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Sample records for all-atom computer simulations

  1. All-atom Simulation of Amyloid Aggregates

    NASA Astrophysics Data System (ADS)

    Berhanu, Workalemahu M.; Alred, Erik J.; Bernhardt, Nathan A.; Hansmann, Ulrich H. E.

    Molecular simulations are now commonly used to complement experiments in the investigation of amyloid formation and their role in human diseases. While various simulations based on enhanced sampling techniques are used in amyloid formation simulations, this article will focus on those using standard atomistic simulations to evaluate the stability of fibril models. Such studies explore the limitations that arise from the choice of force field or polymorphism; and explore the stability of in vivo and in vitro forms of Aβ fibril aggregates, and the role of heterologous seeding as a link between different amyloid diseases.

  2. All-atom simulations of crowding effects on ubiquitin dynamics

    NASA Astrophysics Data System (ADS)

    Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo

    2013-08-01

    It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (˜0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.

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

    PubMed Central

    2016-01-01

    Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886

  4. All-atom crystal simulations of DNA and RNA duplexes

    PubMed Central

    Liu, Chunmei; Janowski, Pawel A.; Case, David A.

    2014-01-01

    Background Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data. Methods We report simulations of a DNA and RNA duplex in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2], and contain 8 unit cells, each with 4 copies of the Watson-Crick duplex; this yields in aggregate 64 µs of duplex sampling for DNA and 16 µs for RNA. Results The duplex structures conform much more closely to the average structure seen in the crystal than do structures extracted from a solution simulation with the same force field. Sequence-dependent variations in helical parameters, and in groove widths, are largely maintained in the crystal structure, but are smoothed out in solution. However, the integrity of the crystal lattice is slowly degraded in both simulations, with the result that the interfaces between chains become heterogeneous. This problem is more severe for the DNA crystal, which has fewer inter-chain hydrogen bond contacts than does the RNA crystal. Conclusions Crystal simulations using current force fields reproduce many features of observed crystal structures, but suffer from a gradual degradation of the integrity of the crystal lattice. General significance The results offer insights into force-field simulations that tests their ability to preserve weak interactions between chains, which will be of importance also in non-crystalline applications that involve binding and recognition. PMID:25255706

  5. Benchmarking all-atom simulations using hydrogen exchange

    PubMed Central

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations. PMID:25349413

  6. All-atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling

    PubMed Central

    Miao, Yinglong; Johnson, John E.; Ortoleva, Peter J.

    2010-01-01

    An all-atom multiscale computational modeling approach, Molecular Dynamics/Order Parameter eXtrapolation (MD/OPX), has recently been developed for simulating large bionanosystems. It accelerates MD simulations and addresses rapid atomistic fluctuations and slowly-varying nanoscale dynamics of bionanosystems simultaneously. With modules added to account for water molecules and ions, MD/OPX is applied to simulate the swelling of cowpea chlorotic mottle virus (CCMV) capsid solvated in a host medium in this study. Simulation results show that the N-terminal arms of capsid proteins undergo large deviations from the initial configurations with their length extended quickly during the early stage of capsid swelling. The capsid swelling is a symmetry-breaking process involving local initiation and front propagation. The capsid swelling rate is ~0.25 nm/ns (npn) during early stage of the simulation and propagation of the structural transition across the capsid is roughly 0.6npn. The system conditions that affect swelling of the capsid are analyzed. Prospects for creating a phase diagram for CCMV capsid swelling and using predictions to guide experiments are discussed. PMID:20695471

  7. On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations.

    PubMed

    Kuhn, Alexander B; Gopal, Srinivasa M; Schäfer, Lars V

    2015-09-01

    Hybrid all-atom/coarse-grained (AA-CG) simulations in which AA solutes are embedded in a CG environment can provide a significant computational speed-up over conventional fully atomistic simulations and thus alleviate the current length and time scale limitations of molecular dynamics (MD) simulations of large biomolecular systems. On one hand, coarse graining the solvent is particularly appealing, since it typically constitutes the largest part of the simulation system and thus dominates computational cost. On the other hand, retaining atomic-level solvent layers around the solute is desirable for a realistic description of hydrogen bonds and other local solvation effects. Here, we devise and systematically validate fixed resolution AA-CG schemes, both with and without atomistic water layers. To quantify the accuracy and diagnose possible pitfalls, Gibbs free energies of solvation of amino acid side chain analogues were calculated, and the influence of the nature of the CG solvent surrounding (polarizable vs nonpolarizable CG water) and the size of the AA solvent region was investigated. We show that distance restraints to keep the AA solvent around the solute lead to too high of a density in the inner shell. Together with a long-ranged effect due to orientational ordering of water molecules at the AA-CG boundary, this affects solvation free energies. Shifting the onset of the distance restraints slightly away from the central solute significantly improves solvation free energies, down to mean unsigned errors with respect to experiment of 2.3 and 2.6 kJ/mol for the polarizable and nonpolarizable CG water surrounding, respectively. The speed-up of the nonpolarizable model renders it computationally more attractive. The present work thus highlights challenges, and outlines possible solutions, involved with modeling the boundary between different levels of resolution in hybrid AA-CG simulations. PMID:26575936

  8. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost. PMID:24676684

  9. All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

    NASA Astrophysics Data System (ADS)

    Kim, Seung-Yeon; Kwak, Wooseop

    2014-12-01

    We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z( T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z( T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T 1 and the lower transition temperature T 2 of PTH(1-34) can be interpreted as the collapse temperature T θ and the folding temperature T f , respectively.

  10. Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

    PubMed

    Zhang, Liqun; Borthakur, Susmita; Buck, Matthias

    2016-02-23

    The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in

  11. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

    PubMed

    Zheng, Wenjun

    2014-07-01

    The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins. PMID:24403006

  12. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    PubMed

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases. PMID:27071540

  13. All-atom molecular dynamics simulation studies of fully hydrated gel phase DPPG and DPPE bilayers

    NASA Astrophysics Data System (ADS)

    Pimthon, Jutarat; Willumeit, Regine; Lendlein, Andreas; Hofmann, Dieter

    2009-03-01

    Here in silico lipid membranes are described providing a structural background of the organization of the lipid components of membranes and aiding further biological or biophysical studies. An all-atom molecular dynamics simulations has been performed to investigate structural and dynamical properties of two fully hydrated gel-phase bilayers of 1,2-dipalmitoyl- sn-glycero-3-phosphoglycerol (DPPG) and 1,2-dipalmitoyl- sn-glycero-3-phospho-ethanolamine (DPPE) bilayers at 303 K. The respective starting configuration of lipids in the simulation bilayer unit cells were taken on the basis of scattering data. In both simulations, we found overall reasonably good agreement with the available experimental data (area per lipid, phosphorus-phosphorus distance). The distribution of the water/counterions at the membrane interface, interactions/orientations of lipid headgroups, and hydrocarbon chain organization were extensively studied in terms of pair distribution functions between main structural components of the system. Intra/intermolecular hydrogen bond formation was discussed in detail. The water orientation at the lipid membrane interface was explored thoroughly in terms of dipole moment as a function of the water molecule positions along the membrane, where we found that the counterions changed the orientation of the water at the interface. Special attention has been devoted to the distribution of the sodium counterions around the DPPG headgroup. We found preferential binding of Na + ions to the phosphate oxygen species.

  14. Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations

    NASA Astrophysics Data System (ADS)

    Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  15. Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.

    PubMed

    Pepłowski, Lukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-28

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids. PMID:21361557

  16. Local elasticity of strained DNA studied by all-atom simulations

    NASA Astrophysics Data System (ADS)

    Mazur, Alexey K.

    2011-08-01

    Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light on earlier experimental observations.

  17. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

    PubMed

    Roberts, Christopher C; Chang, Chia-En A

    2016-08-25

    We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

  18. Human Inducible Hsp70: Structures, Dynamics, and Interdomain Communication from All-Atom Molecular Dynamics Simulations.

    PubMed

    Nicolaï, Adrien; Senet, Patrick; Delarue, Patrice; Ripoll, Daniel R

    2010-08-10

    The 70 kDa human heat shock protein is a major molecular chaperone involved in de novo folding of proteins in vivo and refolding of proteins under stress conditions. Hsp70 is related to several "misfolding diseases" and other major pathologies, such as cancer, and is a target for new therapies. Hsp70 is comprised of two main domains: an N-terminal nucleotide binding domain (NBD) and a C-terminal substrate protein binding domain (SBD). The chaperone function of Hsp70 is based on an allosteric mechanism. Binding of ATP in NBD decreases the affinity of the substrate for SBD, and hydrolysis of ATP is promoted by binding of polypeptide segments in the SBD. No complete structure of human Hsp70 is known. Here, we report two models of human Hsp70, constructed by homology with Saccharomyces cerevisiae cochaperone protein Hsp110 (open model) and with Escherichia coli 70 kDa DnaK (closed model) and relaxed for several tens to hundreds of nanoseconds by using all-atom molecular dynamics simulations in explicit solvent. We obtain two stable states, Hsp70 with SBD open and SBD closed, which agree with experimental and structural information for ATP-Hsp70 and ADP-Hsp70, respectively. The dynamics of the transition from the open to closed states is investigated with a coarse-grained model and normal-mode analysis. The results show that the conformational change between the two states can be represented by a relatively small number of collective modes which involved major conformational changes in the two domains. These modes provide a mechanistic representation of the communication between NBD and SBD and allow us to identify subdomains and residues that appear to have a critical role in the conformational change mechanism that guides the chaperoning cycle of Hsp70. PMID:26613502

  19. Lipid receptor S1P₁ activation scheme concluded from microsecond all-atom molecular dynamics simulations.

    PubMed

    Yuan, Shuguang; Wu, Rongliang; Latek, Dorota; Trzaskowski, Bartosz; Filipek, Slawomir

    2013-01-01

    Sphingosine 1-phosphate (S1P) is a lysophospholipid mediator which activates G protein-coupled sphingosine 1-phosphate receptors and thus evokes a variety of cell and tissue responses including lymphocyte trafficking, endothelial development, integrity, and maturation. We performed five all-atom 700 ns molecular dynamics simulations of the sphingosine 1-phosphate receptor 1 (S1P₁) based on recently released crystal structure of that receptor with an antagonist. We found that the initial movements of amino acid residues occurred in the area of highly conserved W269⁶·⁴⁸ in TM6 which is close to the ligand binding location. Those residues located in the central part of the receptor and adjacent to kinks of TM helices comprise of a transmission switch. Side chains movements of those residues were coupled to the movements of water molecules inside the receptor which helped in the gradual opening of intracellular part of the receptor. The most stable parts of the protein were helices TM1 and TM2, while the largest movement was observed for TM7, possibly due to the short intracellular part starting with a helix kink at P⁷·⁵⁰, which might be the first helix to move at the intracellular side. We show for the first time the detailed view of the concerted action of the transmission switch and Trp (W⁶·⁴⁸) rotamer toggle switch leading to redirection of water molecules flow in the central part of the receptor. That event is a prerequisite for subsequent changes in intracellular part of the receptor involving water influx and opening of the receptor structure. PMID:24098103

  20. Reorientation and Dimerization of the Membrane-Bound Antimicrobial Peptide PGLa from Microsecond All-Atom MD Simulations

    PubMed Central

    Ulmschneider, Jakob P.; Smith, Jeremy C.; Ulmschneider, Martin B.; Ulrich, Anne S.; Strandberg, Erik

    2012-01-01

    The membrane-active antimicrobial peptide PGLa from Xenopus laevis is known from solid-state 2H-, 15N-, and 19F-NMR spectroscopy to occupy two distinct α-helical surface adsorbed states in membranes: a surface-bound S-state with a tilt angle of ∼95° at low peptide/lipid molar ratio (P/L = 1:200), and an obliquely tilted T-state with a tilt angle of 127° at higher peptide concentration (P/L = 1:50). Using a rapid molecular-dynamics insertion protocol in combination with microsecond-scale simulation, we have characterized the structure of both states in detail. As expected, the amphiphilic peptide resides horizontally on the membrane surface in a monomeric form at a low P/L, whereas the T-state is seen in the simulations to be a symmetric antiparallel dimer, with close contacts between small glycine and alanine residues at the interface. The computed tilt angles and azimuthal rotations, as well as the quadrupolar splittings predicted from the simulations agree with the experimental NMR data. The simulations reveal many structural details previously inaccessible, such as the immersion depth of the peptide in the membrane and the packing of the dimerization interface. The study highlights the ability and limitations of current state-of-the-art multimicrosecond all-atom simulations of membrane-active peptides to complement experimental data from solid-state NMR. PMID:22947863

  1. A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

    PubMed Central

    Qin, Feng

    2015-01-01

    The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

  2. Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows

    NASA Astrophysics Data System (ADS)

    Wang, Guan M.; Sandberg, William C.

    2007-04-01

    In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated

  3. Improving an all-atom force field.

    PubMed

    Mohanty, Sandipan; Hansmann, U H E

    2007-07-01

    Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve the force field's range of applicability. PMID:17677516

  4. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

    PubMed Central

    2015-01-01

    We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically

  5. Application of principal component analysis in protein unfolding: An all-atom molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Das, Atanu; Mukhopadhyay, Chaitali

    2007-10-01

    We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide—ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.

  6. Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization.

    PubMed

    Jeon, Joohyun; Mills, Carolyn E; Shell, M Scott

    2013-04-18

    Self-assembling peptides represent a growing class of inexpensive, environmentally benign, nanostructured materials. In particular, diphenylalanine (FF) self-assembles into nanotubes with remarkable strength and thermal stability that have found use in a wide variety of applications, including as sacrificial templates and scaffolds for structuring inorganic materials and as interfacial "nanoforests" for superhydrophobic surfaces and high-performance supercapacitors and biosensors. However, little is known about the assembly mechanisms of FF nanotubes or the forces underlying their stability. Here, we perform a variety of molecular dynamics simulations on both zwitterionic and capped (uncharged) versions of the FF peptide to understand the early stages of self-assembly. We compare these results to simulations of the proposed nanotube X-ray crystal structure. When comparing the zwitterionic and uncharged FF peptides, we find that, while electrostatic interactions steer the former into more ordered dimers and trimers, the hydrophobic side chain interactions play a strong role in determining the structures of larger oligomers. Simulations of the crystal structure fragment also suggest that the strongest interactions occur between side chains, not between the charged termini that form salt bridges. We conclude that the amphiphilic nature of FF is key to understanding its self-assembly, and that the early precursors to nanotube structures are likely to involve substantial hydrophobic clustering, rather than hexamer ring motifs as has been previously suggested. PMID:23521630

  7. Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations.

    PubMed

    Cota, Junio; Oliveira, Leandro C; Damásio, André R L; Citadini, Ana P; Hoffmam, Zaira B; Alvarez, Thabata M; Codima, Carla A; Leite, Vitor B P; Pastore, Glaucia; de Oliveira-Neto, Mario; Murakami, Mario T; Ruller, Roberto; Squina, Fabio M

    2013-08-01

    Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (kcat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. PMID:23459129

  8. Simplified protein models can rival all atom simulations in predicting folding pathways and structure

    PubMed Central

    Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    We demonstrate the ability of simultaneously determining a protein’s folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing native-like substructures or "foldons". Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R.O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that native-like propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the MD study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo. PMID:23889448

  9. Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations

    PubMed Central

    Kamiya, Narutoshi; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki

    2016-01-01

    Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA+ ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named ‘the ADP model’ and ‘the ATP model’, where ADP and ATP are bound to AAA1 in the AAA+ ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results. PMID:27334455

  10. Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations.

    PubMed

    Kamiya, Narutoshi; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki

    2016-08-01

    Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA(+) ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named 'the ADP model' and 'the ATP model', where ADP and ATP are bound to AAA1 in the AAA(+) ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results. PMID:27334455

  11. Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

    PubMed

    Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen

    2016-04-14

    Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties. PMID:27007011

  12. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations.

    PubMed

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-07-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  13. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations*

    PubMed Central

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-01-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  14. Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations.

    PubMed

    Murtola, Teemu; Vattulainen, Ilpo; Falck, Emma

    2008-06-01

    Tryptophan biosynthesis in Bacillus stearothermophilus is regulated by a trp RNA binding attenuation protein (TRAP). It is a ring-shaped 11-mer of identical 74 residue subunits. Tryptophan binding pockets are located between adjacent subunits, and tryptophan binding activates TRAP to bind RNA. Here, we report results from all-atom molecular dynamics simulations of the system, complementing existing extensive experimental studies. We focus on two questions. First, we look at the activation mechanism, of which relatively little is known experimentally. We find that the absence of tryptophan allows larger motions close to the tryptophan binding site, and we see indication of a conformational change in the BC loop. However, complete deactivation seems to occur on much longer time scales than the 40 ns studied here. Second, we study the TRAP-RNA interactions. We look at the relative flexibilities of the different bases in the complex and analyze the hydrogen bonds between the protein and RNA. We also study the role of Lys37, Lys56, and Arg58, which have been experimentally identified as essential for RNA binding. Hydrophobic stacking of Lys37 with the nearby RNA base is confirmed, but we do not see direct hydrogen bonding between RNA and the other two residues, in contrast to the crystal structure. Rather, these residues seem to stabilize the RNA-binding surface, and their positive charge may also play a role in RNA binding. Simulations also indicate that TRAP is able to attract RNA nonspecifically, and the interactions are quantified in more detail using binding energy calculations. The formation of the final binding complex is a very slow process: within the simulation time scale of 40 ns, only two guanine bases become bound (and no others), indicating that the binding initiates at these positions. In general, our results are in good agreement with experimental studies, and provide atomic-scale insights into the processes. PMID:18186477

  15. Probing the Huntingtin 1-17 Membrane Anchor on a Phospholipid Bilayer by Using All-Atom Simulations

    PubMed Central

    Côté, Sébastien; Binette, Vincent; Salnikov, Evgeniy S.; Bechinger, Burkhard; Mousseau, Normand

    2015-01-01

    Mislocalization and aggregation of the huntingtin protein are related to Huntington’s disease. Its first exon—more specifically the first 17 amino acids (Htt17)—is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin’s activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties—order parameter, thickness, and area per lipid—of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions. PMID:25762330

  16. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect

    Markutsya, Sergiy; Lamm, Monica H

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  17. The Ensemble Folding Kinetics of the FBP28 WW Domain Revealed by an All-atom Monte Carlo Simulation in a Knowledge-based Potential

    PubMed Central

    Xu, Jiabin; Huang, Lei; Shakhnovich, Eugene I.

