package, and to form some preliminary conclusions regarding the tradeoffs involved in a path selection system design.

Python-based geometry preparation and simulation visualization toolkits for STEPS

PubMed Central

Chen, Weiliang; De Schutter, Erik

2014-01-01

STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations. PMID:24782754

McStas 1.7 - a new version of the flexible Monte Carlo neutron scattering package

NASA Astrophysics Data System (ADS)

Willendrup, Peter; Farhi, Emmanuel; Lefmann, Kim

2004-07-01

Current neutron instrumentation is both complex and expensive, and accurate simulation has become essential both for building new instruments and for using them effectively. The McStas neutron ray-trace simulation package is a versatile tool for producing such simulations, developed in collaboration between Risø and ILL. The new version (1.7) has many improvements, among these added support for the popular Microsoft Windows platform. This presentation will demonstrate a selection of the new features through a simulation of the ILL IN6 beamline.

High-power UV-LED degradation: Continuous and cycled working condition influence

NASA Astrophysics Data System (ADS)

Arques-Orobon, F. J.; Nuñez, N.; Vazquez, M.; Segura-Antunez, C.; González-Posadas, V.

2015-09-01

High-power (HP) UV-LEDs can replace UV lamps for real-time fluoro-sensing applications by allowing portable and autonomous systems. However, HP UV-LEDs are not a mature technology, and there are still open issues regarding their performance evolution over time. This paper presents a reliability study of 3 W UV-LEDs, with special focus on LED degradation for two working conditions: continuous and cycled (30 s ON and 30 s OFF). Accelerated life tests are developed to evaluate the influence of temperature and electrical working conditions in high-power LEDs degradation, being the predominant failure mechanism the degradation of the package. An analysis that includes dynamic thermal and optical HP UV-LED measurements has been performed. Static thermal and stress simulation analysis with the finite element method (FEM) identifies the causes of package degradation. Accelerated life test results prove that HP UV-LEDs working in cycled condition have a better performance than those working in continuous condition.

Validation of a RANS transition model using a high-order weighted compact nonlinear scheme

NASA Astrophysics Data System (ADS)

Tu, GuoHua; Deng, XiaoGang; Mao, MeiLiang

2013-04-01

A modified transition model is given based on the shear stress transport (SST) turbulence model and an intermittency transport equation. The energy gradient term in the original model is replaced by flow strain rate to saving computational costs. The model employs local variables only, and then it can be conveniently implemented in modern computational fluid dynamics codes. The fifth-order weighted compact nonlinear scheme and the fourth-order staggered scheme are applied to discrete the governing equations for the purpose of minimizing discretization errors, so as to mitigate the confusion between numerical errors and transition model errors. The high-order package is compared with a second-order TVD method on simulating the transitional flow of a flat plate. Numerical results indicate that the high-order package give better grid convergence property than that of the second-order method. Validation of the transition model is performed for transitional flows ranging from low speed to hypersonic speed.

Assessing the accuracy of different simplified frictional rolling contact algorithms

NASA Astrophysics Data System (ADS)

Vollebregt, E. A. H.; Iwnicki, S. D.; Xie, G.; Shackleton, P.

2012-01-01

This paper presents an approach for assessing the accuracy of different frictional rolling contact theories. The main characteristic of the approach is that it takes a statistically oriented view. This yields a better insight into the behaviour of the methods in diverse circumstances (varying contact patch ellipticities, mixed longitudinal, lateral and spin creepages) than is obtained when only a small number of (basic) circumstances are used in the comparison. The range of contact parameters that occur for realistic vehicles and tracks are assessed using simulations with the Vampire vehicle system dynamics (VSD) package. This shows that larger values for the spin creepage occur rather frequently. Based on this, our approach is applied to typical cases for which railway VSD packages are used. The results show that particularly the USETAB approach but also FASTSIM give considerably better results than the linear theory, Vermeulen-Johnson, Shen-Hedrick-Elkins and Polach methods, when compared with the 'complete theory' of the CONTACT program.

Towards a general object-oriented software development methodology

NASA Technical Reports Server (NTRS)

Seidewitz, ED; Stark, Mike

1986-01-01

An object is an abstract software model of a problem domain entity. Objects are packages of both data and operations of that data (Goldberg 83, Booch 83). The Ada (tm) package construct is representative of this general notion of an object. Object-oriented design is the technique of using objects as the basic unit of modularity in systems design. The Software Engineering Laboratory at the Goddard Space Flight Center is currently involved in a pilot program to develop a flight dynamics simulator in Ada (approximately 40,000 statements) using object-oriented methods. Several authors have applied object-oriented concepts to Ada (e.g., Booch 83, Cherry 85). It was found that these methodologies are limited. As a result a more general approach was synthesized with allows a designer to apply powerful object-oriented principles to a wide range of applications and at all stages of design. An overview is provided of this approach. Further, how object-oriented design fits into the overall software life-cycle is considered.

Comparison of long-term numerical simulations at the Ketzin pilot site using the Schlumberger ECLIPSE and LBNL TOUGH2 simulators

NASA Astrophysics Data System (ADS)

Kempka, T.; Norden, B.; Tillner, E.; Nakaten, B.; Kühn, M.

2012-04-01

Geological modelling and dynamic flow simulations were conducted at the Ketzin pilot site showing a good agreement of history matched geological models with CO2 arrival times in both observation wells and timely development of reservoir pressure determined in the injection well. Recently, a re-evaluation of the seismic 3D data enabled a refinement of the structural site model and the implementation of the fault system present at the top of the Ketzin anticline. The updated geological model (model size: 5 km x 5 km) shows a horizontal discretization of 5 x 5 m and consists of three vertical zones, with the finest discretization at the top (0.5 m). According to the revised seismic analysis, the facies modelling to simulate the channel and floodplain facies distribution at Ketzin was updated. Using a sequential Gaussian simulator for the distribution of total and effective porosities and an empiric porosity-permeability relationship based on site and literature data available, the structural model was parameterized. Based on this revised reservoir model of the Stuttgart formation, numerical simulations using the TOUGH2-MP/ECO2N and Schlumberger Information Services (SIS) ECLIPSE 100 black-oil simulators were undertaken in order to evaluate the long-term (up to 10,000 years) migration of the injected CO2 (about 57,000 t at the end of 2011) and the development of reservoir pressure over time. The simulation results enabled us to quantitatively compare both reservoir simulators based on current operational data considering the long-term effects of CO2 storage including CO2 dissolution in the formation fluid. While the integration of the static geological model developed in the SIS Petrel modelling package into the ECLIPSE simulator is relatively flawless, a work-flow allowing for the export of Petrel models into the TOUGH2-MP input file format had to be implemented within the scope of this study. The challenge in this task was mainly determined by the presence of a complex faulted system in the revised reservoir model demanding for an integrated concept to deal with connections between the elements aligned to faults in the TOUGH2-MP simulator. Furthermore, we developed a methodology to visualize and compare the TOUGH2-MP simulation results with those of the Eclipse simulator using the Petrel software package. The long-term simulation results of both simulators are generally in good agreement. Spatial and timely migration of the CO2 plume as well as residual gas saturation are almost identical for both simulators, even though a time-dependent approach of CO2 dissolution in the formation fluid was chosen in the ECLIPSE simulator. Our results confirmed that a scientific open-source simulator as the TOUGH2-MP software package is capable to provide the same accuracy as the industrial standard simulator ECLIPSE 100. However, the computational time and additional efforts to implement a suitable workflow for using the TOUGH2-MP simulator are significantly higher, while the open-source concept of TOUGH2 provides more flexibility regarding process adaptation.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

PubMed

Parton, Daniel L; Grinaway, Patrick B; Hanson, Sonya M; Beauchamp, Kyle A; Chodera, John D

2016-06-01

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences-from a single sequence to an entire superfamily-and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics-such as Markov state models (MSMs)-which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates. Ensembler is free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded from https://github.com/choderalab/ensembler.