    2011-01-01

    In this work, we apply a detailed all-atom model with a transferable knowledge-based potential to study the folding kinetics of Formin-Binding protein, FBP28, which is a canonical three-stranded β-sheet WW domain. Replica exchange Monte Carlo (REMC) simulations starting from random coils find native-like (C α RMSD of 2.68Å) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two β –hairpins, the folding mechanism of each individual β– hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous Pfold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Φ values. Our analysis shows that the turn structure between first and second β strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation. PMID:21365688

  18. Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.

    PubMed

    Bottaro, Sandro; Lindorff-Larsen, Kresten; Best, Robert B

    2013-12-10

    The development of accurate implicit solvation models with low computational cost is essential for addressing many large-scale biophysical problems. Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit solvent simulations, particularly for unfolded and disordered states - as would be needed for multiscale applications. In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution obtained from explicit water simulations. Via this methodology, we have optimized both a charge screening parameter and a backbone torsion term against explicit solvent simulations of an α-helical and a β-stranded peptide. The performance of the resulting effective energy function, termed EEF1-SB, is tested with respect to the properties of folded proteins, the folding of small peptides or fast-folding proteins, and NMR data for intrinsically disordered proteins. The results show that EEF1-SB provides a reasonable description of a wide range of systems, but its key advantage over other methods tested is that it captures very well the structure and dimension of disordered or weakly structured peptides. EEF1-SB is thus a computationally inexpensive (~ 10 times faster than Generalized-Born methods) and transferable approximation for treating solvent effects. PMID:24748852

  19. Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions.

    PubMed

    Date, Atsushi; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2016-05-21

    Energetic analysis was conducted for nonpolar and polar solutes bound in a cationic micelle of dodecyl trimethyl ammonium bromide (DTAB), an anionic micelle of sodium dodecyl sulfate (SDS), and a nonionic micelle of tetraethylene glycol monododecyl ether (Brij30). All-atom molecular dynamics simulation was performed, and the free energies of binding the solutes in the hydrophobic-core and headgroup regions of the micelles were computed using the energy-representation method. It was found in all the micelles examined that aromatic naphthalene is preferably located more outward than aliphatic propane and that the polar solutes are localized at the interface of the hydrophobic and hydrophilic regions. The roles of the surfactant and water were then elucidated by decomposing the free energy into the contributions from the respective species. Water was observed to play a decisive role in determining the binding location of the solute, while the surfactant was found to be more important for the overall stabilization of the solute within the micelle. The effects of attractive and repulsive interactions of the solute with the surfactant and water were further examined, and their competition was analyzed in connection with the preferable location of the solute in the micellar system. PMID:27117093

  20. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  1. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  2. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    PubMed

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  3. Free Energetics of Carbon Nanotube Association in Aqueous Inorganic NaI Salt Solutions: Temperature Effects using All-Atom Molecular Dynamics Simulations

    PubMed Central

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-01-01

    In this study we examine the temperature dependence of free energetics of nanotube association by using GPU-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intra-tube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation also shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of

  4. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

    PubMed

    Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

    2012-05-01

    Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups. PMID:26593668

  5. Poly(Ethylene Glycol) in Drug Delivery, Why Does it Work, and Can We do Better? All Atom Molecular Dynamics Simulation Provides Some Answers

    NASA Astrophysics Data System (ADS)

    Bunker, Alex

    We summarize our recent work, using all atom molecular dynamics simulation to study the role of poly(ethylene glycol) (PEG) in drug delivery. We have simulated the drug delivery liposome membrane, in both the Gel and Liquid crystalline states. The simulations of the PEGylated membrane have been carried out in the presence of a physiological concentration of NaCl, and two other salts encountered in physiological conditions, KCL and CaCl2. We also simulated targeting moieties on the PEGylated membrane, comparing the behavior of two targeting moieties. We also simulated PEG with three drug molecules for which it is used as a delivery aid: paclitaxel, piroxicam, and hematoporphyrin. We found that the specific properties of PEG, its solubility in both polar and non-polar solvents, and its acting as a polymer electrolyte, have a significant e_ect on its behavior when used in drug delivery.

  6. Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

    NASA Astrophysics Data System (ADS)

    Takemura, Kazuhiro; Burri, Raghunadha Reddy; Ishikawa, Takeshi; Ishikura, Takakazu; Sakuraba, Shun; Matubayasi, Nobuyuki; Kuwata, Kazuo; Kitao, Akio

    2013-02-01

    We propose a method for calculating the binding free energy of protein-ligand complexes using all-atom molecular dynamics simulation combined with the solution theory in the energy representation. Four distinct modes for the binding of tri-N-acetyl-D-glucosamine (triNAG) to hen egg-white lysozyme were investigated, one from the crystal structure and three generated by docking predictions. The proposed method was demonstrated to be used to distinguish the most plausible binding mode (crystal model) as the lowest binding energy mode.

  7. Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations.

    PubMed

    Wambo, Thierry O; Chen, Liao Y; McHardy, Stanton F; Tsin, Andrew T

    2016-01-01

    Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn(2+) (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO2 and HCO3(-); what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn(2+) is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn(2+), the characteristics of hCAII-Zn(2+) complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn(2+) complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases. PMID:27232456

  8. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

    NASA Astrophysics Data System (ADS)

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-01

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  9. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

    PubMed

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems. PMID:25612718

  10. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-01

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  11. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    SciTech Connect

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  12. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics.

    PubMed

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  13. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    PubMed Central

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  14. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    NASA Astrophysics Data System (ADS)

    Woo, Sun Young; Lee, Hwankyu

    2016-03-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

  15. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase

    PubMed Central

    Nguyen, Trang Truc; Viet, Man Hoang

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔGbind of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔGbind is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔGbind decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM. PMID:24672329

  16. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    NASA Astrophysics Data System (ADS)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  17. Discriminate protein decoys from native by using a scoring function based on ubiquitous Phi and Psi angles computed for all atom.

    PubMed

    Mishra, Avdesh; Iqbal, Sumaiya; Hoque, Md Tamjidul

    2016-06-01

    The success of solving the protein folding and structure prediction problems in molecular and structural biology relies on an accurate energy function. With the rapid advancement in the computational biology and bioinformatics fields, there is a growing need of solving unknown fold and structure faster and thus an accurate energy function is indispensable. To address this need, we develop a new potential function, namely 3DIGARS3.0, which is a linearly weighted combination of 3DIGARS, mined accessible surface area (ASA) and ubiquitously computed Phi (uPhi) and Psi (uPsi) energies - optimized by a Genetic Algorithm (GA). We use a dataset of 4332 protein-structures to generate uPhi and uPsi based score libraries to be used within the core 3DIGARS method. The optimized weight of each component is obtained by applying Genetic Algorithm based optimization on three challenging decoy sets. The improved 3DIGARS3.0 outperformed state-of-the-art methods significantly based on a set of independent test datasets. PMID:27029514

  18. An effective all-atom potential for proteins

    PubMed Central

    Irbäck, Anders; Mitternacht, Simon; Mohanty, Sandipan

    2009-01-01

    We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed α/β protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49–67-residue systems with high statistical accuracy, using only modest computational resources by today's standards. PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc PMID:19356242

  19. Quantum and all-atom molecular dynamics simulations of protonation and divalent ion binding to phosphatidylinositol 4,5-bisphosphate (PIP2).

    PubMed

    Slochower, David R; Huwe, Peter J; Radhakrishnan, Ravi; Janmey, Paul A

    2013-07-18

    Molecular dynamics calculations have been used to determine the structure of phosphatidylinositol 4,5 bisphosphate (PIP2) at the quantum level and to quantify the propensity for PIP2 to bind two physiologically relevant divalent cations, Mg(2+) and Ca(2+). We performed a geometry optimization at the Hartree-Fock 6-31+G(d) level of theory in vacuum and with a polarized continuum dielectric to determine the conformation of the phospholipid headgroup in the presence of water and its partial charge distribution. The angle between the headgroup and the acyl chains is nearly perpendicular, suggesting that in the absence of other interactions the inositol ring would lie flat along the cytoplasmic surface of the plasma membrane. Next, we employed hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to investigate the protonation state of PIP2 and its interactions with magnesium or calcium. We test the hypothesis suggested by prior experiments that binding of magnesium to PIP2 is mediated by a water molecule that is absent when calcium binds. These results may explain the selective ability of calcium to induce the formation of PIP2 clusters and phase separation from other lipids. PMID:23786273

  20. Quantum and All-Atom Molecular Dynamics Simulations of Protonation and Divalent Ion Binding to Phosphatidylinositol 4,5-Bisphosphate (PIP2)

    PubMed Central

    Slochower, David R.; Huwe, Peter J.; Radhakrishnan, Ravi; Janmey, Paul A.

    2014-01-01

    Molecular dynamics calculations have been used to determine the structure of phosphatidylinositol 4,5 bisphosphate (PIP2) at the quantum level and to quantify the propensity for PIP2 to bind two physiologically relevant divalent cations, Mg2+ and Ca2+. We performed a geometry optimization at the Hartree-Fock 6-31+G(d) level of theory in vacuum and with a polarized continuum dielectric to determine the conformation of the phospholipid headgroup in the presence of water and its partial charge distribution. The angle between the headgroup and the acyl chains is nearly perpendicular, suggesting that in the absence of other interactions, the inositol ring would lie flat along the cytoplasmic surface of the plasma membrane. Next, we employed hybrid quantum mechanics / molecular mechanics (QM/MM) simulations to investigate the protonation state of PIP2 and its interactions with magnesium or calcium. We test the hypothesis suggested by prior experiments that binding of magnesium to PIP2 is mediated by a water molecule that is absent when calcium binds. These results may explain the selective ability of calcium to induce the formation of PIP2 clusters and phase separation from other lipids. PMID:23786273

  1. Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

    PubMed Central

    Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

    2015-01-01

    Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

  2. Computationally efficient multibody simulations

    NASA Technical Reports Server (NTRS)

    Ramakrishnan, Jayant; Kumar, Manoj

    1994-01-01

    Computationally efficient approaches to the solution of the dynamics of multibody systems are presented in this work. The computational efficiency is derived from both the algorithmic and implementational standpoint. Order(n) approaches provide a new formulation of the equations of motion eliminating the assembly and numerical inversion of a system mass matrix as required by conventional algorithms. Computational efficiency is also gained in the implementation phase by the symbolic processing and parallel implementation of these equations. Comparison of this algorithm with existing multibody simulation programs illustrates the increased computational efficiency.

  3. Computer Modeling and Simulation

    SciTech Connect

    Pronskikh, V. S.

    2014-05-09

    Verification and validation of computer codes and models used in simulation are two aspects of the scientific practice of high importance and have recently been discussed by philosophers of science. While verification is predominantly associated with the correctness of the way a model is represented by a computer code or algorithm, validation more often refers to model’s relation to the real world and its intended use. It has been argued that because complex simulations are generally not transparent to a practitioner, the Duhem problem can arise for verification and validation due to their entanglement; such an entanglement makes it impossible to distinguish whether a coding error or model’s general inadequacy to its target should be blamed in the case of the model failure. I argue that in order to disentangle verification and validation, a clear distinction between computer modeling (construction of mathematical computer models of elementary processes) and simulation (construction of models of composite objects and processes by means of numerical experimenting with them) needs to be made. Holding on to that distinction, I propose to relate verification (based on theoretical strategies such as inferences) to modeling and validation, which shares the common epistemology with experimentation, to simulation. To explain reasons of their intermittent entanglement I propose a weberian ideal-typical model of modeling and simulation as roles in practice. I suggest an approach to alleviate the Duhem problem for verification and validation generally applicable in practice and based on differences in epistemic strategies and scopes

  4. Accelerator simulation using computers

    SciTech Connect

    Lee, M.; Zambre, Y.; Corbett, W.

    1992-01-01

    Every accelerator or storage ring system consists of a charged particle beam propagating through a beam line. Although a number of computer programs exits that simulate the propagation of a beam in a given beam line, only a few provide the capabilities for designing, commissioning and operating the beam line. This paper shows how a multi-track'' simulation and analysis code can be used for these applications.

  5. Accelerator simulation using computers

    SciTech Connect

    Lee, M.; Zambre, Y.; Corbett, W.

    1992-01-01

    Every accelerator or storage ring system consists of a charged particle beam propagating through a beam line. Although a number of computer programs exits that simulate the propagation of a beam in a given beam line, only a few provide the capabilities for designing, commissioning and operating the beam line. This paper shows how a ``multi-track`` simulation and analysis code can be used for these applications.

  6. Computer-simulated phacoemulsification

    NASA Astrophysics Data System (ADS)

    Laurell, Carl-Gustaf; Nordh, Leif; Skarman, Eva; Andersson, Mats; Nordqvist, Per

    2001-06-01

    Phacoemulsification makes the cataract operation easier for the patient but involves a demanding technique for the surgeon. It is therefore important to increase the quality of surgical training in order to shorten the learning period for the beginner. This should diminish the risks of the patient. We are developing a computer-based simulator for training of phacoemulsification. The simulator is built on a platform that can be used as a basis for several different training simulators. A prototype has been made that has been partly tested by experienced surgeons.

  7. Probabilistic Fatigue: Computational Simulation

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.

    2002-01-01

    Fatigue is a primary consideration in the design of aerospace structures for long term durability and reliability. There are several types of fatigue that must be considered in the design. These include low cycle, high cycle, combined for different cyclic loading conditions - for example, mechanical, thermal, erosion, etc. The traditional approach to evaluate fatigue has been to conduct many tests in the various service-environment conditions that the component will be subjected to in a specific design. This approach is reasonable and robust for that specific design. However, it is time consuming, costly and needs to be repeated for designs in different operating conditions in general. Recent research has demonstrated that fatigue of structural components/structures can be evaluated by computational simulation based on a novel paradigm. Main features in this novel paradigm are progressive telescoping scale mechanics, progressive scale substructuring and progressive structural fracture, encompassed with probabilistic simulation. These generic features of this approach are to probabilistically telescope scale local material point damage all the way up to the structural component and to probabilistically scale decompose structural loads and boundary conditions all the way down to material point. Additional features include a multifactor interaction model that probabilistically describes material properties evolution, any changes due to various cyclic load and other mutually interacting effects. The objective of the proposed paper is to describe this novel paradigm of computational simulation and present typical fatigue results for structural components. Additionally, advantages, versatility and inclusiveness of computational simulation versus testing are discussed. Guidelines for complementing simulated results with strategic testing are outlined. Typical results are shown for computational simulation of fatigue in metallic composite structures to demonstrate the

  8. Computer simulation of earthquakes

    NASA Technical Reports Server (NTRS)

    Cohen, S. C.

    1977-01-01

    In a computer simulation study of earthquakes a seismically active strike slip fault is represented by coupled mechanical blocks which are driven by a moving plate and which slide on a friction surface. Elastic forces and time independent friction are used to generate main shock events, while viscoelastic forces and time dependent friction add aftershock features. The study reveals that the size, length, and time and place of event occurrence are strongly influenced by the magnitude and degree of homogeneity in the elastic, viscous, and friction parameters of the fault region. For example, periodically reoccurring similar events are observed in simulations with near-homogeneous parameters along the fault, whereas seismic gaps are a common feature of simulations employing large variations in the fault parameters. The study also reveals correlations between strain energy release and fault length and average displacement and between main shock and aftershock displacements.

  9. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

    PubMed

    Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos

    2012-11-21

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging. PMID:23181323

  10. Computer simulation of earthquakes

    NASA Technical Reports Server (NTRS)

    Cohen, S. C.

    1976-01-01

    Two computer simulation models of earthquakes were studied for the dependence of the pattern of events on the model assumptions and input parameters. Both models represent the seismically active region by mechanical blocks which are connected to one another and to a driving plate. The blocks slide on a friction surface. In the first model elastic forces were employed and time independent friction to simulate main shock events. The size, length, and time and place of event occurrence were influenced strongly by the magnitude and degree of homogeniety in the elastic and friction parameters of the fault region. Periodically reoccurring similar events were frequently observed in simulations with near homogeneous parameters along the fault, whereas, seismic gaps were a common feature of simulations employing large variations in the fault parameters. The second model incorporated viscoelastic forces and time-dependent friction to account for aftershock sequences. The periods between aftershock events increased with time and the aftershock region was confined to that which moved in the main event.

  11. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets.

    PubMed

    Perilla, Juan R; Hadden, Jodi A; Goh, Boon Chong; Mayne, Christopher G; Schulten, Klaus

    2016-05-19

    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. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, 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. PMID:27128262

  12. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

    PubMed Central

    2016-01-01

    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. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, 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. PMID:27128262

  13. Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water.