A Multi-Level Parallelization Concept for High-Fidelity Multi-Block Solvers

NASA Technical Reports Server (NTRS)

Hatay, Ferhat F.; Jespersen, Dennis C.; Guruswamy, Guru P.; Rizk, Yehia M.; Byun, Chansup; Gee, Ken; VanDalsem, William R. (Technical Monitor)

1997-01-01

The integration of high-fidelity Computational Fluid Dynamics (CFD) analysis tools with the industrial design process benefits greatly from the robust implementations that are transportable across a wide range of computer architectures. In the present work, a hybrid domain-decomposition and parallelization concept was developed and implemented into the widely-used NASA multi-block Computational Fluid Dynamics (CFD) packages implemented in ENSAERO and OVERFLOW. The new parallel solver concept, PENS (Parallel Euler Navier-Stokes Solver), employs both fine and coarse granularity in data partitioning as well as data coalescing to obtain the desired load-balance characteristics on the available computer platforms. This multi-level parallelism implementation itself introduces no changes to the numerical results, hence the original fidelity of the packages are identically preserved. The present implementation uses the Message Passing Interface (MPI) library for interprocessor message passing and memory accessing. By choosing an appropriate combination of the available partitioning and coalescing capabilities only during the execution stage, the PENS solver becomes adaptable to different computer architectures from shared-memory to distributed-memory platforms with varying degrees of parallelism. The PENS implementation on the IBM SP2 distributed memory environment at the NASA Ames Research Center obtains 85 percent scalable parallel performance using fine-grain partitioning of single-block CFD domains using up to 128 wide computational nodes. Multi-block CFD simulations of complete aircraft simulations achieve 75 percent perfect load-balanced executions using data coalescing and the two levels of parallelism. SGI PowerChallenge, SGI Origin 2000, and a cluster of workstations are the other platforms where the robustness of the implementation is tested. The performance behavior on the other computer platforms with a variety of realistic problems will be included as this on-going study progresses.

A flexible object-oriented software framework for developing complex multimedia simulations.

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

Sydelko, P. J.; Dolph, J. E.; Christiansen, J. H.

Decision makers involved in brownfields redevelopment and long-term stewardship must consider environmental conditions, future-use potential, site ownership, area infrastructure, funding resources, cost recovery, regulations, risk and liability management, community relations, and expected return on investment in a comprehensive and integrated fashion to achieve desired results. Successful brownfields redevelopment requires the ability to assess the impacts of redevelopment options on multiple interrelated aspects of the ecosystem, both natural and societal. Computer-based tools, such as simulation models, databases, and geographical information systems (GISs) can be used to address brownfields planning and project execution. The transparent integration of these tools into a comprehensivemore » and dynamic decision support system would greatly enhance the brownfields assessment process. Such a system needs to be able to adapt to shifting and expanding analytical requirements and contexts. The Dynamic Information Architecture System (DIAS) is a flexible, extensible, object-oriented framework for developing and maintaining complex multidisciplinary simulations of a wide variety of application domains. The modeling domain of a specific DIAS-based simulation is determined by (1) software objects that represent the real-world entities that comprise the problem space (atmosphere, watershed, human), and (2) simulation models and other data processing applications that express the dynamic behaviors of the domain entities. Models and applications used to express dynamic behaviors can be either internal or external to DIAS, including existing legacy models written in various languages (FORTRAN, C, etc.). The flexible design framework of DIAS makes the objects adjustable to the context of the problem without a great deal of recoding. The DIAS Spatial Data Set facility allows parameters to vary spatially depending on the simulation context according to any of a number of 1-D, 2-D, or 3-D topologies. DIAS is also capable of interacting with other GIS packages and can import many standard spatial data formats. DIAS simulation capabilities can also be extended by including societal process models. Models that implement societal behaviors of individuals and organizations within larger DIAS-based natural systems simulations allow for interaction and feedback among natural and societal processes. The ability to simulate the complex interplay of multimedia processes makes DIAS a promising tool for constructing applications for comprehensive community planning, including the assessment of multiple development and redevelopment scenarios.« less

[A research of letter color visibility in package insert information using simulator].

PubMed

Kamimura, Naoki; Kinoshita, Noriyuki; Onaga, Midori; Watanabe, Yurika; Ijuin, Kazushige; Shikamura, Yoshiaki; Negishi, Kenichi; Kaiho, Fusao; Ohta, Takafumi

2012-01-01

Package insert of pharmaceutical drug is one of the most prioritized information for pharmacists to secure safety of patients. However, the color of character, size, font and so on are various company by company product to product from a viewpoint of visibility. It may be cause a serious accident in case visibility is unclear, although it is the most important information. Moreover, package insert with high visibility is required for color vision defectives from a viewpoint of a universal design. Then, the authors selected the package insert which has the boxed warning in the ethical pharmaceutical currently stored mostly in the present health insurance pharmacy and quantified the red color using the color meter. We advocate the state of a suitable package insert from a viewpoint of a universal design, whether the red color is high visible or not for color vision defectives using simulator.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

PubMed Central

Martinez, Michael; Romanowska, Julia; Kokh, Daria B.; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan

2015-01-01

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26123630

Visualization for Molecular Dynamics Simulation of Gas and Metal Surface Interaction

NASA Astrophysics Data System (ADS)

Puzyrkov, D.; Polyakov, S.; Podryga, V.

2016-02-01

The development of methods, algorithms and applications for visualization of molecular dynamics simulation outputs is discussed. The visual analysis of the results of such calculations is a complex and actual problem especially in case of the large scale simulations. To solve this challenging task it is necessary to decide on: 1) what data parameters to render, 2) what type of visualization to choose, 3) what development tools to use. In the present work an attempt to answer these questions was made. For visualization it was offered to draw particles in the corresponding 3D coordinates and also their velocity vectors, trajectories and volume density in the form of isosurfaces or fog. We tested the way of post-processing and visualization based on the Python language with use of additional libraries. Also parallel software was developed that allows processing large volumes of data in the 3D regions of the examined system. This software gives the opportunity to achieve desired results that are obtained in parallel with the calculations, and at the end to collect discrete received frames into a video file. The software package "Enthought Mayavi2" was used as the tool for visualization. This visualization application gave us the opportunity to study the interaction of a gas with a metal surface and to closely observe the adsorption effect.

Simulating wind and marine hydrokinetic turbines with actuator lines in RANS and LES

NASA Astrophysics Data System (ADS)

Bachant, Peter; Wosnik, Martin

2015-11-01

As wind and marine hydrokinetic (MHK) turbine designs mature, focus is shifting towards improving turbine array layouts for maximizing overall power output, i.e., minimizing wake interference for axial-flow or horizontal-axis turbines, or taking advantage of constructive wake interaction for cross-flow or vertical-axis turbines. Towards this goal, an actuator line model (ALM) was developed to provide a computationally feasible method for simulating full turbine arrays inside Navier-Stokes models. The ALM predicts turbine loading with the blade element method combined with sub-models for dynamic stall and flow curvature. The open-source software is written as an extension library for the OpenFOAM CFD package, which allows the ALM body force to be applied to their standard RANS and LES solvers. Turbine forcing is also applied to volume of fluid (VOF) models, e.g., for predicting free surface effects on submerged MHK devices. An additional sub-model is considered for injecting turbulence model scalar quantities based on actuator line element loading. Results are presented for the simulation of performance and wake dynamics of axial- and cross-flow turbines and compared with moderate Reynolds number experiments and body-fitted mesh, blade-resolving CFD. Work supported by NSF-CBET grant 1150797.

ProtSqueeze: simple and effective automated tool for setting up membrane protein simulations.

PubMed

Yesylevskyy, Semen O

2007-01-01

The major challenge in setting up membrane protein simulations is embedding the protein into the pre-equilibrated lipid bilayer. Several techniques were proposed to achieve optimal packing of the lipid molecules around the protein. However, all of them possess serious disadvantages, which limit their applicability and discourage the users of simulation packages from using them. In the present work, we analyzed existing approaches and proposed a new procedure of protein insertion into the lipid bilayer, which is implemented in the ProtSqueeze software. The advantages of ProtSqueeze are as follows: (1) the insertion algorithm is simple, understandable, and controllable; (2) the software can work with virtually any simulation package on virtually any platform; (3) no modification of the source code of the simulation package is needed; (4) the procedure of insertion is as automated as possible; (5) ProtSqueeze is distributed for free under a general public license. In this work, we present the architecture and the algorithm of ProtSqueeze and demonstrate its usage in case studies.

VS2DI: Model use, calibration, and validation

USGS Publications Warehouse

Healy, Richard W.; Essaid, Hedeff I.

2012-01-01

VS2DI is a software package for simulating water, solute, and heat transport through soils or other porous media under conditions of variable saturation. The package contains a graphical preprocessor for constructing simulations, a postprocessor for displaying simulation results, and numerical models that solve for flow and solute transport (VS2DT) and flow and heat transport (VS2DH). Flow is described by the Richards equation, and solute and heat transport are described by advection-dispersion equations; the finite-difference method is used to solve these equations. Problems can be simulated in one, two, or three (assuming radial symmetry) dimensions. This article provides an overview of calibration techniques that have been used with VS2DI; included is a detailed description of calibration procedures used in simulating the interaction between groundwater and a stream fed by drainage from agricultural fields in central Indiana. Brief descriptions of VS2DI and the various types of problems that have been addressed with the software package are also presented.

Comment on "Evaluating interactions between groundwater and vadose zone using the HYDRUS-based flow package for MODFLOW" by Navin Kumar C. Twarakavi, Jirka Šimůnek and Sophia Seo

USGS Publications Warehouse

Niswonger, R.G.; Prudic, David E.

2009-01-01

Twarakavi et al (2008) compared four packages that can be used to estimate recharge for regional-scale groundwater flow simulations using MODFLOW (Harbaugh, 2005). This comment is focused on the comparisons made between two of these packages, namely, UZF1 (Niswonger et al., 2006) and a derivative of HYDRUS referred to herein as HYDRUS (Seo et al., 2007). In their paper, Twarakavi et al. (2008) stated that HYDRUS more accurately simulates unsaturated flow processes and groundwater recharge as compared to UZF1. However, Twarakavi et al. (2008) did not address several important differences between these models that undermine the advantages of HYDRUS as compared to UZF1 for simulating recharge. These differences were not revealed by the comparisons presented by Twarakavi et al. because the test simulations used to compare the models were too simple

Migration of perfluoroalkyl acids from food packaging to food simulants.

PubMed

Xu, Y; Noonan, G O; Begley, T H

2013-01-01

A broad range of fluorochemicals is used to impart oil and water barrier properties to paper and paperboard food packaging. Many of the fluorochemicals are applied to paper and paperboard as complex mixtures containing reaction products and by-products and unreacted starting materials. This work primarily focussed on the determination of seven perfluorocarboxylic acids (PFCAs) in two commercially available food contact papers: a di-perfluoro-alkyloxy-amino-acid and a perfluoroalkyl phosphate surfactant. In addition, the migration of the PFCAs into five food simulants from two commercial packages was evaluated. All seven PFCAs were detected in the range of 700-2220 µg kg⁻¹ of paper, while three perfluoroalkyl sulphonates were under the LOD. Results from migration tests showed that migration depends on paper characteristics, time and food simulant. The percentage of migration after 10 days at 40°C ranged from 4.8% to 100% for the two papers and different food simulants.

Implications of Sea Level Rise on Coastal Flood Hazards

NASA Astrophysics Data System (ADS)

Roeber, V.; Li, N.; Cheung, K.; Lane, P.; Evans, R. L.; Donnelly, J. P.; Ashton, A. D.

2012-12-01

Recent global and local projections suggest the sea level will be on the order of 1 m or higher than the current level by the end of the century. Coastal communities and ecosystems in low-lying areas are vulnerable to impacts resulting from hurricane or large swell events in combination with sea-level rise. This study presents the implementation and results of an integrated numerical modeling package to delineate coastal inundation due to storm landfalls at future sea levels. The modeling package utilizes a suite of numerical models to capture both large-scale phenomena in the open ocean and small-scale processes in coastal areas. It contains four components to simulate (1) meteorological conditions, (2) astronomical tides and surge, (3) wave generation, propagation, and nearshore transformation, and (4) surf-zone processes and inundation onto dry land associated with a storm event. Important aspects of this package are the two-way coupling of a spectral wave model and a storm surge model as well as a detailed representation of surf and swash zone dynamics by a higher-order Boussinesq-type wave model. The package was validated with field data from Hurricane Ivan of 2005 on the US Gulf coast and applied to tropical and extratropical storm scenarios respectively at Eglin, Florida and Camp Lejeune, North Carolina. The results show a nonlinear increase of storm surge level and nearshore wave energy with a rising sea level. The exacerbated flood hazard can have major consequences for coastal communities with respect to erosion and damage to infrastructure.

Water boiling inside carbon nanotubes: toward efficient drug release.

PubMed

Chaban, Vitaly V; Prezhdo, Oleg V

2011-07-26

We show using molecular dynamics simulation that spatial confinement of water inside carbon nanotubes (CNTs) substantially increases its boiling temperature and that a small temperature growth above the boiling point dramatically raises the inside pressure. Capillary theory successfully predicts the boiling point elevation down to 2 nm, below which large deviations between the theory and atomistic simulation take place. Water behaves qualitatively different inside narrow CNTs, exhibiting transition into an unusual phase, where pressure is gas-like and grows linearly with temperature, while the diffusion constant is temperature-independent. Precise control over boiling by CNT diameter, together with the rapid growth of inside pressure above the boiling point, suggests a novel drug delivery protocol. Polar drug molecules are packaged inside CNTs; the latter are delivered into living tissues and heated by laser. Solvent boiling facilitates drug release.