    PubMed

    Yan, Xin Cindy; Tirado-Rives, Julian; Jorgensen, William L

    2016-08-25

    Due to the importance of water in chemical and biological systems, a coarse-grained representation of the solvent can greatly simplify the description of the system while retaining key thermodynamic properties of the medium. A multiscale solvation model that couples all-atom solutes and polarizable Martini coarse-grained water (AAX/CGS) is developed to reproduce free energies of hydration of organic solutes. Using Monte Carlo/free energy perturbation (MC/FEP) calculations, results from multiscale and all-atom simulations are compared. Improved accuracy is obtained with the AAX/CGS approach for hydrophobic and sulfur- or halogen-containing solutes, but larger deviations are found for polar solute molecules where hydrogen bonding is featured. Furthermore, solvent effects on conformational and tautomeric equilibria of AA solutes were investigated using AA, CG, and GB/SA solvent models. It is found that the CG solvent model can reproduce well the medium effects from experiment and AA simulations; however, the GB/SA solvent model fails in some cases. A 7-30-fold reduction in computational cost is found for the present AAX/CGS multiscale simulations compared to the AA alternative. PMID:26901452

  14. Computational model for protein unfolding simulation

    NASA Astrophysics Data System (ADS)

    Tian, Xu-Hong; Zheng, Ye-Han; Jiao, Xiong; Liu, Cai-Xing; Chang, Shan

    2011-06-01

    The protein folding problem is one of the fundamental and important questions in molecular biology. However, the all-atom molecular dynamics studies of protein folding and unfolding are still computationally expensive and severely limited by the time scale of simulation. In this paper, a simple and fast protein unfolding method is proposed based on the conformational stability analyses and structure modeling. In this method, two structure-based conditions are considered to identify the unstable regions of proteins during the unfolding processes. The protein unfolding trajectories are mimicked through iterative structure modeling according to conformational stability analyses. Two proteins, chymotrypsin inhibitor 2 (CI2) and α -spectrin SH3 domain (SH3) were simulated by this method. Their unfolding pathways are consistent with the previous molecular dynamics simulations. Furthermore, the transition states of the two proteins were identified in unfolding processes and the theoretical Φ values of these transition states showed significant correlations with the experimental data (the correlation coefficients are >0.8). The results indicate that this method is effective in studying protein unfolding. Moreover, we analyzed and discussed the influence of parameters on the unfolding simulation. This simple coarse-grained model may provide a general and fast approach for the mechanism studies of protein folding.

  15. All-atom force field for molecular dynamics simulations on organotransition metal solids and liquids. Application to M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) compounds.

    PubMed

    Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E

    2013-10-31

    A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row). PMID:24079472

  16. Intelligence Assessment with Computer Simulations

    ERIC Educational Resources Information Center

    Kroner, S.; Plass, J.L.; Leutner, D.

    2005-01-01

    It has been suggested that computer simulations may be used for intelligence assessment. This study investigates what relationships exist between intelligence and computer-simulated tasks that mimic real-world problem-solving behavior, and discusses design requirements that simulations have to meet in order to be suitable for intelligence…

  17. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2015-10-13

    We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264

  18. Massively parallel quantum computer simulator

    NASA Astrophysics Data System (ADS)

    De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.

    2007-01-01

    We describe portable software to simulate universal quantum computers on massive parallel computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray X1E, a SGI Altix 3700 and clusters of PCs running Windows XP. We study the performance of the software by simulating quantum computers containing up to 36 qubits, using up to 4096 processors and up to 1 TB of memory. Our results demonstrate that the simulator exhibits nearly ideal scaling as a function of the number of processors and suggest that the simulation software described in this paper may also serve as benchmark for testing high-end parallel computers.

  19. Software simulator for multiple computer simulation system

    NASA Technical Reports Server (NTRS)

    Ogrady, E. P.

    1983-01-01

    A description is given of the structure and use of a computer program that simulates the operation of a parallel processor simulation system. The program is part of an investigation to determine algorithms that are suitable for simulating continous systems on a parallel processor configuration. The simulator is designed to accurately simulate the problem-solving phase of a simulation study. Care has been taken to ensure the integrity and correctness of data exchanges and to correctly sequence periods of computation and periods of data exchange. It is pointed out that the functions performed during a problem-setup phase or a reset phase are not simulated. In particular, there is no attempt to simulate the downloading process that loads object code into the local, transfer, and mapping memories of processing elements or the memories of the run control processor and the system control processor. The main program of the simulator carries out some problem-setup functions of the system control processor in that it requests the user to enter values for simulation system parameters and problem parameters. The method by which these values are transferred to the other processors, however, is not simulated.

  20. Computer simulation of space charge

    NASA Astrophysics Data System (ADS)

    Yu, K. W.; Chung, W. K.; Mak, S. S.

    1991-05-01

    Using the particle-mesh (PM) method, a one-dimensional simulation of the well-known Langmuir-Child's law is performed on an INTEL 80386-based personal computer system. The program is coded in turbo basic (trademark of Borland International, Inc.). The numerical results obtained were in excellent agreement with theoretical predictions and the computational time required is quite modest. This simulation exercise demonstrates that some simple computer simulation using particles may be implemented successfully on PC's that are available today, and hopefully this will provide the necessary incentives for newcomers to the field who wish to acquire a flavor of the elementary aspects of the practice.

  1. Computer Simulation of Mutagenesis.

    ERIC Educational Resources Information Center

    North, J. C.; Dent, M. T.

    1978-01-01

    A FORTRAN program is described which simulates point-substitution mutations in the DNA strands of typical organisms. Its objective is to help students to understand the significance and structure of the genetic code, and the mechanisms and effect of mutagenesis. (Author/BB)

  2. High performance computing in biology: multimillion atom simulations of nanoscale systems.

    PubMed

    Sanbonmatsu, K Y; Tung, C-S

    2007-03-01

    Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nano-scale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

  3. Computer Simulation and Library Management.

    ERIC Educational Resources Information Center

    Main, Linda

    1992-01-01

    Reviews the literature on computer simulation modeling for library management and examines whether simulation is underutilized because the models are too complex and mathematical. Other problems with implementation are considered, including incomplete problem definition, lack of a conceptual framework, system constraints, lack of interaction…

  4. Plasma physics via computer simulation

    SciTech Connect

    Birdsall, C.K.; Langdon, A.B.

    1985-01-01

    This book describes the computerized simulation of plasma kinetics. Topics considered include why attempting to do plasma physics via computer simulation using particles makes good physical sense; overall view of a one-dimensional electrostatic program; a one-dimensional electrostatic program; introduction to the numerical methods used; a 1d electromagnetic program; projects for EM1; effects of the spatial grid; effects of the finite time step; energy-conserving simulation models; multipole models; kinetic theory for fluctuations and noise; collisions; statistical mechanics of a sheet plasma; electrostatic programs in two and three dimensions; electromagnetic programs in 2D and 3D; design of computer experiments; and the choice of parameters.

  5. Composite Erosion by Computational Simulation

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.

    2006-01-01

    Composite degradation is evaluated by computational simulation when the erosion degradation occurs on a ply-by-ply basis and the degrading medium (device) is normal to the ply. The computational simulation is performed by a multi factor interaction model and by a multi scale and multi physics available computer code. The erosion process degrades both the fiber and the matrix simultaneously in the same slice (ply). Both the fiber volume ratio and the matrix volume ratio approach zero while the void volume ratio increases as the ply degrades. The multi factor interaction model simulates the erosion degradation, provided that the exponents and factor ratios are selected judiciously. Results obtained by the computational composite mechanics show that most composite characterization properties degrade monotonically and approach "zero" as the ply degrades completely.

  6. Computer Simulation of Aircraft Aerodynamics

    NASA Technical Reports Server (NTRS)

    Inouye, Mamoru

    1989-01-01

    The role of Ames Research Center in conducting basic aerodynamics research through computer simulations is described. The computer facilities, including supercomputers and peripheral equipment that represent the state of the art, are described. The methodology of computational fluid dynamics is explained briefly. Fundamental studies of turbulence and transition are being pursued to understand these phenomena and to develop models that can be used in the solution of the Reynolds-averaged Navier-Stokes equations. Four applications of computer simulations for aerodynamics problems are described: subsonic flow around a fuselage at high angle of attack, subsonic flow through a turbine stator-rotor stage, transonic flow around a flexible swept wing, and transonic flow around a wing-body configuration that includes an inlet and a tail.

  7. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer. PMID:26930454

  8. Taxis through Computer Simulation Programs.

    ERIC Educational Resources Information Center

    Park, David

    1983-01-01

    Describes a sequence of five computer programs (listings for Apple II available from author) on tactic responses (oriented movement of a cell, cell group, or whole organism in reponse to stimuli). The simulation programs are useful in helping students examine mechanisms at work in real organisms. (JN)

  9. Computer Simulation of Diffraction Patterns.

    ERIC Educational Resources Information Center

    Dodd, N. A.

    1983-01-01

    Describes an Apple computer program (listing available from author) which simulates Fraunhofer and Fresnel diffraction using vector addition techniques (vector chaining) and allows user to experiment with different shaped multiple apertures. Graphics output include vector resultants, phase difference, diffraction patterns, and the Cornu spiral…

  10. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution. PMID:20160980

  11. Computer simulation of martensitic transformations

    SciTech Connect

    Xu, Ping

    1993-11-01

    The characteristics of martensitic transformations in solids are largely determined by the elastic strain that develops as martensite particles grow and interact. To study the development of microstructure, a finite-element computer simulation model was constructed to mimic the transformation process. The transformation is athermal and simulated at each incremental step by transforming the cell which maximizes the decrease in the free energy. To determine the free energy change, the elastic energy developed during martensite growth is calculated from the theory of linear elasticity for elastically homogeneous media, and updated as the transformation proceeds.

  12. Temperature estimators in computer simulation

    NASA Astrophysics Data System (ADS)

    Jara, César; González-Cataldo, Felipe; Davis, Sergio; Gutiérrez, Gonzalo

    2016-05-01

    Temperature is a key physical quantity that is used to describe equilibrium between two bodies in thermal contact. In computer simulations, the temperature is usually estimated by means of the equipartition theorem, as an average over the kinetic energy. However, recent studies have shown that the temperature can be estimated using only the particles positions, which has been called configurational temperature. Through classical molecular dynamics simulations of 108-argon-atoms system, we compare the performance of four different temperature estimators: the usual kinetic temperature and three configurational temperatures, Our results show that the different estimators converge to the same value, but their fluctuations are different.

  13. Computer Simulations of Space Plasmas

    NASA Astrophysics Data System (ADS)

    Goertz, C. K.

    Even a superficial scanning of the latest issues of the Journal of Geophysical Research reveals that numerical simulation of space plasma processes is an active and growing field. The complexity and sophistication of numerically produced “data” rivals that of the real stuff. Sometimes numerical results need interpretation in terms of a simple “theory,” very much as the results of real experiments and observations do. Numerical simulation has indeed become a third independent tool of space physics, somewhere between observations and analytic theory. There is thus a strong need for textbooks and monographs that report the latest techniques and results in an easily accessible form. This book is an attempt to satisfy this need. The editors want it not only to be “proceedings of selected lectures (given) at the first ISSS (International School of Space Simulations in Kyoto, Japan, November 1-2, 1982) but rather…a form of textbook of computer simulations of space plasmas.” This is, of course, a difficult task when many authors are involved. Unavoidable redundancies and differences in notation may confuse the beginner. Some important questions, like numerical stability, are not discussed in sufficient detail. The recent book by C.K. Birdsall and A.B. Langdon (Plasma Physics via Computer Simulations, McGraw-Hill, New York, 1985) is more complete and detailed and seems more suitable as a textbook for simulations. Nevertheless, this book is useful to the beginner and the specialist because it contains not only descriptions of various numerical techniques but also many applications of simulations to space physics phenomena.

  14. Biomes computed from simulated climatologies

    SciTech Connect

    Claussen, M.; Esch, M.

    1994-01-01

    The biome model of Prentice et al. is used to predict global patterns of potential natural plant formations, or biomes, from climatologies simulated by ECHAM, a model used for climate simulations at the Max-Planck-Institut fuer Meteorologie. This study undertaken in order to show the advantage of this biome model in diagnosing the performance of a climate model and assessing effects of past and future climate changes predicted by a climate model. Good overall agreement is found between global patterns of biomes computed from observed and simulated data of present climate. But there are also major discrepancies indicated by a difference in biomes in Australia, in the Kalahari Desert, and in the Middle West of North America. These discrepancies can be traced back to in simulated rainfall as well as summer or winter temperatures. Global patterns of biomes computed from an ice age simulation reveal that North America, Europe, and Siberia should have been covered largely by tundra and taiga, whereas only small differences are for the tropical rain forests. A potential northeast shift of biomes is expected from a simulation with enhanced CO{sub 2} concentration according to the IPCC Scenario A. Little change is seen in the tropical rain forest and the Sahara. Since the biome model used is not capable of predicting chances in vegetation patterns due to a rapid climate change, the latter simulation to be taken as a prediction of chances in conditions favourable for the existence of certain biomes, not as a reduction of a future distribution of biomes. 15 refs., 8 figs., 2 tabs.

  15. Computer simulation of nonequilibrium processes

    SciTech Connect

    Wallace, D.C.

    1985-07-01

    The underlying concepts of nonequilibrium statistical mechanics, and of irreversible thermodynamics, will be described. The question at hand is then, how are these concepts to be realize in computer simulations of many-particle systems. The answer will be given for dissipative deformation processes in solids, on three hierarchical levels: heterogeneous plastic flow, dislocation dynamics, an molecular dynamics. Aplication to the shock process will be discussed.

  16. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    PubMed

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

  17. Inversion based on computational simulations

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.; Saquib, S.S.

    1998-09-01

    A standard approach to solving inversion problems that involve many parameters uses gradient-based optimization to find the parameters that best match the data. The authors discuss enabling techniques that facilitate application of this approach to large-scale computational simulations, which are the only way to investigate many complex physical phenomena. Such simulations may not seem to lend themselves to calculation of the gradient with respect to numerous parameters. However, adjoint differentiation allows one to efficiently compute the gradient of an objective function with respect to all the variables of a simulation. When combined with advanced gradient-based optimization algorithms, adjoint differentiation permits one to solve very large problems of optimization or parameter estimation. These techniques will be illustrated through the simulation of the time-dependent diffusion of infrared light through tissue, which has been used to perform optical tomography. The techniques discussed have a wide range of applicability to modeling including the optimization of models to achieve a desired design goal.

  18. An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders.

    PubMed

    Qin, Sanbo; Zhou, Huan-Xiang

    2013-10-01

    It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments. PMID:24187527

  19. Computer simulations of particle packing

    SciTech Connect

    Cesarano, J. III; McEuen, M.J.; Swiler, T.

    1996-09-01

    Computer code has been developed to rapidly simulate the random packing of disks and spheres in two and three dimensions. Any size distribution may be packed. The code simulates varying degrees of inter particle conditions ranging from sticky to free flowing. The code will also calculate the overall packing density, density distributions, and void size distributions (in two dimensions). An important aspect of the code is that it is written in C++ and incorporates a user-friendly graphical interface for standard Macintosh and Power PC platforms. Investigations as to how well the code simulates the realistic random packing have begun. The code has been developed in consideration of the problem of filling a container (or die) with spray-dried granules of ceramic powder (represented by spheres). Although not presented here, the futuristic goal of this work is to give users the ability to predict homogeneity of filled dies prior to dry pressing. Additionally, this software has educational utility for studying relationships between particle size distributions and macrostructures.

  20. Computer simulation of microstructural dynamics

    SciTech Connect

    Grest, G.S.; Anderson, M.P.; Srolovitz, D.J.

    1985-01-01

    Since many of the physical properties of materials are determined by their microstructure, it is important to be able to predict and control microstructural development. A number of approaches have been taken to study this problem, but they assume that the grains can be described as spherical or hexagonal and that growth occurs in an average environment. We have developed a new technique to bridge the gap between the atomistic interactions and the macroscopic scale by discretizing the continuum system such that the microstructure retains its topological connectedness, yet is amenable to computer simulations. Using this technique, we have studied grain growth in polycrystalline aggregates. The temporal evolution and grain morphology of our model are in excellent agreement with experimental results for metals and ceramics.

  1. Priority Queues for Computer Simulations

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S. (Inventor)

    1998-01-01

    The present invention is embodied in new priority queue data structures for event list management of computer simulations, and includes a new priority queue data structure and an improved event horizon applied to priority queue data structures. ne new priority queue data structure is a Qheap and is made out of linked lists for robust, fast, reliable, and stable event list management and uses a temporary unsorted list to store all items until one of the items is needed. Then the list is sorted, next, the highest priority item is removed, and then the rest of the list is inserted in the Qheap. Also, an event horizon is applied to binary tree and splay tree priority queue data structures to form the improved event horizon for event management.

  2. Computer simulations of liquid crystals

    NASA Astrophysics Data System (ADS)

    Smondyrev, Alexander M.