Method for CFD Simulation of Propellant Slosh in a Spherical Tank

NASA Technical Reports Server (NTRS)

Benson, David J.; Mason, Paul A.

2011-01-01

Propellant sloshing can impart unwanted disturbances to spacecraft, especially if the spacecraft controller is driving the system at the slosh frequency. This paper describes the work performed by the authors in simulating propellant slosh in a spherical tank using computational fluid dynamics (CFD). ANSYS-CFX is the CFD package used to perform the analysis. A 42 in spherical tank is studied with various fill fractions. Results are provided for the forces on the walls and the frequency of the slosh. Snapshots of slosh animation give a qualitative understanding of the propellant slosh. The results show that maximum slosh forces occur at a tank fill fraction of 0.4 and 0.6 due to the amount of mass participating in the slosh and the room available for sloshing to occur. The slosh frequency increases as the tank fill fraction increases.

Copper Tube Compression in Z-Current Geometry, Numerical Simulations and Comparison with Cyclope Experiments

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

Lefrancois, A.; L'Eplattenier, P.; Burger, M.

2006-02-13

Metallic tubes compressions in Z-current geometry were performed at the Cyclope facility from Gramat Research Center in order to study the behavior of metals under large strain at high strain rate. 3D configurations of cylinder compressions have been calculated here to benchmark the new beta version of the electromagnetism package coupled with the dynamics in Ls-Dyna and compared with the Cyclope experiments. The electromagnetism module is being developed in the general-purpose explicit and implicit finite element program LS-DYNA{reg_sign} in order to perform coupled mechanical/thermal/electromagnetism simulations. The Maxwell equations are solved using a Finite Element Method (FEM) for the solid conductorsmore » coupled with a Boundary Element Method (BEM) for the surrounding air (or vacuum). More details can be read in the references.« less

Design Approaches and Comparison of TAPS Packages for Engineering

ERIC Educational Resources Information Center

Sidhu, S. Manjit

2007-01-01

Purpose: The paper's purpose is to promote the use of modern technologies such as multimedia packages to engineering students. The aim is to help them to learning in their learning, visualization, problem solving and understanding engineering concepts such as in mechanics dynamics. Design/methodology/approach: TAPS packages are developed to help…

Rapid methods for radionuclide contaminant transport in nuclear fuel cycle simulation

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

Huff, Kathryn

Here, nuclear fuel cycle and nuclear waste disposal decisions are technologically coupled. However, current nuclear fuel cycle simulators lack dynamic repository performance analysis due to the computational burden of high-fidelity hydrolgic contaminant transport models. The Cyder disposal environment and repository module was developed to fill this gap. It implements medium-fidelity hydrologic radionuclide transport models to support assessment appropriate for fuel cycle simulation in the Cyclus fuel cycle simulator. Rapid modeling of hundreds of discrete waste packages in a geologic environment is enabled within this module by a suite of four closed form models for advective, dispersive, coupled, and idealized con-more » taminant transport: a Degradation Rate model, a Mixed Cell model, a Lumped Parameter model, and a 1-D Permeable Porous Medium model. A summary of the Cyder module, its timestepping algorithm, and the mathematical models implemented within it are presented. Additionally, parametric demonstrations simulations performed with Cyder are presented and shown to demonstrate functional agreement with parametric simulations conducted in a standalone hydrologic transport model, the Clay Generic Disposal System Model developed by the Used Fuel Disposition Campaign Department of Energy Office of Nuclear Energy.« less

New algorithms for field-theoretic block copolymer simulations: Progress on using adaptive-mesh refinement and sparse matrix solvers in SCFT calculations

NASA Astrophysics Data System (ADS)

Sides, Scott; Jamroz, Ben; Crockett, Robert; Pletzer, Alexander

2012-02-01

Self-consistent field theory (SCFT) for dense polymer melts has been highly successful in describing complex morphologies in block copolymers. Field-theoretic simulations such as these are able to access large length and time scales that are difficult or impossible for particle-based simulations such as molecular dynamics. The modified diffusion equations that arise as a consequence of the coarse-graining procedure in the SCF theory can be efficiently solved with a pseudo-spectral (PS) method that uses fast-Fourier transforms on uniform Cartesian grids. However, PS methods can be difficult to apply in many block copolymer SCFT simulations (eg. confinement, interface adsorption) in which small spatial regions might require finer resolution than most of the simulation grid. Progress on using new solver algorithms to address these problems will be presented. The Tech-X Chompst project aims at marrying the best of adaptive mesh refinement with linear matrix solver algorithms. The Tech-X code PolySwift++ is an SCFT simulation platform that leverages ongoing development in coupling Chombo, a package for solving PDEs via block-structured AMR calculations and embedded boundaries, with PETSc, a toolkit that includes a large assortment of sparse linear solvers.

Rapid methods for radionuclide contaminant transport in nuclear fuel cycle simulation

DOE PAGES

Huff, Kathryn

2017-08-01

Here, nuclear fuel cycle and nuclear waste disposal decisions are technologically coupled. However, current nuclear fuel cycle simulators lack dynamic repository performance analysis due to the computational burden of high-fidelity hydrolgic contaminant transport models. The Cyder disposal environment and repository module was developed to fill this gap. It implements medium-fidelity hydrologic radionuclide transport models to support assessment appropriate for fuel cycle simulation in the Cyclus fuel cycle simulator. Rapid modeling of hundreds of discrete waste packages in a geologic environment is enabled within this module by a suite of four closed form models for advective, dispersive, coupled, and idealized con-more » taminant transport: a Degradation Rate model, a Mixed Cell model, a Lumped Parameter model, and a 1-D Permeable Porous Medium model. A summary of the Cyder module, its timestepping algorithm, and the mathematical models implemented within it are presented. Additionally, parametric demonstrations simulations performed with Cyder are presented and shown to demonstrate functional agreement with parametric simulations conducted in a standalone hydrologic transport model, the Clay Generic Disposal System Model developed by the Used Fuel Disposition Campaign Department of Energy Office of Nuclear Energy.« less

Getting started with package sampSurf

Treesearch

Jeffrey H. Gove

2014-01-01

The sampSurf package is designed to facilitate the comparison of new and existing areal sampling methods through simulation. The package is thoroughly documented in several vignettes as mentioned below. This document is meant to point you in the right direction in finding the needed information to get started using sampSurf.

A New Streamflow-Routing (SFR1) Package to Simulate Stream-Aquifer Interaction with MODFLOW-2000

USGS Publications Warehouse

Prudic, David E.; Konikow, Leonard F.; Banta, Edward R.

2004-01-01

The increasing concern for water and its quality require improved methods to evaluate the interaction between streams and aquifers and the strong influence that streams can have on the flow and transport of contaminants through many aquifers. For this reason, a new Streamflow-Routing (SFR1) Package was written for use with the U.S. Geological Survey's MODFLOW-2000 ground-water flow model. The SFR1 Package is linked to the Lake (LAK3) Package, and both have been integrated with the Ground-Water Transport (GWT) Process of MODFLOW-2000 (MODFLOW-GWT). SFR1 replaces the previous Stream (STR1) Package, with the most important difference being that stream depth is computed at the midpoint of each reach instead of at the beginning of each reach, as was done in the original Stream Package. This approach allows for the addition and subtraction of water from runoff, precipitation, and evapotranspiration within each reach. Because the SFR1 Package computes stream depth differently than that for the original package, a different name was used to distinguish it from the original Stream (STR1) Package. The SFR1 Package has five options for simulating stream depth and four options for computing diversions from a stream. The options for computing stream depth are: a specified value; Manning's equation (using a wide rectangular channel or an eight-point cross section); a power equation; or a table of values that relate flow to depth and width. Each stream segment can have a different option. Outflow from lakes can be computed using the same options. Because the wetted perimeter is computed for the eight-point cross section and width is computed for the power equation and table of values, the streambed conductance term no longer needs to be calculated externally whenever the area of streambed changes as a function of flow. The concentration of solute is computed in a stream network when MODFLOW-GWT is used in conjunction with the SFR1 Package. The concentration of a solute in a stream reach is based on a mass-balance approach and accounts for exchanges with (inputs from or losses to) ground-water systems. Two test examples are used to illustrate some of the capabilities of the SFR1 Package. The first test simulation was designed to illustrate how pumping of ground water from an aquifer connected to streams can affect streamflow, depth, width, and streambed conductance using the different options. The second test simulation was designed to illustrate solute transport through interconnected lakes, streams, and aquifers. Because of the need to examine time series results from the model simulations, the Gage Package first described in the LAK3 documentation was revised to include time series results of selected variables (streamflows, stream depth and width, streambed conductance, solute concentrations, and solute loads) for specified stream reaches. The mass-balance or continuity approach for routing flow and solutes through a stream network may not be applicable for all interactions between streams and aquifers. The SFR1 Package is best suited for modeling long-term changes (months to hundreds of years) in ground-water flow and solute concentrations using averaged flows in streams. The Package is not recommended for modeling the transient exchange of water between streams and aquifers when the objective is to examine short-term (minutes to days) effects caused by rapidly changing streamflows.

Motion synthesis and force distribution analysis for a biped robot.

PubMed

Trojnacki, Maciej T; Zielińska, Teresa

2011-01-01

In this paper, the method of generating biped robot motion using recorded human gait is presented. The recorded data were modified taking into account the velocity available for robot drives. Data includes only selected joint angles, therefore the missing values were obtained considering the dynamic postural stability of the robot, which means obtaining an adequate motion trajectory of the so-called Zero Moment Point (ZMT). Also, the method of determining the ground reaction forces' distribution during the biped robot's dynamic stable walk is described. The method was developed by the authors. Following the description of equations characterizing the dynamics of robot's motion, the values of the components of ground reaction forces were symbolically determined as well as the coordinates of the points of robot's feet contact with the ground. The theoretical considerations have been supported by computer simulation and animation of the robot's motion. This was done using Matlab/Simulink package and Simulink 3D Animation Toolbox, and it has proved the proposed method.

Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.

PubMed

Bameta, Tripti; Das, Dibyendu; Padinhateeri, Ranjith

2018-06-01

Positioning of nucleosomes along the genomic DNA is crucial for many cellular processes that include gene regulation and higher order packaging of chromatin. The question of how nucleosome-positioning information from a parent chromatin gets transferred to the daughter chromatin is highly intriguing. Accounting for experimentally known coupling between replisome movement and nucleosome dynamics, we propose a model that can obtain de novo nucleosome assembly similar to what is observed in recent experiments. Simulating nucleosome dynamics during replication, we argue that short pausing of the replication fork, associated with nucleosome disassembly, can be a event crucial for communicating nucleosome positioning information from parent to daughter. We show that the interplay of timescales between nucleosome disassembly (τp) at the replication fork and nucleosome sliding behind the fork (τs) can give rise to a rich 'phase diagram' having different inherited patterns of nucleosome organization. Our model predicts that only when τp ≥ τs the daughter chromatin can inherit nucleosome positioning of the parent.

Simple method for the selection of the appropriate food simulant for the evaluation of a specific food/packaging interaction.

PubMed

Hernández-Muñoz, P; Catalá, R; Gavara, R

2002-01-01

Knowledge of the extent of food/packaging interactions is essential to provide assurance of food quality and shelf life, especially in migration and sorption processes that commonly reach equilibrium during the lifetime of a commercial packaged foodstuff. The limits of sorption and migration must be measured in the presence of the specific food or an appropriate food simulant. The partition equilibrium of food aroma compounds between plastic films and foods or food simulants (K(A,P/L) has been characterized. Two polymers (LLDPE and PET), three organic compounds (ethyl caproate, hexanal and 2-phenylethanol), four food products with varying fat content (milk cream, mayonnaise, margarine and oil) and three simulants (ethanol 95%, n-heptane and isooctane) were selectedfor study. The results show the effect of the aroma compound volatility, and polarity, as well as its compatibility with the polymer and the food or food simulant. Equilibrium constants for the organic compound between the polymers and a gaseous phase (K(A,P/V)) as well as between the food (or food simulant) and a gaseous phase (K(A,L/V)) were also determined. An approach is presented to estimate K(A,P/V) from the binary equilibrium constants K(A,P/V) and K(A,L/V). Calculated results were shown to describe experimental data very well and indicated that compatibility between the aroma and the food or food simulant is the main contributing factor to the partition equilibrium describing the extent of food/packaging interactions. Therefore, the measurement of liquid/vapour equilibrium can be regarded as a powerful tool to compare the effectiveness of food simulants as substitutes of a particular food product and can be used as a guide for the selection of the appropriate simulant.

Maestro Workflow Conductor

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

Di Natale, Francesco

2017-06-01

MaestroWF is a Python tool and software package for loading YAML study specifications that represents a simulation campaign. The package is capable of parameterizing a study, pulling dependencies automatically, formatting output directories, and managing the flow and execution of the campaign. MaestroWF also provides a set of abstracted objects that can also be used to develop user specific scripts for launching simulation campaigns.

Dynamics of bacteriophage genome ejection in vitro and in vivo

NASA Astrophysics Data System (ADS)

Panja, Debabrata; Molineux, Ian J.

2010-12-01

Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg ml-1. This high density requires substantial compression of the normal B-form helix, leading to the conjecture that DNA in mature phage virions is under significant pressure, and that pressure is used to eject the DNA during infection. A large number of theoretical, computer simulation and in vitro experimental studies surrounding this conjecture have revealed many—though often isolated and/or contradictory—aspects of packaged DNA. This prompts us to present a unified view of the statistical physics and thermodynamics of DNA packaged in phage capsids. We argue that the DNA in a mature phage is in a (meta)stable state, wherein electrostatic self-repulsion is balanced by curvature stress due to confinement in the capsid. We show that in addition to the osmotic pressure associated with the packaged DNA and its counterions, there are four different pressures within the capsid: pressure on the DNA, hydrostatic pressure, the pressure experienced by the capsid and the pressure associated with the chemical potential of DNA ejection. Significantly, we analyze the mechanism of force transmission in the packaged DNA and demonstrate that the pressure on DNA is not important for ejection. We derive equations showing a strong hydrostatic pressure difference across the capsid shell. We propose that when a phage is triggered to eject by interaction with its receptor in vitro, the (thermodynamic) incentive of water molecules to enter the phage capsid flushes the DNA out of the capsid. In vivo, the difference between the osmotic pressures in the bacterial cell cytoplasm and the culture medium similarly results in a water flow that drags the DNA out of the capsid and into the bacterial cell.