    Liquid crystal physics is an exciting interdisciplinary field of research with important practical applications. Their complexity and the presence of strong translational and orientational fluctuations require a computational approach, especially in the studies of nonequlibrium phenomena. In this dissertation we present the results of computer simulation studies of liquid crystals using the molecular dynamics technique. We employed the Gay-Berne phenomenological model of liquid crystals to describe the interaction between the molecules. Both equilibrium and non-equilibrium phenomena were studied. In the first case we studied the flow properties of the liquid crystal system in equilibrium as well as the dynamics of the director. We measured the viscosities of the Gay-Berne model in the nematic and isotropic phases. The temperature-dependence of the rotational and shear viscosities, including the nonmonotonic behavior of one shear viscosity, are in good agreement with experimental data. The bulk viscosities are significantly larger than the shear viscosities, again in agreement with experiment. The director motion was found to be ballistic at short times and diffusive at longer times. The second class of problems we focused on is the properties of the system which was rapidly quenched to very low temperatures from the nematic phase. We find a glass transition to a metastable phase with nematic order and frozen translational and orientational degrees of freedom. For fast quench rates the local structure is nematic-like, while for slower quench rates smectic order is present as well. Finally, we considered a system in the isotropic phase which is then cooled to temperatures below the isotropic-nematic transition temperature. We expect topological defects to play a central role in the subsequent equilibration of the system. To identify and study these defects we require a simulation of a system with several thousand particles. We present the results of large

  3. An all-atom force field developed for Zn₄O(RCO₂)₆ metal organic frameworks.

    PubMed

    Sun, Yingxin; Sun, Huai

    2014-03-01

    An all-atom force field is developed for metal organic frameworks Zn₄O(RCO₂)₆ by fitting to quantum mechanics data. Molecular simulations are conducted to validate the force field by calculating thermal expansion coefficients, crystal bulk and Young's moduli, power spectra, self-diffusion coefficients, and activation energies of self-diffusions for benzene and n-hexane. The calculated results are in good agreement with available experimental data. The proposed force field is suitable for simulations of adsorption or diffusion of organic molecules with flexible frameworks. PMID:24562858

  4. The Shuttle Mission Simulator computer generated imagery

    NASA Technical Reports Server (NTRS)

    Henderson, T. H.

    1984-01-01

    Equipment available in the primary training facility for the Space Transportation System (STS) flight crews includes the Fixed Base Simulator, the Motion Base Simulator, the Spacelab Simulator, and the Guidance and Navigation Simulator. The Shuttle Mission Simulator (SMS) consists of the Fixed Base Simulator and the Motion Base Simulator. The SMS utilizes four visual Computer Generated Image (CGI) systems. The Motion Base Simulator has a forward crew station with six-degrees of freedom motion simulation. Operation of the Spacelab Simulator is planned for the spring of 1983. The Guidance and Navigation Simulator went into operation in 1982. Aspects of orbital visual simulation are discussed, taking into account the earth scene, payload simulation, the generation and display of 1079 stars, the simulation of sun glare, and Reaction Control System jet firing plumes. Attention is also given to landing site visual simulation, and night launch and landing simulation.

  5. Development of simulation computer complex specification

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The Training Simulation Computer Complex Study was one of three studies contracted in support of preparations for procurement of a shuttle mission simulator for shuttle crew training. The subject study was concerned with definition of the software loads to be imposed on the computer complex to be associated with the shuttle mission simulator and the development of procurement specifications based on the resulting computer requirements. These procurement specifications cover the computer hardware and system software as well as the data conversion equipment required to interface the computer to the simulator hardware. The development of the necessary hardware and software specifications required the execution of a number of related tasks which included, (1) simulation software sizing, (2) computer requirements definition, (3) data conversion equipment requirements definition, (4) system software requirements definition, (5) a simulation management plan, (6) a background survey, and (7) preparation of the specifications.

  6. Space Ultrareliable Modular Computer (SUMC) instruction simulator

    NASA Technical Reports Server (NTRS)

    Curran, R. T.

    1972-01-01

    The design principles, description, functional operation, and recommended expansion and enhancements are presented for the Space Ultrareliable Modular Computer interpretive simulator. Included as appendices are the user's manual, program module descriptions, target instruction descriptions, simulator source program listing, and a sample program printout. In discussing the design and operation of the simulator, the key problems involving host computer independence and target computer architectural scope are brought into focus.

  7. Simulating Drosophila Genetics with the Computer.

    ERIC Educational Resources Information Center

    Small, James W., Jr.; Edwards, Kathryn L.

    1979-01-01

    Presents some techniques developed to help improve student understanding of Mendelian principles through the use of a computer simulation model by the genetic system of the fruit fly. Includes discussion and evaluation of this computer assisted program. (MA)

  8. Protocols for Handling Messages Between Simulation Computers

    NASA Technical Reports Server (NTRS)

    Balcerowski, John P.; Dunnam, Milton

    2006-01-01

    Practical Simulator Network (PSimNet) is a set of data-communication protocols designed especially for use in handling messages between computers that are engaging cooperatively in real-time or nearly-real-time training simulations. In a typical application, computers that provide individualized training at widely dispersed locations would communicate, by use of PSimNet, with a central host computer that would provide a common computational- simulation environment and common data. Originally intended for use in supporting interfaces between training computers and computers that simulate the responses of spacecraft scientific payloads, PSimNet could be especially well suited for a variety of other applications -- for example, group automobile-driver training in a classroom. Another potential application might lie in networking of automobile-diagnostic computers at repair facilities to a central computer that would compile the expertise of numerous technicians and engineers and act as an expert consulting technician.

  9. Chip level simulation of fault tolerant computers

    NASA Technical Reports Server (NTRS)

    Armstrong, J. R.

    1982-01-01

    Chip-level modeling techniques in the evaluation of fault tolerant systems were researched. A fault tolerant computer was modeled. An efficient approach to functional fault simulation was developed. Simulation software was also developed.

  10. Monte Carlo Computer Simulation of a Rainbow.

    ERIC Educational Resources Information Center

    Olson, Donald; And Others

    1990-01-01

    Discusses making a computer-simulated rainbow using principles of physics, such as reflection and refraction. Provides BASIC program for the simulation. Appends a program illustrating the effects of dispersion of the colors. (YP)

  11. Computer Based Simulation of Laboratory Experiments.

    ERIC Educational Resources Information Center

    Edward, Norrie S.

    1997-01-01

    Examines computer based simulations of practical laboratory experiments in engineering. Discusses the aims and achievements of lab work (cognitive, process, psychomotor, and affective); types of simulations (model building and behavioral); and the strengths and weaknesses of simulations. Describes the development of a centrifugal pump simulation,…

  12. Constructivist Design of Graphic Computer Simulations.

    ERIC Educational Resources Information Center

    Black, John B.; And Others

    Two graphic computer simulations have been prepared for teaching high school and middle school students about how business organizations and financial systems work: "Parkside," which simulates managing a hotel; and "Guestwear," which simulates managing a clothing manufacturer. Both simulations are based on six principles of constructivist design…

  13. Computer Simulation in Chemical Kinetics

    ERIC Educational Resources Information Center

    Anderson, Jay Martin

    1976-01-01

    Discusses the use of the System Dynamics technique in simulating a chemical reaction for kinetic analysis. Also discusses the use of simulation modelling in biology, ecology, and the social sciences, where experimentation may be impractical or impossible. (MLH)

  14. Computer simulation of CPM dye lasers

    SciTech Connect

    Wang Qingyue; Zhao Xingjun )

    1990-01-01

    Quantative analysis of the laser pulses of various intracavity elements in a CPM dye laser is carried out in this study. The pulse formation is simulated with a computer, resulting in an asymmetric numerical solution for the pulse shape. The mechanisms of pulse formation are also discussed based on the results of computer simulation.

  15. VLSI circuit simulation using a vector computer

    NASA Technical Reports Server (NTRS)

    Mcgrogan, S. K.

    1984-01-01

    Simulation of circuits having more than 2000 active devices requires the largest, fastest computers available. A vector computer, such as the CYBER 205, can yield great speed and cost advantages if efforts are made to adapt the simulation program to the strengths of the computer. ASPEC and SPICE (1), two widely used circuit simulation programs, are discussed. ASPECV and VAMOS (5) are respectively vector adaptations of these two simulators. They demonstrate the substantial performance enhancements possible for this class of algorithm on the CYBER 205.

  16. Peptides (P1, P2 and its mutations) binding with a graphene sheet: an all-atom to all-residue hierarchical coarse-grained approach

    NASA Astrophysics Data System (ADS)

    Kuang, Zhifeng; Farmer, Barry; Pandey, Ras

    2013-03-01

    Binding of peptide P2 (EPLQLKM) [1] and its mutations (P2G, P2Q) to a graphene sheet are studied by a coarse-grained computer simulation. Our hierarchical coarse-grained approach involves all-atom MD simulation to assess the binding interaction of each residue with the graphene sheet. Data from all-atom simulations are then used as input to phenomenological interaction in a coarse-grained MC simulation [2]. Binding of each peptide and its residue in corresponding sequence (P2, P2G, P2Q) are evaluated by analyzing the adsorption of each residue, its mobility, and structural profiles. Although it is difficult to identify overall morphological differences in adsorbed peptides by visual inspections, quantitative analysis of the conformational changes of adsorbed peptides shows variations in size among P2E and its mutations. Results on binding of peptide P1 (HSSYWYAFNNKT) may also be presented if data become available. This work is supported by the Air Force Research Laboratory.

  17. Optimum spaceborne computer system design by simulation

    NASA Technical Reports Server (NTRS)

    Williams, T.; Kerner, H.; Weatherbee, J. E.; Taylor, D. S.; Hodges, B.

    1973-01-01

    A deterministic simulator is described which models the Automatically Reconfigurable Modular Multiprocessor System (ARMMS), a candidate computer system for future manned and unmanned space missions. Its use as a tool to study and determine the minimum computer system configuration necessary to satisfy the on-board computational requirements of a typical mission is presented. The paper describes how the computer system configuration is determined in order to satisfy the data processing demand of the various shuttle booster subsytems. The configuration which is developed as a result of studies with the simulator is optimal with respect to the efficient use of computer system resources.

  18. Analyzing Robotic Kinematics Via Computed Simulations

    NASA Technical Reports Server (NTRS)

    Carnahan, Timothy M.

    1992-01-01

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

  19. Computationally Lightweight Air-Traffic-Control Simulation

    NASA Technical Reports Server (NTRS)

    Knight, Russell

    2005-01-01

    An algorithm for computationally lightweight simulation of automated air traffic control (ATC) at a busy airport has been derived. The algorithm is expected to serve as the basis for development of software that would be incorporated into flight-simulator software, the ATC component of which is not yet capable of handling realistic airport loads. Software based on this algorithm could also be incorporated into other computer programs that simulate a variety of scenarios for purposes of training or amusement.

  20. Folding peptides and proteins with all-atom physics: methods and applications

    NASA Astrophysics Data System (ADS)

    Shell, M. Scott

    2008-03-01

    Computational methods offer powerful tools for investigating proteins and peptides at the molecular-level; however, it has proven challenging to reproduce the long time scale folding processes of these molecules at a level that is both faithful to the atomic driving forces and attainable with modern commodity cluster computing. Alternatively, the past decade has seen significant progress in using bioinformatics-based approaches to infer the three dimensional native structures of proteins, drawing upon extensive knowledge databases of known protein structures [1]. These methods work remarkably well when a homologous protein can be found to provide a structural template for a candidate sequence. However, in cases where homology to database proteins is low, where the folding pathway is of interest, or where conformational flexibility is substantial---as in many emerging protein and peptide technologies---bioinformatics methods perform poorly. There is therefore great interest in seeing purely physics-based approaches succeed. We discuss a purely physics-based, database-free folding method, relying on proper thermal sampling (replica exchange molecular dynamics) and molecular potential energy functions. In order to surmount the tremendous computational demands of all-atom folding simulations, our approach implements a conformational search strategy based on a putative protein folding mechanism called zipping and assembly [2-4]. That is, we explicitly seek out potential folding pathways inferred from short simulations, and iteratively pursue all such routes by coaxing a polypeptide chain along them. The method is called the Zipping and Assembly Method (ZAM) and it works in two parts: (1) the full polypeptide chain is broken into small fragments that are first simulated independently and then successively re-assembled into larger segments with further sampling, and (2) consistently stable structure in fragments is detected and locked into place, in order to avoid re

  1. Computer Clinical Simulations in Health Sciences.

    ERIC Educational Resources Information Center

    Jones, Gary L; Keith, Kenneth D.

    1983-01-01

    Discusses the key characteristics of clinical simulation, some developmental foundations, two current research studies, and some implications for the future of health science education. Investigations of the effects of computer-based simulation indicate that acquisition of decision-making skills is greater than with noncomputerized simulations.…

  2. Computer simulation of nonequilibrium processes

    SciTech Connect

    Hoover, W.G.; Moran, B.; Holian, B.L.; Posch, H.A.; Bestiale, S.

    1987-01-01

    Recent atomistic simulations of irreversible macroscopic hydrodynamic flows are illustrated. An extension of Nose's reversible atomistic mechanics makes it possible to simulate such non-equilibrium systems with completely reversible equations of motion. The new techniques show that macroscopic irreversibility is a natural inevitable consequence of time-reversible Lyapunov-unstable microscopic equations of motion.

  3. Filtration theory using computer simulations

    SciTech Connect

    Bergman, W.; Corey, I.

    1997-08-01

    We have used commercially available fluid dynamics codes based on Navier-Stokes theory and the Langevin particle equation of motion to compute the particle capture efficiency and pressure drop through selected two- and three-dimensional fiber arrays. The approach we used was to first compute the air velocity vector field throughout a defined region containing the fiber matrix. The particle capture in the fiber matrix is then computed by superimposing the Langevin particle equation of motion over the flow velocity field. Using the Langevin equation combines the particle Brownian motion, inertia and interception mechanisms in a single equation. In contrast, most previous investigations treat the different capture mechanisms separately. We have computed the particle capture efficiency and the pressure drop through one, 2-D and two, 3-D fiber matrix elements. 5 refs., 11 figs.

  4. Evaluation of Visual Computer Simulator for Computer Architecture Education

    ERIC Educational Resources Information Center

    Imai, Yoshiro; Imai, Masatoshi; Moritoh, Yoshio

    2013-01-01

    This paper presents trial evaluation of a visual computer simulator in 2009-2011, which has been developed to play some roles of both instruction facility and learning tool simultaneously. And it illustrates an example of Computer Architecture education for University students and usage of e-Learning tool for Assembly Programming in order to…

  5. Computer simulation of upset welding

    SciTech Connect

    Spingarn, J R; Mason, W E; Swearengen, J C

    1982-04-01

    Useful process modeling of upset welding requires contributions from metallurgy, welding engineering, thermal analysis and experimental mechanics. In this report, the significant milestones for such an effort are outlined and probable difficult areas are pointed out. Progress to date is summarized and directions for future research are offered. With regard to the computational aspects of this problem, a 2-D heat conduction computer code has been modified to incorporate electrical heating, and computations have been run for an axisymmetric problem with simple viscous material laws and d.c. electrical boundary conditions. In the experimental endeavor, the boundary conditions have been measured during the welding process, although interpretation of voltage drop measurements is not straightforward. The ranges of strain, strain rate and temperature encountered during upset welding have been measured or calculated, and the need for a unifying constitutive law is described. Finally, the possible complications of microstructure and interfaces are clarified.

  6. Computational Spectrum of Agent Model Simulation

    SciTech Connect

    Perumalla, Kalyan S

    2010-01-01

    The study of human social behavioral systems is finding renewed interest in military, homeland security and other applications. Simulation is the most generally applied approach to studying complex scenarios in such systems. Here, we outline some of the important considerations that underlie the computational aspects of simulation-based study of human social systems. The fundamental imprecision underlying questions and answers in social science makes it necessary to carefully distinguish among different simulation problem classes and to identify the most pertinent set of computational dimensions associated with those classes. We identify a few such classes and present their computational implications. The focus is then shifted to the most challenging combinations in the computational spectrum, namely, large-scale entity counts at moderate to high levels of fidelity. Recent developments in furthering the state-of-the-art in these challenging cases are outlined. A case study of large-scale agent simulation is provided in simulating large numbers (millions) of social entities at real-time speeds on inexpensive hardware. Recent computational results are identified that highlight the potential of modern high-end computing platforms to push the envelope with respect to speed, scale and fidelity of social system simulations. Finally, the problem of shielding the modeler or domain expert from the complex computational aspects is discussed and a few potential solution approaches are identified.

  7. All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations

    PubMed Central

    Kuroda, Yutaka; Suenaga, Atsushi; Sato, Yuji; Kosuda, Satoshi; Taiji, Makoto

    2016-01-01

    In order to investigate the contribution of individual amino acids to protein and peptide solubility, we carried out 100 ns molecular dynamics (MD) simulations of 106 Å3 cubic boxes containing ~3 × 104 water molecules and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calculations were performed using Amber with a standard force field on a special purpose MDGRAPE-3 computer, without introducing any “artificial” hydrophobic interactions. Tetra-peptides composed of I, V, L, M, N, Q, F, W, Y, and H formed large amorphous clusters, and those containing A, P, S, and T formed smaller ones. Tetra-peptides made of D, E, K, and R did not cluster at all. These observations correlated well with experimental solubility tendencies as well as hydrophobicity scales with correlation coefficients of 0.5 to > 0.9. Repulsive Coulomb interactions were dominant in ensuring high solubility, whereas both Coulomb and van der Waals (vdW) energies contributed to the aggregations of low solubility amino acids. Overall, this very first all-atom molecular dynamics simulation of a multi-peptide system appears to reproduce the basic properties of peptide solubility, essentially in line with experimental observations. PMID:26817663

  8. Economic Analysis. Computer Simulation Models.

    ERIC Educational Resources Information Center

    Sterling Inst., Washington, DC. Educational Technology Center.