Temperature-package power correlations for open-mode geologic disposal concepts.

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

Hardin, Ernest.

2013-02-01

Logistical simulation of spent nuclear fuel (SNF) management in the U.S. combines storage, transportation and disposal elements to evaluate schedule, cost and other resources needed for all major operations leading to final geologic disposal. Geologic repository reference options are associated with limits on waste package thermal power output at emplacement, in order to meet limits on peak temperature for certain key engineered and natural barriers. These package power limits are used in logistical simulation software such as CALVIN, as threshold requirements that must be met by means of decay storage or SNF blending in waste packages, before emplacement in amore » repository. Geologic repository reference options include enclosed modes developed for crystalline rock, clay or shale, and salt. In addition, a further need has been addressed for open modes in which SNF can be emplaced in a repository, then ventilated for decades or longer to remove heat, prior to permanent repository closure. For each open mode disposal concept there are specified durations for surface decay storage (prior to emplacement), repository ventilation, and repository closure operations. This study simulates those steps for several timing cases, and for SNF with three fuel-burnup characteristics, to develop package power limits at which waste packages can be emplaced without exceeding specified temperature limits many years later after permanent closure. The results are presented in the form of correlations that span a range of package power and peak postclosure temperature, for each open-mode disposal concept, and for each timing case. Given a particular temperature limit value, the corresponding package power limit for each case can be selected for use in CALVIN and similar tools.« less

The One-Water Hydrologic Flow Model - The next generation in fully integrated hydrologic simulation software

NASA Astrophysics Data System (ADS)

Boyce, S. E.; Hanson, R. T.

2015-12-01

The One-Water Hydrologic Flow Model (MF-OWHM) is a MODFLOW-based integrated hydrologic flow model that is the most complete version, to date, of the MODFLOW family of hydrologic simulators needed for the analysis of a broad range of conjunctive-use issues. MF-OWHM fully links the movement and use of groundwater, surface water, and imported water for consumption by agriculture and natural vegetation on the landscape, and for potable and other uses within a supply-and-demand framework. MF-OWHM is based on the Farm Process for MODFLOW-2005 combined with Local Grid Refinement, Streamflow Routing, Surface-water Routing Process, Seawater Intrusion, Riparian Evapotranspiration, and the Newton-Raphson solver. MF-OWHM also includes linkages for deformation-, flow-, and head-dependent flows; additional observation and parameter options for higher-order calibrations; and redesigned code for facilitation of self-updating models and faster simulation run times. The next version of MF-OWHM, currently under development, will include a new surface-water operations module that simulates dynamic reservoir operations, the conduit flow process for karst aquifers and leaky pipe networks, a new subsidence and aquifer compaction package, and additional features and enhancements to enable more integration and cross communication between traditional MODFLOW packages. By retaining and tracking the water within the hydrosphere, MF-OWHM accounts for "all of the water everywhere and all of the time." This philosophy provides more confidence in the water accounting by the scientific community and provides the public a foundation needed to address wider classes of problems such as evaluation of conjunctive-use alternatives and sustainability analysis, including potential adaptation and mitigation strategies, and best management practices. By Scott E. Boyce and Randall T. Hanson

Description and field analysis of a coupled ground-water/surface-water flow model (MODFLOW/BRANCH) with modifications for structures and wetlands in southern Dade County, Florida

USGS Publications Warehouse

Swain, E.D.; Howie, Barbara; Dixon, Joann

1996-01-01

A coupled surface-water model (BRANCH) and ground-water model (MODFLOW) model were tested to simulate the interacting wetlands/surface-water/ ground-water system of southern Dade County. Several options created for the MODFLOW ground- ground-water model were used in representing this field situation. The primary option is the MODBRANCH interfacing software, which allows leakage to be accounted for between the MODFLOW ground-water model and the BRANCH dynamic model for simulation of flow in an interconnected network of open channels. A modification to an existing software routine, which is referred to as BCF2, allows cells in MODFLOW to rewet when dry--a requirement in representing the seasonal wetlands in Dade County. A companion to BCF2 is the modified evapotranspiration routine EVT2. The EVT2 routine changes the cells where evapotranspiration occurs, depending on which cells are wet. The Streamlink package represents direct connections between the canals and wetlands at locations where canals open directly into overland flow. Within the BRANCH model, the capability to represent the numerous hydraulic structures, gated spillways, gated culverts, and pumps was added. The application of these modifications to model surface-water/ground-water interactions in southern Dade County demonstrated the usefulness of the coupled MODFLOW/BRANCH model. Ground-water and surface-water flows are both simulated with dynamic models. Flow exchange between models, intermittent wetting and drying, evapotranspiration, and hydraulic structure operations are all represented appropriately. Comparison was made with a simulation using the RIV1 package instead of MODBRANCH to represent the canals. RIV1 represents the canals by user-defined stages, and computes leakage to the aquifer. Greater accuracy in reproducing measured ground- water heads was achieved with MODBRANCH, which also computes dynamic flow conditions in the canals, unlike RIV1. The surface-water integrated flow and transport two-dimensional model (SWIFT2D) was also applied to the southeastern coastal wetlands for comparison with the wetlands flow approximation made in MODFLOW. MODFLOW simulates the wetlands as a highly conductive upper layer of the aquifer, whereas SWIFT2D solves the hydrodynamic equations. Comparison in this limited test demonstrated no specific advantage for either method of representation. However, much additional testing on a wider variety of geometric and hydraulic situations, such as in areas with greater tidal or other dynamic forcing effects, is needed to make definite conclusions. A submodel of the existing southern Dade County model schematization was used to examine water-delivery alternatives proposed by the U.S. Army Corps of Engineers. For this application, the coupled MODFLOW/BRANCH model was used as a design tool. A new canal and several pumps to be tested to maintain lower water levels in a residential area (while water levels in the Everglades are raised) were added to the model schematization. The pumps were assumed to have infinite supply capacity in the model so that their maximum pumping rates during the simulation could be used to determine pump sizes.

FRACOR-software toolbox for deterministic mapping of fracture corridors in oil fields on AutoCAD platform

NASA Astrophysics Data System (ADS)

Ozkaya, Sait I.

2018-03-01

Fracture corridors are interconnected large fractures in a narrow sub vertical tabular array, which usually traverse entire reservoir vertically and extended for several hundreds of meters laterally. Fracture corridors with their huge conductivities constitute an important element of many fractured reservoirs. Unlike small diffuse fractures, actual fracture corridors must be mapped deterministically for simulation or field development purposes. Fracture corridors can be identified and quantified definitely with borehole image logs and well testing. However, there are rarely sufficient image logs or well tests, and it is necessary to utilize various fracture corridor indicators with varying degrees of reliability. Integration of data from many different sources, in turn, requires a platform with powerful editing and layering capability. Available commercial reservoir characterization software packages, with layering and editing capabilities, can be cost intensive. CAD packages are far more affordable and may easily acquire the versatility and power of commercial software packages with addition of a small software toolbox. The objective of this communication is to present FRACOR, a software toolbox which enables deterministic 2D fracture corridor mapping and modeling on AutoCAD platform. The FRACOR toolbox is written in AutoLISPand contains several independent routines to import and integrate available fracture corridor data from an oil field, and export results as text files. The resulting fracture corridor maps consists mainly of fracture corridors with different confidence levels from combination of static and dynamic data and exclusion zones where no fracture corridor can exist. The exported text file of fracture corridors from FRACOR can be imported into an upscaling programs to generate fracture grid for dual porosity simulation or used for field development and well planning.

Modeling hydraulic regenerative hybrid vehicles using AMESim and Matlab/Simulink

NASA Astrophysics Data System (ADS)

Lynn, Alfred; Smid, Edzko; Eshraghi, Moji; Caldwell, Niall; Woody, Dan

2005-05-01

This paper presents the overview of the simulation modeling of a hydraulic system with regenerative braking used to improve vehicle emissions and fuel economy. Two simulation software packages were used together to enhance the simulation capability for fuel economy results and development of vehicle and hybrid control strategy. AMESim, a hydraulic simulation software package modeled the complex hydraulic circuit and component hardware and was interlinked with a Matlab/Simulink model of the vehicle, engine and the control strategy required to operate the vehicle and the hydraulic hybrid system through various North American and European drive cycles.

IN-PACKAGE CHEMISTRY ABSTRACTION

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

E. Thomas

2005-07-14

This report was developed in accordance with the requirements in ''Technical Work Plan for Postclosure Waste Form Modeling'' (BSC 2005 [DIRS 173246]). The purpose of the in-package chemistry model is to predict the bulk chemistry inside of a breached waste package and to provide simplified expressions of that chemistry as a function of time after breach to Total Systems Performance Assessment for the License Application (TSPA-LA). The scope of this report is to describe the development and validation of the in-package chemistry model. The in-package model is a combination of two models, a batch reactor model, which uses the EQ3/6more » geochemistry-modeling tool, and a surface complexation model, which is applied to the results of the batch reactor model. The batch reactor model considers chemical interactions of water with the waste package materials, and the waste form for commercial spent nuclear fuel (CSNF) waste packages and codisposed (CDSP) waste packages containing high-level waste glass (HLWG) and DOE spent fuel. The surface complexation model includes the impact of fluid-surface interactions (i.e., surface complexation) on the resulting fluid composition. The model examines two types of water influx: (1) the condensation of water vapor diffusing into the waste package, and (2) seepage water entering the waste package as a liquid from the drift. (1) Vapor-Influx Case: The condensation of vapor onto the waste package internals is simulated as pure H{sub 2}O and enters at a rate determined by the water vapor pressure for representative temperature and relative humidity conditions. (2) Liquid-Influx Case: The water entering a waste package from the drift is simulated as typical groundwater and enters at a rate determined by the amount of seepage available to flow through openings in a breached waste package.« less

Experimental characterisation and modelling of deformation- induced microstructure in an A6061 aluminium alloy

NASA Astrophysics Data System (ADS)

Kreyca, J. F.; Falahati, A.; Kozeschnik, E.

2016-03-01

For industry, the mechanical properties of a material in form of flow curves are essential input data for finite element simulations. Current practice is to obtain flow curves experimentally and to apply fitting procedures to obtain constitutive equations that describe the material response to external loading as a function of temperature and strain rate. Unfortunately, the experimental procedure for characterizing flow curves is complex and expensive, which is why the prediction of flow-curves by computer modelling becomes increasingly important. In the present work, we introduce a state parameter based model that is capable of predicting the flow curves of an A6061 aluminium alloy in different heat-treatment conditions. The model is implemented in the thermo-kinetic software package MatCalc and takes into account precipitation kinetics, subgrain formation, dynamic recovery by spontaneous annihilation and dislocation climb. To validate the simulation results, a series of compression tests is performed on the thermo-mechanical simulator Gleeble 1500.

Design of an ammonia closed-loop storage system in a CSP power plant with a power tower cavity receiver

NASA Astrophysics Data System (ADS)

Abdiwe, Ramadan; Haider, Markus

2017-06-01

In this study the thermochemical system using ammonia as energy storage carrier is investigated and a transient mathematical model using MATLAB software was developed to predict the behavior of the ammonia closed-loop storage system including but not limited to the ammonia solar reactor and the ammonia synthesis reactor. The MATLAB model contains transient mass and energy balances as well as chemical equilibrium model for each relevant system component. For the importance of the dissociation and formation processes in the system, a Computational Fluid Dynamics (CFD) simulation on the ammonia solar and synthesis reactors has been performed. The CFD commercial package FLUENT is used for the simulation study and all the important mechanisms for packed bed reactors are taken into account, such as momentum, heat and mass transfer, and chemical reactions. The FLUENT simulation reveals the profiles inside both reactors and compared them with the profiles from the MATLAB code.

Coal conversion systems design and process modeling. Volume 1: Application of MPPR and Aspen computer models

NASA Technical Reports Server (NTRS)

1981-01-01

The development of a coal gasification system design and mass and energy balance simulation program for the TVA and other similar facilities is described. The materials-process-product model (MPPM) and the advanced system for process engineering (ASPEN) computer program were selected from available steady state and dynamic models. The MPPM was selected to serve as the basis for development of system level design model structure because it provided the capability for process block material and energy balance and high-level systems sizing and costing. The ASPEN simulation serves as the basis for assessing detailed component models for the system design modeling program. The ASPEN components were analyzed to identify particular process blocks and data packages (physical properties) which could be extracted and used in the system design modeling program. While ASPEN physical properties calculation routines are capable of generating physical properties required for process simulation, not all required physical property data are available, and must be user-entered.

Numerical simulation on the powder propellant pickup characteristics of feeding system at high pressure

NASA Astrophysics Data System (ADS)

Sun, Haijun; Hu, Chunbo; Zhu, Xiaofei

2017-10-01

A numerical study of powder propellant pickup progress at high pressure was presented in this paper by using two-fluid model with kinetic theory of granular flow in the computational fluid dynamics software package ANSYS/Fluent. Simulations were conducted to evaluate the effects of initial pressure, initial powder packing rate and mean particle diameter on the flow characteristics in terms of velocity vector distribution, granular temperature, pressure drop, particle velocity and volume. The numerical results of pressure drop were also compared with experiments to verify the TFM model. The simulated results show that the pressure drop value increases as the initial pressure increases, and the granular temperature under the conditions of different initial pressures and packing rates is almost the same in the area of throttling orifice plate. While there is an appropriate value for particle size and packing rate to form a ;core-annulus; structure in powder box, and the time-averaged velocity vector distribution of solid phase is inordinate.

NY TBO Research: Integrated Demand Management (IDM): IDM Concept, Tools, and Training Package

NASA Technical Reports Server (NTRS)

Smith, Nancy

2016-01-01

A series of human-in-the-loop simulation sessions were conducted in the Airspace Operations Laboratory (AOL) to evaluate a new traffic management concept called Integrated Demand Management (IDM). The simulation explored how to address chronic equity, throughput and delay issues associated with New Yorks high-volume airports by operationally integrating three current and NextGen capabilities the Collaborative Trajectory Options Program (CTOP), Time-Based Flow Management (TBFM) and Required Time of Arrival (RTA) in order to better manage traffic demand within the National Air Traffic System. A package of presentation slides was developed to describe the concept, tools, and training materials used in the simulation sessions. The package will be used to outbrief our stakeholders by both presenting orally and disseminating of the materials via email.