    A multimedia course in economic analysis was developed and used in conjunction with the United States Naval Academy. (See ED 043 790 and ED 043 791 for final reports of the project evaluation and development model.) This volume of the text discusses the simulation of behavioral relationships among variable elements in an economy and presents…

  9. Astronomy Simulation with Computer Graphics.

    ERIC Educational Resources Information Center

    Thomas, William E.

    1982-01-01

    "Planetary Motion Simulations" is a system of programs designed for students to observe motions of a superior planet (one whose orbit lies outside the orbit of the earth). Programs run on the Apple II microcomputer and employ high-resolution graphics to present the motions of Saturn. (Author/JN)

  10. Computer simulation of engine systems

    NASA Technical Reports Server (NTRS)

    Fishbach, L. H.

    1980-01-01

    The use of computerized simulations of the steady state and transient performance of jet engines throughout the flight regime is discussed. In addition, installation effects on thrust and specific fuel consumption is accounted for as well as engine weight, dimensions and cost. The availability throughout the government and industry of analytical methods for calculating these quantities are pointed out.

  11. Fiber Composite Sandwich Thermostructural Behavior: Computational Simulation

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Aiello, R. A.; Murthy, P. L. N.

    1986-01-01

    Several computational levels of progressive sophistication/simplification are described to computationally simulate composite sandwich hygral, thermal, and structural behavior. The computational levels of sophistication include: (1) three-dimensional detailed finite element modeling of the honeycomb, the adhesive and the composite faces; (2) three-dimensional finite element modeling of the honeycomb assumed to be an equivalent continuous, homogeneous medium, the adhesive and the composite faces; (3) laminate theory simulation where the honeycomb (metal or composite) is assumed to consist of plies with equivalent properties; and (4) derivations of approximate, simplified equations for thermal and mechanical properties by simulating the honeycomb as an equivalent homogeneous medium. The approximate equations are combined with composite hygrothermomechanical and laminate theories to provide a simple and effective computational procedure for simulating the thermomechanical/thermostructural behavior of fiber composite sandwich structures.

  12. Augmented Reality Simulations on Handheld Computers

    ERIC Educational Resources Information Center

    Squire, Kurt; Klopfer, Eric

    2007-01-01

    Advancements in handheld computing, particularly its portability, social interactivity, context sensitivity, connectivity, and individuality, open new opportunities for immersive learning environments. This article articulates the pedagogical potential of augmented reality simulations in environmental engineering education by immersing students in…

  13. Computer Simulation of F=m/a.

    ERIC Educational Resources Information Center

    Hayden, Howard C.

    1984-01-01

    Discusses a computer simulation which: (1) describes an experiment investigating F=m/a; (2) generates data; (3) allows students to see the data; and (4) generates the equation with a least-squares fit. (JN)

  14. Computer simulation and optimization of radioelectronic devices

    NASA Astrophysics Data System (ADS)

    Benenson, Z. M.; Elistratov, M. R.; Ilin, L. K.; Kravchenko, S. V.; Sukhov, D. M.; Udler, M. A.

    Methods of simulating and optimizing radioelectronic devices in an automated design system are discussed. Also treated are algorithms used in the computer-aided design of these devices. The special language of description for these devices is described.

  15. Computer-simulated phacoemulsification improvements

    NASA Astrophysics Data System (ADS)

    Soederberg, Per G.; Laurell, Carl-Gustaf; Artzen, D.; Nordh, Leif; Skarman, Eva; Nordqvist, P.; Andersson, Mats

    2002-06-01

    A simulator for phacoemulsification cataract extraction is developed. A three-dimensional visual interface and foot pedals for phacoemulsification power, x-y positioning, zoom and focus were established. An algorithm that allows real time visual feedback of the surgical field was developed. Cataract surgery is the most common surgical procedure. The operation requires input from both feet and both hands and provides visual feedback through the operation microscope essentially without tactile feedback. Experience demonstrates that the number of complications for an experienced surgeon learning phacoemulsification, decreases exponentially, reaching close to the asymptote after the first 500 procedures despite initial wet lab training on animal eyes. Simulator training is anticipated to decrease training time, decrease complication rate for the beginner and reduce expensive supervision by a high volume surgeon.

  16. An All-Atom Model of the Structure of Human Copper Transporter 1

    PubMed Central

    Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.

    2013-01-01

    Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin. PMID:22569840

  17. Teaching Environmental Systems Modelling Using Computer Simulation.

    ERIC Educational Resources Information Center

    Moffatt, Ian

    1986-01-01

    A computer modeling course in environmental systems and dynamics is presented. The course teaches senior undergraduates to analyze a system of interest, construct a system flow chart, and write computer programs to simulate real world environmental processes. An example is presented along with a course evaluation, figures, tables, and references.…

  18. Psychology on Computers: Simulations, Experiments and Projects.

    ERIC Educational Resources Information Center

    Belcher, Duane M.; Smith, Stephen D.

    PSYCOM is a unique mixed media package which combines high interest projects on the computer with a written text of expository material. It goes beyond most computer-assisted instruction which emphasizes drill and practice and testing of knowledge. A project might consist of a simulation or an actual experiment, or it might be a demonstration, a…

  19. Computer Simulation Of A Small Turboshaft Engine

    NASA Technical Reports Server (NTRS)

    Ballin, Mark G.

    1991-01-01

    Component-type mathematical model of small turboshaft engine developed for use in real-time computer simulations of dynamics of helicopter flight. Yields shaft speeds, torques, fuel-consumption rates, and other operating parameters with sufficient accuracy for use in real-time simulation of maneuvers involving large transients in power and/or severe accelerations.

  20. Simulations of Probabilities for Quantum Computing

    NASA Technical Reports Server (NTRS)

    Zak, M.

    1996-01-01

    It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-LIpschitz dynamics, without utilization of any man-made devices (such as random number generators). Self-organizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed.

  1. Criterion Standards for Evaluating Computer Simulation Courseware.

    ERIC Educational Resources Information Center

    Wholeben, Brent Edward

    This paper explores the role of computerized simulations as a decision-modeling intervention strategy, and views the strategy's different attribute biases based upon the varying primary missions of instruction versus application. The common goals associated with computer simulations as a training technique are discussed and compared with goals of…

  2. Salesperson Ethics: An Interactive Computer Simulation

    ERIC Educational Resources Information Center

    Castleberry, Stephen

    2014-01-01

    A new interactive computer simulation designed to teach sales ethics is described. Simulation learner objectives include gaining a better understanding of legal issues in selling; realizing that ethical dilemmas do arise in selling; realizing the need to be honest when selling; seeing that there are conflicting demands from a salesperson's…

  3. Computer simulation of gear tooth manufacturing processes

    NASA Technical Reports Server (NTRS)

    Mavriplis, Dimitri; Huston, Ronald L.

    1990-01-01

    The use of computer graphics to simulate gear tooth manufacturing procedures is discussed. An analytical basis for the simulation is established for spur gears. The simulation itself, however, is developed not only for spur gears, but for straight bevel gears as well. The applications of the developed procedure extend from the development of finite element models of heretofore intractable geometrical forms, to exploring the fabrication of nonstandard tooth forms.

  4. Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD

    NASA Astrophysics Data System (ADS)

    Giorgino, Toni

    2014-01-01

    Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to analyze simulated trajectories, either interactively or via scripts, to derive quantities of interest and provide insight for further experiments. This paper presents the Density Profile Tool, a package that enhances the Visual Molecular Dynamics environment with the ability to interactively compute and visualize 1-D projections of various density functions of molecular models. We describe how the plugin is used to perform computations both via a graphical interface and programmatically. Results are presented for realistic examples, all-atom bilayer models, showing how mass and electron densities readily provide measurements such as membrane thickness, location of structural elements, and how they compare to X-ray diffraction experiments.

  5. Optimum spaceborne computer system design by simulation

    NASA Technical Reports Server (NTRS)

    Williams, T.; Weatherbee, J. E.; Taylor, D. S.

    1972-01-01

    A deterministic digital simulation model is described which models the Automatically Reconfigurable Modular Multiprocessor System (ARMMS), a candidate computer system for future manned and unmanned space missions. Use of the model as a tool in configuring a minimum computer system for a typical mission is demonstrated. The configuration which is developed as a result of studies with the simulator is optimal with respect to the efficient use of computer system resources, i.e., the configuration derived is a minimal one. Other considerations such as increased reliability through the use of standby spares would be taken into account in the definition of a practical system for a given mission.

  6. Computer simulation of bubble formation.

    SciTech Connect

    Insepov, Z.; Bazhirov, T.; Norman, G.; Stegailov, V.; Mathematics and Computer Science; Institute for High Energy Densities of Joint Institute for High Temperatures of RAS

    2007-01-01

    Properties of liquid metals (Li, Pb, Na) containing nanoscale cavities were studied by atomistic Molecular Dynamics (MD). Two atomistic models of cavity simulation were developed that cover a wide area in the phase diagram with negative pressure. In the first model, the thermodynamics of cavity formation, stability and the dynamics of cavity evolution in bulk liquid metals have been studied. Radial densities, pressures, surface tensions, and work functions of nano-scale cavities of various radii were calculated for liquid Li, Na, and Pb at various temperatures and densities, and at small negative pressures near the liquid-gas spinodal, and the work functions for cavity formation in liquid Li were calculated and compared with the available experimental data. The cavitation rate can further be obtained by using the classical nucleation theory (CNT). The second model is based on the stability study and on the kinetics of cavitation of the stretched liquid metals. A MD method was used to simulate cavitation in a metastable Pb and Li melts and determine the stability limits. States at temperatures below critical (T < 0.5Tc) and large negative pressures were considered. The kinetic boundary of liquid phase stability was shown to be different from the spinodal. The kinetics and dynamics of cavitation were studied. The pressure dependences of cavitation frequencies were obtained for several temperatures. The results of MD calculations were compared with estimates based on classical nucleation theory.

  7. Computer Code for Nanostructure Simulation

    NASA Technical Reports Server (NTRS)

    Filikhin, Igor; Vlahovic, Branislav

    2009-01-01

    Due to their small size, nanostructures can have stress and thermal gradients that are larger than any macroscopic analogue. These gradients can lead to specific regions that are susceptible to failure via processes such as plastic deformation by dislocation emission, chemical debonding, and interfacial alloying. A program has been developed that rigorously simulates and predicts optoelectronic properties of nanostructures of virtually any geometrical complexity and material composition. It can be used in simulations of energy level structure, wave functions, density of states of spatially configured phonon-coupled electrons, excitons in quantum dots, quantum rings, quantum ring complexes, and more. The code can be used to calculate stress distributions and thermal transport properties for a variety of nanostructures and interfaces, transport and scattering at nanoscale interfaces and surfaces under various stress states, and alloy compositional gradients. The code allows users to perform modeling of charge transport processes through quantum-dot (QD) arrays as functions of inter-dot distance, array order versus disorder, QD orientation, shape, size, and chemical composition for applications in photovoltaics and physical properties of QD-based biochemical sensors. The code can be used to study the hot exciton formation/relation dynamics in arrays of QDs of different shapes and sizes at different temperatures. It also can be used to understand the relation among the deposition parameters and inherent stresses, strain deformation, heat flow, and failure of nanostructures.

  8. Pseudospark discharges via computer simulation

    SciTech Connect

    Boeuf, J.P.; Pitchford, L.C. )

    1991-04-01

    The authors of this paper developed a hybrid fluid-particle (Monte Carlo) model to describe the initiation phase of pseudospark discharges. In this model, time-dependent fluid equations for the electrons and positive ions are solved self-consistently with Poisson's equation for the electric field in a two-dimensional, cylindrically symmetrical geometry. The Monte Carlo simulation is used to determine the ionization source term in the fluid equations. This model has been used to study the evolution of a discharge in helium at 0.5 torr, with an applied voltage of 2 kV and in a typical pseudospark geometry. From the numerical results, the authors have identified a sequence of physical events that lead to the rapid rise in current associated with the onset of the pseudospark discharge mode. For the conditions the authors have simulated, they find that there is a maximum in the electron multiplication at the time which corresponds to the onset of the hollow cathode effect, and although the multiplication later decreases, it is always greater than needed for a steady-state discharge. Thus the sheaths inside the hollow cathode tend to collapse against the walls, and eventually cathode emission mechanisms (such as field-enhanced thermionic emission) which the authors have not included will start to play a role. In spite of the approximation in this model, the picture which has emerged provides insight into the mechanisms controlling the onset of this potentially important discharge mode.

  9. Rotorcraft Damage Tolerance Evaluated by Computational Simulation

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Minnetyan, Levon; Abdi, Frank

    2000-01-01

    An integrally stiffened graphite/epoxy composite rotorcraft structure is evaluated via computational simulation. A computer code that scales up constituent micromechanics level material properties to the structure level and accounts for all possible failure modes is used for the simulation of composite degradation under loading. Damage initiation, growth, accumulation, and propagation to fracture are included in the simulation. Design implications with regard to defect and damage tolerance of integrally stiffened composite structures are examined. A procedure is outlined regarding the use of this type of information for setting quality acceptance criteria, design allowables, damage tolerance, and retirement-for-cause criteria.

  10. Cluster computing software for GATE simulations

    SciTech Connect

    Beenhouwer, Jan de; Staelens, Steven; Kruecker, Dirk; Ferrer, Ludovic; D'Asseler, Yves; Lemahieu, Ignace; Rannou, Fernando R.

    2007-06-15

    Geometry and tracking (GEANT4) is a Monte Carlo package designed for high energy physics experiments. It is used as the basis layer for Monte Carlo simulations of nuclear medicine acquisition systems in GEANT4 Application for Tomographic Emission (GATE). GATE allows the user to realistically model experiments using accurate physics models and time synchronization for detector movement through a script language contained in a macro file. The downside of this high accuracy is long computation time. This paper describes a platform independent computing approach for running GATE simulations on a cluster of computers in order to reduce the overall simulation time. Our software automatically creates fully resolved, nonparametrized macros accompanied with an on-the-fly generated cluster specific submit file used to launch the simulations. The scalability of GATE simulations on a cluster is investigated for two imaging modalities, positron emission tomography (PET) and single photon emission computed tomography (SPECT). Due to a higher sensitivity, PET simulations are characterized by relatively high data output rates that create rather large output files. SPECT simulations, on the other hand, have lower data output rates but require a long collimator setup time. Both of these characteristics hamper scalability as a function of the number of CPUs. The scalability of PET simulations is improved here by the development of a fast output merger. The scalability of SPECT simulations is improved by greatly reducing the collimator setup time. Accordingly, these two new developments result in higher scalability for both PET and SPECT simulations and reduce the computation time to more practical values.

  11. Cluster computing software for GATE simulations.

    PubMed

    De Beenhouwer, Jan; Staelens, Steven; Kruecker, Dirk; Ferrer, Ludovic; D'Asseler, Yves; Lemahieu, Ignace; Rannou, Fernando R

    2007-06-01

    Geometry and tracking (GEANT4) is a Monte Carlo package designed for high energy physics experiments. It is used as the basis layer for Monte Carlo simulations of nuclear medicine acquisition systems in GEANT4 Application for Tomographic Emission (GATE). GATE allows the user to realistically model experiments using accurate physics models and time synchronization for detector movement through a script language contained in a macro file. The downside of this high accuracy is long computation time. This paper describes a platform independent computing approach for running GATE simulations on a cluster of computers in order to reduce the overall simulation time. Our software automatically creates fully resolved, nonparametrized macros accompanied with an on-the-fly generated cluster specific submit file used to launch the simulations. The scalability of GATE simulations on a cluster is investigated for two imaging modalities, positron emission tomography (PET) and single photon emission computed tomography (SPECT). Due to a higher sensitivity, PET simulations are characterized by relatively high data output rates that create rather large output files. SPECT simulations, on the other hand, have lower data output rates but require a long collimator setup time. Both of these characteristics hamper scalability as a function of the number of CPUs. The scalability of PET simulations is improved here by the development of a fast output merger. The scalability of SPECT simulations is improved by greatly reducing the collimator setup time. Accordingly, these two new developments result in higher scalability for both PET and SPECT simulations and reduce the computation time to more practical values. PMID:17654895

  12. Polymer Composites Corrosive Degradation: A Computational Simulation

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Minnetyan, Levon

    2007-01-01

    A computational simulation of polymer composites corrosive durability is presented. The corrosive environment is assumed to manage the polymer composite degradation on a ply-by-ply basis. The degradation is correlated with a measured pH factor and is represented by voids, temperature and moisture which vary parabolically for voids and linearly for temperature and moisture through the laminate thickness. The simulation is performed by a computational composite mechanics computer code which includes micro, macro, combined stress failure and laminate theories. This accounts for starting the simulation from constitutive material properties and up to the laminate scale which exposes the laminate to the corrosive environment. Results obtained for one laminate indicate that the ply-by-ply degradation degrades the laminate to the last one or the last several plies. Results also demonstrate that the simulation is applicable to other polymer composite systems as well.

  13. Computer simulations of lung surfactant.

    PubMed

    Baoukina, Svetlana; Tieleman, D Peter

    2016-10-01

    Lung surfactant lines the gas-exchange interface in the lungs and reduces the surface tension, which is necessary for breathing. Lung surfactant consists mainly of lipids with a small amount of proteins and forms a monolayer at the air-water interface connected to bilayer reservoirs. Lung surfactant function involves transfer of material between the monolayer and bilayers during the breathing cycle. Lipids and proteins are organized laterally in the monolayer; selected species are possibly preferentially transferred to bilayers. The complex 3D structure of lung surfactant and the exact roles of lipid organization and proteins remain important goals for research. We review recent simulation studies on the properties of lipid monolayers, monolayers with phase coexistence, monolayer-bilayer transformations, lipid-protein interactions, and effects of nanoparticles on lung surfactant. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26922885

  14. Creating science simulations through Computational Thinking Patterns

    NASA Astrophysics Data System (ADS)

    Basawapatna, Ashok Ram

    Computational thinking aims to outline fundamental skills from computer science that everyone should learn. As currently defined, with help from the National Science Foundation (NSF), these skills include problem formulation, logically organizing data, automating solutions through algorithmic thinking, and representing data through abstraction. One aim of the NSF is to integrate these and other computational thinking concepts into the classroom. End-user programming tools offer a unique opportunity to accomplish this goal. An end-user programming tool that allows students with little or no prior experience the ability to create simulations based on phenomena they see in-class could be a first step towards meeting most, if not all, of the above computational thinking goals. This thesis describes the creation, implementation and initial testing of a programming tool, called the Simulation Creation Toolkit, with which users apply high-level agent interactions called Computational Thinking Patterns (CTPs) to create simulations. Employing Computational Thinking Patterns obviates lower behavior-level programming and allows users to directly create agent interactions in a simulation by making an analogy with real world phenomena they are trying to represent. Data collected from 21 sixth grade students with no prior programming experience and 45 seventh grade students with minimal programming experience indicates that this is an effective first step towards enabling students to create simulations in the classroom environment. Furthermore, an analogical reasoning study that looked at how users might apply patterns to create simulations from high- level descriptions with little guidance shows promising results. These initial results indicate that the high level strategy employed by the Simulation Creation Toolkit is a promising strategy towards incorporating Computational Thinking concepts in the classroom environment.

  15. Computer simulation of space station computer steered high gain antenna

    NASA Technical Reports Server (NTRS)

    Beach, S. W.

    1973-01-01

    The mathematical modeling and programming of a complete simulation program for a space station computer-steered high gain antenna are described. The program provides for reading input data cards, numerically integrating up to 50 first order differential equations, and monitoring up to 48 variables on printed output and on plots. The program system consists of a high gain antenna, an antenna gimbal control system, an on board computer, and the environment in which all are to operate.

  16. Airport Simulations Using Distributed Computational Resources

    NASA Technical Reports Server (NTRS)

    McDermott, William J.; Maluf, David A.; Gawdiak, Yuri; Tran, Peter; Clancy, Daniel (Technical Monitor)

    2002-01-01

    The Virtual National Airspace Simulation (VNAS) will improve the safety of Air Transportation. In 2001, using simulation and information management software running over a distributed network of super-computers, researchers at NASA Ames, Glenn, and Langley Research Centers developed a working prototype of a virtual airspace. This VNAS prototype modeled daily operations of the Atlanta airport by integrating measured operational data and simulation data on up to 2,000 flights a day. The concepts and architecture developed by NASA for this prototype are integral to the National Airspace Simulation to support the development of strategies improving aviation safety, identifying precursors to component failure.

  17. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

    PubMed Central

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-01-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

  18. Symbolic computation in system simulation and design

    NASA Astrophysics Data System (ADS)

    Evans, Brian L.; Gu, Steve X.; Kalavade, Asa; Lee, Edward A.

    1995-06-01

    This paper examines some of the roles that symbolic computation plays in assisting system- level simulation and design. By symbolic computation, we mean programs like Mathematica that perform symbolic algebra and apply transformation rules based on algebraic identities. At a behavioral level, symbolic computation can compute parameters, generate new models, and optimize parameter settings. At the synthesis level, symbolic computation can work in tandem with synthesis tools to rewrite cascade and parallel combinations on components in sub- systems to meet design constraints. Symbolic computation represents one type of tool that may be invoked in the complex flow of the system design process. The paper discusses the qualities that a formal infrastructure for managing system design should have. The paper also describes an implementation of this infrastructure called DesignMaker, implemented in the Ptolemy environment, which manages the flow of tool invocations in an efficient manner using a graphical file dependency mechanism.

  19. Computer Series, 108. Computer Simulation of Chemical Equilibrium.

    ERIC Educational Resources Information Center

    Cullen, John F., Jr.

    1989-01-01

    Presented is a computer simulation called "The Great Chemical Bead Game" which can be used to teach the concepts of equilibrium and kinetics to introductory chemistry students more clearly than through an experiment. Discussed are the rules of the game, the application of rate laws and graphical analysis. (CW)

  20. Enabling Computational Technologies for Terascale Scientific Simulations

    SciTech Connect

    Ashby, S.F.

    2000-08-24

    We develop scalable algorithms and object-oriented code frameworks for terascale scientific simulations on massively parallel processors (MPPs). Our research in multigrid-based linear solvers and adaptive mesh refinement enables Laboratory programs to use MPPs to explore important physical phenomena. For example, our research aids stockpile stewardship by making practical detailed 3D simulations of radiation transport. The need to solve large linear systems arises in many applications, including radiation transport, structural dynamics, combustion, and flow in porous media. These systems result from discretizations of partial differential equations on computational meshes. Our first research objective is to develop multigrid preconditioned iterative methods for such problems and to demonstrate their scalability on MPPs. Scalability describes how total computational work grows with problem size; it measures how effectively additional resources can help solve increasingly larger problems. Many factors contribute to scalability: computer architecture, parallel implementation, and choice of algorithm. Scalable algorithms have been shown to decrease simulation times by several orders of magnitude.

  1. Computer simulation of breathing systems for divers

    SciTech Connect

    Sexton, P.G.; Nuckols, M.L.

    1983-02-01

    A powerful new tool for the analysis and design of underwater breathing gas systems is being developed. A versatile computer simulator is described which makes possible the modular ''construction'' of any conceivable breathing gas system from computer memory-resident components. The analysis of a typical breathing gas system is demonstrated using this simulation technique, and the effects of system modifications on performance of the breathing system are shown. This modeling technique will ultimately serve as the foundation for a proposed breathing system simulator under development by the Navy. The marriage of this computer modeling technique with an interactive graphics system will provide the designer with an efficient, cost-effective tool for the development of new and improved diving systems.

  2. Software Engineering for Scientific Computer Simulations

    NASA Astrophysics Data System (ADS)

    Post, Douglass E.; Henderson, Dale B.; Kendall, Richard P.; Whitney, Earl M.

    2004-11-01

    Computer simulation is becoming a very powerful tool for analyzing and predicting the performance of fusion experiments. Simulation efforts are evolving from including only a few effects to many effects, from small teams with a few people to large teams, and from workstations and small processor count parallel computers to massively parallel platforms. Successfully making this transition requires attention to software engineering issues. We report on the conclusions drawn from a number of case studies of large scale scientific computing projects within DOE, academia and the DoD. The major lessons learned include attention to sound project management including setting reasonable and achievable requirements, building a good code team, enforcing customer focus, carrying out verification and validation and selecting the optimum computational mathematics approaches.

  3. Structural Composites Corrosive Management by Computational Simulation

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Minnetyan, Levon

    2006-01-01

    A simulation of corrosive management on polymer composites durability is presented. The corrosive environment is assumed to manage the polymer composite degradation on a ply-by-ply basis. The degradation is correlated with a measured Ph factor and is represented by voids, temperature, and moisture which vary parabolically for voids and linearly for temperature and moisture through the laminate thickness. The simulation is performed by a computational composite mechanics computer code which includes micro, macro, combined stress failure, and laminate theories. This accounts for starting the simulation from constitutive material properties and up to the laminate scale which exposes the laminate to the corrosive environment. Results obtained for one laminate indicate that the ply-by-ply managed degradation degrades the laminate to the last one or the last several plies. Results also demonstrate that the simulation is applicable to other polymer composite systems as well.

  4. Learning features in computer simulation skills training.

    PubMed

    Johannesson, Eva; Olsson, Mats; Petersson, Göran; Silén, Charlotte

    2010-09-01

    New simulation tools imply new opportunities to teach skills and train health care professionals. The aim of this study was to investigate the learning gained from computer simulation skills training. The study was designed for optimal educational settings, which benefit student-centred learning. Twenty-four second year undergraduate nursing students practised intravenous catheterization with the computer simulation program CathSim. Questionnaires were answered before and after the skills training, and after the skills examination. When using CathSim, the students appreciated the variation in patient cases, the immediate feedback, and a better understanding of anatomy, but they missed having an arm model to hold. We concluded that CathSim was useful in the students' learning process and skills training when appropriately integrated into the curriculum. Learning features to be aware of when organizing curricula with simulators are motivation, realism, variation, meaningfulness and feedback. PMID:20015690

  5. Task simulation in computer-based training

    SciTech Connect

    Gardner, P.R.

    1988-02-01

    Westinghouse Hanford Company (WHC) makes extensive use of job-task simulations in company-developed computer-based training (CBT) courseware. This courseware is different from most others because it does not simulate process control machinery or other computer programs, instead the WHC Excerises model day-to-day tasks such as physical work preparations, progress, and incident handling. These Exercises provide a higher level of motivation and enable the testing of more complex patterns of behavior than those typically measured by multiple-choice and short questions. Examples from the WHC Radiation Safety and Crane Safety courses will be used as illustrations. 3 refs.

  6. Student Choices when Learning with Computer Simulations

    NASA Astrophysics Data System (ADS)

    Podolefsky, Noah S.; Adams, Wendy K.; Wieman, Carl E.

    2009-11-01

    We examine student choices while using PhET computer simulations (sims) to learn physics content. In interviews, students were given questions from the Force Concept Inventory (FCI) and were allowed to choose from 12 computer simulations in order to answer these questions. We investigate students' choices when answering FCI questions with sims. We find that while students' initially choose sims that match problem situations at a surface level, deeper connections may be noticed by students later on. These results inform us on how people may choose education resources when learning on their own.

  7. Computer simulation: A modern day crystal ball?

    NASA Technical Reports Server (NTRS)

    Sham, Michael; Siprelle, Andrew

    1994-01-01

    It has long been the desire of managers to be able to look into the future and predict the outcome of decisions. With the advent of computer simulation and the tremendous capability provided by personal computers, that desire can now be realized. This paper presents an overview of computer simulation and modeling, and discusses the capabilities of Extend. Extend is an iconic-driven Macintosh-based software tool that brings the power of simulation to the average computer user. An example of an Extend based model is presented in the form of the Space Transportation System (STS) Processing Model. The STS Processing Model produces eight shuttle launches per year, yet it takes only about ten minutes to run. In addition, statistical data such as facility utilization, wait times, and processing bottlenecks are produced. The addition or deletion of resources, such as orbiters or facilities, can be easily modeled and their impact analyzed. Through the use of computer simulation, it is possible to look into the future to see the impact of today's decisions.

  8. Virtual ambulatory care. Computer simulation applications.

    PubMed

    Zilm, Frank; Culp, Kristyna; Dorney, Beverley

    2003-01-01

    Computer simulation modeling has evolved during the past twenty years into an effective tool for analyzing and planning ambulatory care facilities. This article explains the use of this tool in three case-study, ambulatory care settings--a GI lab, holding beds for a cardiac catheterization laboratory, and in emergency services. These examples also illustrate the use of three software packages currently available: MedModel, Simul8, and WITNESS. PMID:12545512

  9. Perspective: Computer simulations of long time dynamics.

    PubMed

    Elber, Ron

    2016-02-14

    Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473

  10. Perspective: Computer simulations of long time dynamics

    PubMed Central

    Elber, Ron

    2016-01-01

    Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473

  11. Uncertainty and error in computational simulations

    SciTech Connect

    Oberkampf, W.L.; Diegert, K.V.; Alvin, K.F.; Rutherford, B.M.

    1997-10-01

    The present paper addresses the question: ``What are the general classes of uncertainty and error sources in complex, computational simulations?`` This is the first step of a two step process to develop a general methodology for quantitatively estimating the global modeling and simulation uncertainty in computational modeling and simulation. The second step is to develop a general mathematical procedure for representing, combining and propagating all of the individual sources through the simulation. The authors develop a comprehensive view of the general phases of modeling and simulation. The phases proposed are: conceptual modeling of the physical system, mathematical modeling of the system, discretization of the mathematical model, computer programming of the discrete model, numerical solution of the model, and interpretation of the results. This new view is built upon combining phases recognized in the disciplines of operations research and numerical solution methods for partial differential equations. The characteristics and activities of each of these phases is discussed in general, but examples are given for the fields of computational fluid dynamics and heat transfer. They argue that a clear distinction should be made between uncertainty and error that can arise in each of these phases. The present definitions for uncertainty and error are inadequate and. therefore, they propose comprehensive definitions for these terms. Specific classes of uncertainty and error sources are then defined that can occur in each phase of modeling and simulation. The numerical sources of error considered apply regardless of whether the discretization procedure is based on finite elements, finite volumes, or finite differences. To better explain the broad types of sources of uncertainty and error, and the utility of their categorization, they discuss a coupled-physics example simulation.

  12. Simulating physical phenomena with a quantum computer

    NASA Astrophysics Data System (ADS)

    Ortiz, Gerardo

    2003-03-01

    In a keynote speech at MIT in 1981 Richard Feynman raised some provocative questions in connection to the exact simulation of physical systems using a special device named a ``quantum computer'' (QC). At the time it was known that deterministic simulations of quantum phenomena in classical computers required a number of resources that scaled exponentially with the number of degrees of freedom, and also that the probabilistic simulation of certain quantum problems were limited by the so-called sign or phase problem, a problem believed to be of exponential complexity. Such a QC was intended to mimick physical processes exactly the same as Nature. Certainly, remarks coming from such an influential figure generated widespread interest in these ideas, and today after 21 years there are still some open questions. What kind of physical phenomena can be simulated with a QC?, How?, and What are its limitations? Addressing and attempting to answer these questions is what this talk is about. Definitively, the goal of physics simulation using controllable quantum systems (``physics imitation'') is to exploit quantum laws to advantage, and thus accomplish efficient imitation. Fundamental is the connection between a quantum computational model and a physical system by transformations of operator algebras. This concept is a necessary one because in Quantum Mechanics each physical system is naturally associated with a language of operators and thus can be considered as a possible model of quantum computation. The remarkable result is that an arbitrary physical system is naturally simulatable by another physical system (or QC) whenever a ``dictionary'' between the two operator algebras exists. I will explain these concepts and address some of Feynman's concerns regarding the simulation of fermionic systems. Finally, I will illustrate the main ideas by imitating simple physical phenomena borrowed from condensed matter physics using quantum algorithms, and present experimental

  13. Quantitative computer simulations of extraterrestrial processing operations

    NASA Technical Reports Server (NTRS)

    Vincent, T. L.; Nikravesh, P. E.

    1989-01-01

    The automation of a small, solid propellant mixer was studied. Temperature control is under investigation. A numerical simulation of the system is under development and will be tested using different control options. Control system hardware is currently being put into place. The construction of mathematical models and simulation techniques for understanding various engineering processes is also studied. Computer graphics packages were utilized for better visualization of the simulation results. The mechanical mixing of propellants is examined. Simulation of the mixing process is being done to study how one can control for chaotic behavior to meet specified mixing requirements. An experimental mixing chamber is also being built. It will allow visual tracking of particles under mixing. The experimental unit will be used to test ideas from chaos theory, as well as to verify simulation results. This project has applications to extraterrestrial propellant quality and reliability.

  14. Computer simulation of screw dislocation in aluminum

    NASA Technical Reports Server (NTRS)

    Esterling, D. M.

    1976-01-01

    The atomic structure in a 110 screw dislocation core for aluminum is obtained by computer simulation. The lattice statics technique is employed since it entails no artificially imposed elastic boundary around the defect. The interatomic potential has no adjustable parameters and was derived from pseudopotential theory. The resulting atomic displacements were allowed to relax in all three dimensions.

  15. Eliminating Computational Instability In Multibody Simulations

    NASA Technical Reports Server (NTRS)

    Watts, Gaines L.

    1994-01-01

    TWOBODY implements improved version of Lagrange multiplier method. Program ultilizes programming technique eliminating computational instability in multibody simulations in which Lagrange multipliers used. In technique, one uses constraint equations, instead of integration, to determine coordinates that are not independent. To illustrate technique, it includes simple mathematical model of solid rocket booster and parachute connected by frictionless swivel. Written in FORTRAN 77.

  16. Macromod: Computer Simulation For Introductory Economics

    ERIC Educational Resources Information Center

    Ross, Thomas

    1977-01-01

    The Macroeconomic model (Macromod) is a computer assisted instruction simulation model designed for introductory economics courses. An evaluation of its utilization at a community college indicates that it yielded a 10 percent to 13 percent greater economic comprehension than lecture classes and that it met with high student approval. (DC)

  17. Designing Online Scaffolds for Interactive Computer Simulation

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  18. Assessing Moderator Variables: Two Computer Simulation Studies.