Efficient implementation of constant pH molecular dynamics on modern graphics processors.

PubMed

Arthur, Evan J; Brooks, Charles L

2016-09-15

The treatment of pH sensitive ionization states for titratable residues in proteins is often omitted from molecular dynamics (MD) simulations. While static charge models can answer many questions regarding protein conformational equilibrium and protein-ligand interactions, pH-sensitive phenomena such as acid-activated chaperones and amyloidogenic protein aggregation are inaccessible to such models. Constant pH molecular dynamics (CPHMD) coupled with the Generalized Born with a Simple sWitching function (GBSW) implicit solvent model provide an accurate framework for simulating pH sensitive processes in biological systems. Although this combination has demonstrated success in predicting pKa values of protein structures, and in exploring dynamics of ionizable side-chains, its speed has been an impediment to routine application. The recent availability of low-cost graphics processing unit (GPU) chipsets with thousands of processing cores, together with the implementation of the accurate GBSW implicit solvent model on those chipsets (Arthur and Brooks, J. Comput. Chem. 2016, 37, 927), provide an opportunity to improve the speed of CPHMD and ionization modeling greatly. Here, we present a first implementation of GPU-enabled CPHMD within the CHARMM-OpenMM simulation package interface. Depending on the system size and nonbonded force cutoff parameters, we find speed increases of between one and three orders of magnitude. Additionally, the algorithm scales better with system size than the CPU-based algorithm, thus allowing for larger systems to be modeled in a cost effective manner. We anticipate that the improved performance of this methodology will open the door for broad-spread application of CPHMD in its modeling pH-mediated biological processes. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Lattice dynamics calculations based on density-functional perturbation theory in real space

NASA Astrophysics Data System (ADS)

Shang, Honghui; Carbogno, Christian; Rinke, Patrick; Scheffler, Matthias

2017-06-01

A real-space formalism for density-functional perturbation theory (DFPT) is derived and applied for the computation of harmonic vibrational properties in molecules and solids. The practical implementation using numeric atom-centered orbitals as basis functions is demonstrated exemplarily for the all-electron Fritz Haber Institute ab initio molecular simulations (FHI-aims) package. The convergence of the calculations with respect to numerical parameters is carefully investigated and a systematic comparison with finite-difference approaches is performed both for finite (molecules) and extended (periodic) systems. Finally, the scaling tests and scalability tests on massively parallel computer systems demonstrate the computational efficiency.

Enhancing 4-propylheptane dissociation with nickel nanocluster based on molecular dynamics simulations.

PubMed

Ilyina, Margarita G; Khamitov, Edward M; Galiakhmetov, Rail N; Mustafin, Ildar A; Mustafin, Akhat G

2017-03-01

In the present work, a 0.4nm nickel cluster has been theoretically studied. Its equilibrium structural parameters have been calculated by the DFT method based on the PBEH1PBE hybrid functional and split-valence basis set Lanl2DZ including effective core potentials. We have systematically considered diverse spin states of this cluster and find out its ground state. The relative stability of these states depends on the HOMO-LUMO gap. The interaction of the Ni 6 with 4-propylheptane С 10 Н 22 has been studied to simulate the process of catalytic cracking of hydrocarbons. The optimization of this structure has been performed by the ωPBE/Lanl2DZ_ecp method (the TeraChem V.1.9 program package) with no symmetry restrictions; the electron shells of the metal were described by effective core pseudopotentials. For visualization and quantitative estimation of the bonding bonds between the nickel nanocluster and 4-propylheptane, the analysis of weak interactions based on RGD has been performed. To confirm the proposition about the formation of Ni-H bonds, we have scrutinized critical points of electronic density. Values of laplasian of electronic density and Bader atomic charge distribution in the global minimum of the total energy have been estimated by the AIMAll 15.05.18 program suite. Finally, we have simulated interaction of Ni 6 with 4-propylheptane in terms of the Born-Oppenheimer ab initio molecular dynamics. The results of the molecular dynamics simulation provide pair radial distribution function CH at 1500°C and a detailed picture of the processes occurring in the system. Copyright © 2017 Elsevier Inc. All rights reserved.

MoleculaRnetworks: an integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation.

PubMed

Mooney, Barbara Logan; Corrales, L René; Clark, Aurora E

2012-03-30

This work discusses scripts for processing molecular simulations data written using the software package R: A Language and Environment for Statistical Computing. These scripts, named moleculaRnetworks, are intended for the geometric and solvent network analysis of aqueous solutes and can be extended to other H-bonded solvents. New algorithms, several of which are based on graph theory, that interrogate the solvent environment about a solute are presented and described. This includes a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute and an exploratory approach for describing H-bonding, both based on the PageRank algorithm of Google search fame. The moleculaRnetworks codes include a preprocessor, which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, and correlation analysis, and other data mining. The goal of these scripts is to increase access to the wealth of structural and dynamical information that can be obtained from molecular simulations. Copyright © 2012 Wiley Periodicals, Inc.

Structural transitions in Cowpea chlorotic mottle virus (CCMV)

NASA Astrophysics Data System (ADS)

Liepold, Lars O.; Revis, Jennifer; Allen, Mark; Oltrogge, Luke; Young, Mark; Douglas, Trevor

2005-12-01

Viral capsids act as molecular containers for the encapsulation of genomic nucleic acid. These protein cages can also be used as constrained reaction vessels for packaging and entrapment of synthetic cargos. The icosahedral Cowpea chlorotic mottle virus (CCMV) is an excellent model for understanding the encapsulation and packaging of both genomic and synthetic materials. High-resolution structural information of the CCMV capsid has been invaluable for evaluating structure-function relationships in the assembled capsid but does not allow insight into the capsid dynamics. The dynamic nature of the CCMV capsid might play an important role in the biological function of the virus. The CCMV capsid undergoes a pH and metal ion dependent reversible structural transition where 60 separate pores in the capsid open or close, exposing the interior of the protein cage to the bulk medium. In addition, the highly basic N-terminal domain of the capsid, which is disordered in the crystal structure, plays a significant role in packaging the viral cargo. Interestingly, in limited proteolysis and mass spectrometry experiments the N-terminal domain is the first part of the subunit to be cleaved, confirming its dynamic nature. Based on our fundamental understanding of the capsid dynamics in CCMV, we have utilized these aspects to direct packaging of a range of synthetic materials including drugs and inorganic nanoparticles.

Column compression strength of tubular packaging forms made from paper

Treesearch

Thomas J. Urbanik; Sung K. Lee; Charles G. Johnson

2006-01-01

Tubular packaging forms fabricated and shaped from rolled paper are used as reinforcing corner posts for major appliances packaged in corrugated containers. Tests of column compression strength simulate the expected performance loads from appliances stacked in warehouses. Column strength depends on tube geometry, paper properties, basis weight, and number of...

GDINA and CDM Packages in R

ERIC Educational Resources Information Center

Rupp, André A.; van Rijn, Peter W.

2018-01-01

We review the GIDNA and CDM packages in R for fitting cognitive diagnosis/diagnostic classification models. We first provide a summary of their core capabilities and then use both simulated and real data to compare their functionalities in practice. We found that the most relevant routines in the two packages appear to be more similar than…