    ERIC Educational Resources Information Center

    Mason, Craig A.; And Others

    1996-01-01

    A strategy is proposed for conceptualizing moderating relationships based on their type (strictly correlational and classically correlational) and form, whether continuous, noncontinuous, logistic, or quantum. Results of computer simulations comparing three statistical approaches for assessing moderator variables are presented, and advantages of…

  19. Decision Making in Computer-Simulated Experiments.

    ERIC Educational Resources Information Center

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

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

  20. Progress in Computational Simulation of Earthquakes

    NASA Technical Reports Server (NTRS)

    Donnellan, Andrea; Parker, Jay; Lyzenga, Gregory; Judd, Michele; Li, P. Peggy; Norton, Charles; Tisdale, Edwin; Granat, Robert

    2006-01-01

    GeoFEST(P) is a computer program written for use in the QuakeSim project, which is devoted to development and improvement of means of computational simulation of earthquakes. GeoFEST(P) models interacting earthquake fault systems from the fault-nucleation to the tectonic scale. The development of GeoFEST( P) has involved coupling of two programs: GeoFEST and the Pyramid Adaptive Mesh Refinement Library. GeoFEST is a message-passing-interface-parallel code that utilizes a finite-element technique to simulate evolution of stress, fault slip, and plastic/elastic deformation in realistic materials like those of faulted regions of the crust of the Earth. The products of such simulations are synthetic observable time-dependent surface deformations on time scales from days to decades. Pyramid Adaptive Mesh Refinement Library is a software library that facilitates the generation of computational meshes for solving physical problems. In an application of GeoFEST(P), a computational grid can be dynamically adapted as stress grows on a fault. Simulations on workstations using a few tens of thousands of stress and displacement finite elements can now be expanded to multiple millions of elements with greater than 98-percent scaled efficiency on over many hundreds of parallel processors (see figure).

  1. Computation applied to particle accelerator simulations

    SciTech Connect

    Herrmannsfeldt, W.B. ); Yan, Y.T. )

    1991-07-01

    The rapid growth in the power of large-scale computers has had a revolutionary effect on the study of charged-particle accelerators that is similar to the impact of smaller computers on everyday life. Before an accelerator is built, it is now the absolute rule to simulate every component and subsystem by computer to establish modes of operation and tolerances. We will bypass the important and fruitful areas of control and operation and consider only application to design and diagnostic interpretation. Applications of computers can be divided into separate categories including: component design, system design, stability studies, cost optimization, and operating condition simulation. For the purposes of this report, we will choose a few examples taken from the above categories to illustrate the methods and we will discuss the significance of the work to the project, and also briefly discuss the accelerator project itself. The examples that will be discussed are: (1) the tracking analysis done for the main ring of the Superconducting Supercollider, which contributed to the analysis which ultimately resulted in changing the dipole coil diameter to 5 cm from the earlier design for a 4-cm coil-diameter dipole magnet; (2) the design of accelerator structures for electron-positron linear colliders and circular colliding beam systems (B-factories); (3) simulation of the wake fields from multibunch electron beams for linear colliders; and (4) particle-in-cell simulation of space-charge dominated beams for an experimental liner induction accelerator for Heavy Ion Fusion. 8 refs., 9 figs.

  2. Factors Promoting Engaged Exploration with Computer Simulations

    ERIC Educational Resources Information Center

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

    2010-01-01

    This paper extends prior research on student use of computer simulations (sims) to engage with and explore science topics, in this case wave interference. We describe engaged exploration; a process that involves students actively interacting with educational materials, sense making, and exploring primarily via their own questioning. We analyze…

  3. Spiking network simulation code for petascale computers.

    PubMed

    Kunkel, Susanne; Schmidt, Maximilian; Eppler, Jochen M; Plesser, Hans E; Masumoto, Gen; Igarashi, Jun; Ishii, Shin; Fukai, Tomoki; Morrison, Abigail; Diesmann, Markus; Helias, Moritz

    2014-01-01

    Brain-scale networks exhibit a breathtaking heterogeneity in the dynamical properties and parameters of their constituents. At cellular resolution, the entities of theory are neurons and synapses and over the past decade researchers have learned to manage the heterogeneity of neurons and synapses with efficient data structures. Already early parallel simulation codes stored synapses in a distributed fashion such that a synapse solely consumes memory on the compute node harboring the target neuron. As petaflop computers with some 100,000 nodes become increasingly available for neuroscience, new challenges arise for neuronal network simulation software: Each neuron contacts on the order of 10,000 other neurons and thus has targets only on a fraction of all compute nodes; furthermore, for any given source neuron, at most a single synapse is typically created on any compute node. From the viewpoint of an individual compute node, the heterogeneity in the synaptic target lists thus collapses along two dimensions: the dimension of the types of synapses and the dimension of the number of synapses of a given type. Here we present a data structure taking advantage of this double collapse using metaprogramming techniques. After introducing the relevant scaling scenario for brain-scale simulations, we quantitatively discuss the performance on two supercomputers. We show that the novel architecture scales to the largest petascale supercomputers available today. PMID:25346682

  4. Spiking network simulation code for petascale computers

    PubMed Central

    Kunkel, Susanne; Schmidt, Maximilian; Eppler, Jochen M.; Plesser, Hans E.; Masumoto, Gen; Igarashi, Jun; Ishii, Shin; Fukai, Tomoki; Morrison, Abigail; Diesmann, Markus; Helias, Moritz

    2014-01-01

    Brain-scale networks exhibit a breathtaking heterogeneity in the dynamical properties and parameters of their constituents. At cellular resolution, the entities of theory are neurons and synapses and over the past decade researchers have learned to manage the heterogeneity of neurons and synapses with efficient data structures. Already early parallel simulation codes stored synapses in a distributed fashion such that a synapse solely consumes memory on the compute node harboring the target neuron. As petaflop computers with some 100,000 nodes become increasingly available for neuroscience, new challenges arise for neuronal network simulation software: Each neuron contacts on the order of 10,000 other neurons and thus has targets only on a fraction of all compute nodes; furthermore, for any given source neuron, at most a single synapse is typically created on any compute node. From the viewpoint of an individual compute node, the heterogeneity in the synaptic target lists thus collapses along two dimensions: the dimension of the types of synapses and the dimension of the number of synapses of a given type. Here we present a data structure taking advantage of this double collapse using metaprogramming techniques. After introducing the relevant scaling scenario for brain-scale simulations, we quantitatively discuss the performance on two supercomputers. We show that the novel architecture scales to the largest petascale supercomputers available today. PMID:25346682

  5. Computer simulations of WIGWAM underwater experiment

    SciTech Connect

    Kamegai, Minao; White, J.W.

    1993-11-01

    We performed computer simulations of the WIGWAM underwater experiment with a 2-D hydro-code, CALE. First, we calculated the bubble pulse and the signal strength at the closest gauge in one-dimensional geometry. The calculation shows excellent agreement with the measured data. Next, we made two-dimensional simulations of WIGWAM applying the gravity over-pressure, and calculated the signals at three selected gauge locations where measurements were recorded. The computed peak pressures at those gauge locations come well within the 15% experimental error bars. The signal at the farthest gauge is of the order of 200 bars. This is significant, because at this pressure the CALE output can be linked to a hydro-acoustics computer program, NPE Code (Nonlinear Progressive Wave-equation Code), to analyze the long distance propagation of acoustical signals from the underwater explosions on a global scale.

  6. Computer simulation of underwater nuclear effects

    SciTech Connect

    Kamegai, M.

    1987-01-30

    We investigated underwater nuclear effects by computer simulations. First, we computed a long distance wave propagation in water by the 1-D LASNEX code by modeling the energy source and the underwater environment. The pressure-distance data were calculated for two quite different yields; pressures range from 300 GPa to 15 MPa. They were found to be in good agreement with Snay's theoretical points and the Wigwam measurements. The computed data also agree with the similarity solution at high pressures and the empirical equation at low pressures. After completion of the 1-D study, we investigated a free surface effect commonly referred to as irregular surface rarefaction by applying two hydrocodes (LASNEX and ALE), linked at the appropriate time. Using these codes, we simulated near-surface explosions for three depths of burst (3 m, 21 m and 66.5 m), which represent the strong, intermediate, and weak surface shocks, respectively.

  7. Computational algorithms for simulations in atmospheric optics.

    PubMed

    Konyaev, P A; Lukin, V P

    2016-04-20

    A computer simulation technique for atmospheric and adaptive optics based on parallel programing is discussed. A parallel propagation algorithm is designed and a modified spectral-phase method for computer generation of 2D time-variant random fields is developed. Temporal power spectra of Laguerre-Gaussian beam fluctuations are considered as an example to illustrate the applications discussed. Implementation of the proposed algorithms using Intel MKL and IPP libraries and NVIDIA CUDA technology is shown to be very fast and accurate. The hardware system for the computer simulation is an off-the-shelf desktop with an Intel Core i7-4790K CPU operating at a turbo-speed frequency up to 5 GHz and an NVIDIA GeForce GTX-960 graphics accelerator with 1024 1.5 GHz processors. PMID:27140113

  8. Computer simulation of surface and film processes

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

    Adequate computer methods, based on interactions between discrete particles, provide information leading to an atomic level understanding of various physical processes. The success of these simulation methods, however, is related to the accuracy of the potential energy function representing the interactions among the particles. The development of a potential energy function for crystalline SiO2 forms that can be employed in lengthy computer modelling procedures was investigated. In many of the simulation methods which deal with discrete particles, semiempirical two body potentials were employed to analyze energy and structure related properties of the system. Many body interactions are required for a proper representation of the total energy for many systems. Many body interactions for simulations based on discrete particles are discussed.

  9. Computational Simulation of Composite Structural Fatigue

    NASA Technical Reports Server (NTRS)

    Minnetyan, Levon

    2004-01-01

    Progressive damage and fracture of composite structures subjected to monotonically increasing static, tension-tension cyclic, pressurization, and flexural cyclic loading are evaluated via computational simulation. Constituent material properties, stress and strain limits are scaled up to the structure level to evaluate the overall damage and fracture propagation for composites. Damage initiation, growth, accumulation, and propagation to fracture due to monotonically increasing static and cyclic loads are included in the simulations. Results show the number of cycles to failure at different temperatures and the damage progression sequence during different degradation stages. A procedure is outlined for use of computational simulation data in the assessment of damage tolerance, determination of sensitive parameters affecting fracture, and interpretation of results with insight for design decisions.

  10. Computational Simulation of Composite Structural Fatigue

    NASA Technical Reports Server (NTRS)

    Minnetyan, Levon; Chamis, Christos C. (Technical Monitor)

    2005-01-01

    Progressive damage and fracture of composite structures subjected to monotonically increasing static, tension-tension cyclic, pressurization, and flexural cyclic loading are evaluated via computational simulation. Constituent material properties, stress and strain limits are scaled up to the structure level to evaluate the overall damage and fracture propagation for composites. Damage initiation, growth, accumulation, and propagation to fracture due to monotonically increasing static and cyclic loads are included in the simulations. Results show the number of cycles to failure at different temperatures and the damage progression sequence during different degradation stages. A procedure is outlined for use of computational simulation data in the assessment of damage tolerance, determination of sensitive parameters affecting fracture, and interpretation of results with insight for design decisions.

  11. Computer simulation of underwater nuclear events

    SciTech Connect

    Kamegai, M.

    1986-09-01

    This report describes the computer simulation of two underwater nuclear explosions, Operation Wigwam and a modern hypothetical explosion of greater yield. The computer simulations were done in spherical geometry with the LASNEX computer code. Comparison of the LASNEX calculation with Snay's analytical results and the Wigwam measurements shows that agreement in the shock pressure versus range in water is better than 5%. The results of the calculations are also consistent with the cube root scaling law for an underwater blast wave. The time constant of the wave front was determined from the wave profiles taken at several points. The LASNEX time-constant calculation and Snay's theoretical results agree to within 20%. A time-constant-versus-range relation empirically fitted by Snay is valid only within a limited range at low pressures, whereas a time-constant formula based on Sedov's similarity solution holds at very high pressures. This leaves the intermediate pressure range with neither an empirical nor a theoretical formula for the time constant. These one-dimensional simulations demonstrate applicability of the computer code to investigations of this nature, and justify the use of this technique for more complex two-dimensional problems, namely, surface effects on underwater nuclear explosions. 16 refs., 8 figs., 2 tabs.

  12. Computational Challenges in Nuclear Weapons Simulation

    SciTech Connect

    McMillain, C F; Adams, T F; McCoy, M G; Christensen, R B; Pudliner, B S; Zika, M R; Brantley, P S; Vetter, J S; May, J M

    2003-08-29

    After a decade of experience, the Stockpile Stewardship Program continues to ensure the safety, security and reliability of the nation's nuclear weapons. The Advanced Simulation and Computing (ASCI) program was established to provide leading edge, high-end simulation capabilities needed to meet the program's assessment and certification requirements. The great challenge of this program lies in developing the tools and resources necessary for the complex, highly coupled, multi-physics calculations required to simulate nuclear weapons. This paper describes the hardware and software environment we have applied to fulfill our nuclear weapons responsibilities. It also presents the characteristics of our algorithms and codes, especially as they relate to supercomputing resource capabilities and requirements. It then addresses impediments to the development and application of nuclear weapon simulation software and hardware and concludes with a summary of observations and recommendations on an approach for working with industry and government agencies to address these impediments.

  13. Application of computer simulators in population genetics.

    PubMed

    Feng, Gao; Haipeng, Li

    2016-08-01

    The genomes of more and more organisms have been sequenced due to the advances in next-generation sequencing technologies. As a powerful tool, computer simulators play a critical role in studying the genome-wide DNA polymorphism pattern. Simulations can be performed both forwards-in-time and backwards-in-time, which complement each other and are suitable for meeting different needs, such as studying the effect of evolutionary dynamics, the estimation of parameters, and the validation of evolutionary hypotheses as well as new methods. In this review, we briefly introduced population genetics related theoretical framework and provided a detailed comparison of 32 simulators published over the last ten years. The future development of new simulators was also discussed. PMID:27531609

  14. Computer Simulations Improve University Instructional Laboratories1

    PubMed Central

    2004-01-01

    Laboratory classes are commonplace and essential in biology departments but can sometimes be cumbersome, unreliable, and a drain on time and resources. As university intakes increase, pressure on budgets and staff time can often lead to reduction in practical class provision. Frequently, the ability to use laboratory equipment, mix solutions, and manipulate test animals are essential learning outcomes, and “wet” laboratory classes are thus appropriate. In others, however, interpretation and manipulation of the data are the primary learning outcomes, and here, computer-based simulations can provide a cheaper, easier, and less time- and labor-intensive alternative. We report the evaluation of two computer-based simulations of practical exercises: the first in chromosome analysis, the second in bioinformatics. Simulations can provide significant time savings to students (by a factor of four in our first case study) without affecting learning, as measured by performance in assessment. Moreover, under certain circumstances, performance can be improved by the use of simulations (by 7% in our second case study). We concluded that the introduction of these simulations can significantly enhance student learning where consideration of the learning outcomes indicates that it might be appropriate. In addition, they can offer significant benefits to teaching staff. PMID:15592599

  15. Computational simulation of Faraday probe measurements

    NASA Astrophysics Data System (ADS)

    Boerner, Jeremiah J.

    Electric propulsion devices, including ion thrusters and Hall thrusters, are becoming increasingly popular for long duration space missions. Ground-based experimental testing of such devices is performed in vacuum chambers, which develop an unavoidable background gas due to pumping limitations and facility leakage. Besides directly altering the operating environment, the background gas may indirectly affect the performance of immersed plasma probe diagnostics. This work focuses on computational modeling research conducted to evaluate the performance of a current-collecting Faraday probe. Initial findings from one dimensional analytical models of plasma sheaths are used as reference cases for subsequent modeling. A two dimensional, axisymmetric, hybrid electron fluid and Particle In Cell computational code is used for extensive simulation of the plasma flow around a representative Faraday probe geometry. The hybrid fluid PIC code is used to simulate a range of inflowing plasma conditions, from a simple ion beam consistent with one dimensional models to a multiple component plasma representative of a low-power Hall thruster plume. These simulations produce profiles of plasma properties and simulated current measurements at the probe surface. Interpretation of the simulation results leads to recommendations for probe design and experimental techniques. Significant contributions of this work include the development and use of two new non-neutral detailed electron fluid models and the recent incorporation of multi grid capabilities.

  16. Computer Simulation for Emergency Incident Management

    SciTech Connect

    Brown, D L

    2004-12-03

    This report describes the findings and recommendations resulting from the Department of Homeland Security (DHS) Incident Management Simulation Workshop held by the DHS Advanced Scientific Computing Program in May 2004. This workshop brought senior representatives of the emergency response and incident-management communities together with modeling and simulation technologists from Department of Energy laboratories. The workshop provided an opportunity for incident responders to describe the nature and substance of the primary personnel roles in an incident response, to identify current and anticipated roles of modeling and simulation in support of incident response, and to begin a dialog between the incident response and simulation technology communities that will guide and inform planned modeling and simulation development for incident response. This report provides a summary of the discussions at the workshop as well as a summary of simulation capabilities that are relevant to incident-management training, and recommendations for the use of simulation in both incident management and in incident management training, based on the discussions at the workshop. In addition, the report discusses areas where further research and development will be required to support future needs in this area.

  17. Memory interface simulator: A computer design aid

    NASA Technical Reports Server (NTRS)

    Taylor, D. S.; Williams, T.; Weatherbee, J. E.

    1972-01-01

    Results are presented of a study conducted with a digital simulation model being used in the design of the Automatically Reconfigurable Modular Multiprocessor System (ARMMS), a candidate computer system for future manned and unmanned space missions. The model simulates the activity involved as instructions are fetched from random access memory for execution in one of the system central processing units. A series of model runs measured instruction execution time under various assumptions pertaining to the CPU's and the interface between the CPU's and RAM. Design tradeoffs are presented in the following areas: Bus widths, CPU microprogram read only memory cycle time, multiple instruction fetch, and instruction mix.

  18. Computer Simulation of the VASIMR Engine

    NASA Technical Reports Server (NTRS)

    Garrison, David

    2005-01-01

    The goal of this project is to develop a magneto-hydrodynamic (MHD) computer code for simulation of the VASIMR engine. This code is designed be easy to modify and use. We achieve this using the Cactus framework, a system originally developed for research in numerical relativity. Since its release, Cactus has become an extremely powerful and flexible open source framework. The development of the code will be done in stages, starting with a basic fluid dynamic simulation and working towards a more complex MHD code. Once developed, this code can be used by students and researchers in order to further test and improve the VASIMR engine.

  19. Computer Simulation For Design Of TWT's

    NASA Technical Reports Server (NTRS)

    Bartos, Karen F.; Fite, E. Brian; Shalkhauser, Kurt A.; Sharp, G. Richard

    1992-01-01

    A three-dimensional finite-element analytical technique facilitates design and fabrication of traveling-wave-tube (TWT) slow-wave structures. Used to perform thermal and mechanical analyses of TWT designed with variety of configurations, geometries, and materials. Using three-dimensional computer analysis, designer able to simulate building and testing of TWT, with consequent substantial saving of time and money. Technique enables detailed look into operation of traveling-wave tubes to help improve performance for future communications systems.

  20. Integrated computer simulation on FIR FEL dynamics

    SciTech Connect

    Furukawa, H.; Kuruma, S.; Imasaki, K.

    1995-12-31

    An integrated computer simulation code has been developed to analyze the RF-Linac FEL dynamics. First, the simulation code on the electron beam acceleration and transport processes in RF-Linac: (LUNA) has been developed to analyze the characteristics of the electron beam in RF-Linac and to optimize the parameters of RF-Linac. Second, a space-time dependent 3D FEL simulation code (Shipout) has been developed. The RF-Linac FEL total simulations have been performed by using the electron beam data from LUNA in Shipout. The number of particles using in a RF-Linac FEL total simulation is approximately 1000. The CPU time for the simulation of 1 round trip is about 1.5 minutes. At ILT/ILE, Osaka, a 8.5MeV RF-Linac with a photo-cathode RF-gun is used for FEL oscillation experiments. By using 2 cm wiggler, the FEL oscillation in the wavelength approximately 46 {mu}m are investigated. By the simulations using LUNA with the parameters of an ILT/ILE experiment, the pulse shape and the energy spectra of the electron beam at the end of the linac are estimated. The pulse shape of the electron beam at the end of the linac has sharp rise-up and it slowly decays as a function of time. By the RF-linac FEL total simulations with the parameters of an ILT/ILE experiment, the dependencies of the start up of the FEL oscillations on the pulse shape of the electron beam at the end of the linac are estimated. The coherent spontaneous emission effects and the quick start up of FEL oscillations have been observed by the RF-Linac FEL total simulations.

  1. Computer simulations in the science classroom

    NASA Astrophysics Data System (ADS)

    Richards, John; Barowy, William; Levin, Dov

    1992-03-01

    In this paper we describe software for science instruction that is based upon a constructivist epistemology of learning. From a constructivist perspective, the process of learning is viewed as an active construction of knowledge, rather than a passive reception of information. The computer has the potential to provide an environment in which students can explore their understanding and better construct scientific knowledge. The Explorer is an interactive environment that integrates animated computer models with analytic capabilities for learning and teaching science. The system include graphs, a spreadsheet, scripting, and interactive tools. During formative evaluation of Explorer in the classroom, we have focused on learning the function and effectiveness of computer models in teaching science. Models have helped students relate theory to experiment when used in conjunction with hands-on activities and when the simulation addressed students' naive understanding of the phenomena. Two classroom examples illustrate our findings. The first is based on the dynamics of colliding objects. The second describes a class modeling the function of simple electric circuits. The simulations bridge between phenomena and theory by providing an abstract representation on which students may make measurements. Simulations based on scientific theory help to provide a set of interrelated experiences that challenge students' informal understanding of the science.

  2. Metal matrix composites microfracture: Computational simulation

    NASA Technical Reports Server (NTRS)

    Mital, Subodh K.; Caruso, John J.; Chamis, Christos C.

    1990-01-01

    Fiber/matrix fracture and fiber-matrix interface debonding in a metal matrix composite (MMC) are computationally simulated. These simulations are part of a research activity to develop computational methods for microfracture, microfracture propagation and fracture toughness of the metal matrix composites. The three-dimensional finite element model used in the simulation consists of a group of nine unidirectional fibers in three by three unit cell array of SiC/Ti15 metal matrix composite with a fiber volume ration of 0.35. This computational procedure is used to predict the fracture process and establish the hierarchy of fracture modes based on strain energy release rate. It is also used to predict stress redistribution to surrounding matrix-fibers due to initial and progressive fracture of fiber/matrix and due to debonding of fiber-matrix interface. Microfracture results for various loading cases such as longitudinal, transverse, shear and bending are presented and discussed. Step-by-step procedures are outlined to evaluate composite microfracture for a given composite system.

  3. Accelerating Climate Simulations Through Hybrid Computing

    NASA Technical Reports Server (NTRS)

    Zhou, Shujia; Sinno, Scott; Cruz, Carlos; Purcell, Mark

    2009-01-01

    Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.

  4. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel.

    PubMed

    Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A

    2016-06-01

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

  5. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

    PubMed Central

    Na, Hyuntae; Jernigan, Robert L.; Song, Guang

    2015-01-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491

  6. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    SciTech Connect

    Kouza, Maksim Kolinski, Andrzej; Co, Nguyen Truong; Nguyen, Phuong H.; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  7. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    NASA Astrophysics Data System (ADS)

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H.; Kolinski, Andrzej; Li, Mai Suan

    2015-04-01

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  8. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.

    PubMed

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  9. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    SciTech Connect

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  10. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    PubMed

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688

  11. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    NASA Astrophysics Data System (ADS)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  12. A computer simulation of chromosomal instability

    NASA Astrophysics Data System (ADS)

    Goodwin, E.; Cornforth, M.

    The transformation of a normal cell into a cancerous growth can be described as a process of mutation and selection occurring within the context of clonal expansion. Radiation, in addition to initial DNA damage, induces a persistent and still poorly understood genomic instability process that contributes to the mutational burden. It will be essential to include a quantitative description of this phenomenon in any attempt at science-based risk assessment. Monte Carlo computer simulations are a relatively simple way to model processes that are characterized by an element of randomness. A properly constructed simulation can capture the essence of a phenomenon that, as is often the case in biology, can be extraordinarily complex, and can do so even though the phenomenon itself is incompletely understood. A simple computer simulation of one manifestation of genomic instability known as chromosomal instability will be presented. The model simulates clonal expansion of a single chromosomally unstable cell into a colony. Instability is characterized by a single parameter, the rate of chromosomal rearrangement. With each new chromosome aberration, a unique subclone arises (subclones are defined as having a unique karyotype). The subclone initially has just one cell, but it can expand with cell division if the aberration is not lethal. The computer program automatically keeps track of the number of subclones within the expanding colony, and the number of cells within each subclone. Because chromosome aberrations kill some cells during colony growth, colonies arising from unstable cells tend to be smaller than those arising from stable cells. For any chosen level of instability, the computer program calculates the mean number of cells per colony averaged over many runs. These output should prove useful for investigating how such radiobiological phenomena as slow growth colonies, increased doubling time, and delayed cell death depend on chromosomal instability. Also of

  13. New Computer Simulations of Macular Neural Functioning

    NASA Technical Reports Server (NTRS)

    Ross, Muriel D.; Doshay, D.; Linton, S.; Parnas, B.; Montgomery, K.; Chimento, T.

    1994-01-01

    We use high performance graphics workstations and supercomputers to study the functional significance of the three-dimensional (3-D) organization of gravity sensors. These sensors have a prototypic architecture foreshadowing more complex systems. Scaled-down simulations run on a Silicon Graphics workstation and scaled-up, 3-D versions run on a Cray Y-MP supercomputer. A semi-automated method of reconstruction of neural tissue from serial sections studied in a transmission electron microscope has been developed to eliminate tedious conventional photography. The reconstructions use a mesh as a step in generating a neural surface for visualization. Two meshes are required to model calyx surfaces. The meshes are connected and the resulting prisms represent the cytoplasm and the bounding membranes. A finite volume analysis method is employed to simulate voltage changes along the calyx in response to synapse activation on the calyx or on calyceal processes. The finite volume method insures that charge is conserved at the calyx-process junction. These and other models indicate that efferent processes act as voltage followers, and that the morphology of some afferent processes affects their functioning. In a final application, morphological information is symbolically represented in three dimensions in a computer. The possible functioning of the connectivities is tested using mathematical interpretations of physiological parameters taken from the literature. Symbolic, 3-D simulations are in progress to probe the functional significance of the connectivities. This research is expected to advance computer-based studies of macular functioning and of synaptic plasticity.

  14. Computational Methods for Jet Noise Simulation

    NASA Technical Reports Server (NTRS)

    Goodrich, John W. (Technical Monitor); Hagstrom, Thomas

    2003-01-01

    The purpose of our project is to develop, analyze, and test novel numerical technologies central to the long term goal of direct simulations of subsonic jet noise. Our current focus is on two issues: accurate, near-field domain truncations and high-order, single-step discretizations of the governing equations. The Direct Numerical Simulation (DNS) of jet noise poses a number of extreme challenges to computational technique. In particular, the problem involves multiple temporal and spatial scales as well as flow instabilities and is posed on an unbounded spatial domain. Moreover, the basic phenomenon of interest, the radiation of acoustic waves to the far field, involves only a minuscule fraction of the total energy. The best current simulations of jet noise are at low Reynolds number. It is likely that an increase of one to two orders of magnitude will be necessary to reach a regime where the separation between the energy-containing and dissipation scales is sufficient to make the radiated noise essentially independent of the Reynolds number. Such an increase in resolution cannot be obtained in the near future solely through increases in computing power. Therefore, new numerical methodologies of maximal efficiency and accuracy are required.

  15. Parallel Proximity Detection for Computer Simulations

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S. (Inventor); Wieland, Frederick P. (Inventor)

    1998-01-01

    The present invention discloses a system for performing proximity detection in computer simulations on parallel processing architectures utilizing a distribution list which includes movers and sensor coverages which check in and out of grids. Each mover maintains a list of sensors that detect the mover's motion as the mover and sensor coverages check in and out of the grids. Fuzzy grids are included by fuzzy resolution parameters to allow movers and sensor coverages to check in and out of grids without computing exact grid crossings. The movers check in and out of grids while moving sensors periodically inform the grids of their coverage. In addition, a lookahead function is also included for providing a generalized capability without making any limiting assumptions about the particular application to which it is applied. The lookahead function is initiated so that risk-free synchronization strategies never roll back grid events. The lookahead function adds fixed delays as events are scheduled for objects on other nodes.

  16. Fast computation algorithms for speckle pattern simulation

    SciTech Connect

    Nascov, Victor; Samoilă, Cornel; Ursuţiu, Doru

    2013-11-13

    We present our development of a series of efficient computation algorithms, generally usable to calculate light diffraction and particularly for speckle pattern simulation. We use mainly the scalar diffraction theory in the form of Rayleigh-Sommerfeld diffraction formula and its Fresnel approximation. Our algorithms are based on a special form of the convolution theorem and the Fast Fourier Transform. They are able to evaluate the diffraction formula much faster than by direct computation and we have circumvented the restrictions regarding the relative sizes of the input and output domains, met on commonly used procedures. Moreover, the input and output planes can be tilted each to other and the output domain can be off-axis shifted.

  17. Investigation of Carbohydrate Recognition via Computer Simulation

    SciTech Connect

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

    2015-04-28

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

  18. Parallel Proximity Detection for Computer Simulation

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S. (Inventor); Wieland, Frederick P. (Inventor)

    1997-01-01

    The present invention discloses a system for performing proximity detection in computer simulations on parallel processing architectures utilizing a distribution list which includes movers and sensor coverages which check in and out of grids. Each mover maintains a list of sensors that detect the mover's motion as the mover and sensor coverages check in and out of the grids. Fuzzy grids are includes by fuzzy resolution parameters to allow movers and sensor coverages to check in and out of grids without computing exact grid crossings. The movers check in and out of grids while moving sensors periodically inform the grids of their coverage. In addition, a lookahead function is also included for providing a generalized capability without making any limiting assumptions about the particular application to which it is applied. The lookahead function is initiated so that risk-free synchronization strategies never roll back grid events. The lookahead function adds fixed delays as events are scheduled for objects on other nodes.

  19. Computer simulation of spacecraft/environment interaction.

    PubMed

    Krupnikov, K K; Makletsov, A A; Mileev, V N; Novikov, L S; Sinolits, V V

    1999-10-01

    This report presents some examples of a computer simulation of spacecraft interaction with space environment. We analysed a set data on electron and ion fluxes measured in 1991 1994 on geostationary satellite GORIZONT-35. The influence of spacecraft eclipse and device eclipse by solar-cell panel on spacecraft charging was investigated. A simple method was developed for an estimation of spacecraft potentials in LEO. Effects of various particle flux impact and spacecraft orientation are discussed. A computer engineering model for a calculation of space radiation is presented. This model is used as a client/server model with WWW interface, including spacecraft model description and results representation based on the virtual reality markup language. PMID:11542669

  20. Investigation of Carbohydrate Recognition via Computer Simulation

    DOE PAGESBeta

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

    2015-04-28

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

  1. Molecular physiology of rhodopsin: Computer simulation

    NASA Astrophysics Data System (ADS)

    Fel'Dman, T. B.; Kholmurodov, Kh. T.; Ostrovsky, M. A.

    2008-03-01

    Computer simulation is used for comparative investigation of the molecular dynamics of rhodopsin containing the chromophore group (11- cis-retinal) and free opsin. Molecular dynamics is traced within a time interval of 3000 ps; 3 × 106 discrete conformational states of rhodopsin and opsin are obtained and analyzed. It is demonstrated that the presence of the chromophore group in the chromophore center of opsin influences considerably the nearest protein environment of 11- cis-retinal both in the region of the β-ionone ring and in the region of the protonated Schiff base bond. Based on simulation results, a possible intramolecular mechanism of keeping rhodopsin as a G-protein-coupled receptor in the inactive state, i.e., the chromophore function as an efficient ligand antagonist, is discussed.

  2. Computer Simulation Studies of Gramicidin Channel

    NASA Astrophysics Data System (ADS)

    Song, Hyundeok; Beck, Thomas

    2009-04-01

    Ion channels are large membrane proteins, and their function is to facilitate the passage of ions across biological membranes. Recently, Dr. John Cuppoletti's group at UC showed that the gramicidin channel could function at high temperatures (360 -- 390K) with significant currents. This finding may have large implications for fuel cell technology. In this project, we will examine the experimental system by computer simulation. We will investigate how the temperature affects the current and differences in magnitude of the currents between two forms of Gramicidin, A and D. This research will help to elucidate the underlying molecular mechanism in this promising new technology.

  3. Determining Peptide Partitioning Properties via Computer Simulation

    PubMed Central

    Ulmschneider, Jakob P.; Ulmschneider, Martin B.

    2010-01-01

    The transfer of polypeptide segments into lipid bilayers to form transmembrane helices represents the crucial first step in cellular membrane protein folding and assembly. This process is driven by complex and poorly understood atomic interactions of peptides with the lipid bilayer environment. The lack of suitable experimental techniques that can resolve these processes both at atomic resolution and nanosecond timescales has spurred the development of computational techniques. In this review, we summarize the significant progress achieved in the last few years in elucidating the partitioning of peptides into lipid bilayer membranes using atomic detail molecular dynamics simulations. Indeed, partitioning simulations can now provide a wealth of structural and dynamic information. Furthermore, we show that peptide-induced bilayer distortions, insertion pathways, transfer free energies, and kinetic insertion barriers are now accurate enough to complement experiments. Further advances in simulation methods and force field parameter accuracy promise to turn molecular dynamics simulations into a powerful tool for investigating a wide range of membrane active peptide phenomena. PMID:21107546

  4. Multiscale Computer Simulation of Failure in Aerogels

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2008-01-01

    Aerogels have been of interest to the aerospace community primarily for their thermal properties, notably their low thermal conductivities. While such gels are typically fragile, recent advances in the application of conformal polymer layers to these gels has made them potentially useful as lightweight structural materials as well. We have previously performed computer simulations of aerogel thermal conductivity and tensile and compressive failure, with results that are in qualitative, and sometimes quantitative, agreement with experiment. However, recent experiments in our laboratory suggest that gels having similar densities may exhibit substantially different properties. In this work, we extend our original diffusion limited cluster aggregation (DLCA) model for gel structure to incorporate additional variation in DLCA simulation parameters, with the aim of producing DLCA clusters of similar densities that nevertheless have different fractal dimension and secondary particle coordination. We perform particle statics simulations of gel strain on these clusters, and consider the effects of differing DLCA simulation conditions, and the resultant differences in fractal dimension and coordination, on gel strain properties.

  5. Computer Simulation of Fracture in Aerogels

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2006-01-01

    Aerogels are of interest to the aerospace community primarily for their thermal properties, notably their low thermal conductivities. While the gels are typically fragile, recent advances in the application of conformal polymer layers to these gels has made them potentially useful as lightweight structural materials as well. In this work, we investigate the strength and fracture behavior of silica aerogels using a molecular statics-based computer simulation technique. The gels' structure is simulated via a Diffusion Limited Cluster Aggregation (DLCA) algorithm, which produces fractal structures representing experimentally observed aggregates of so-called secondary particles, themselves composed of amorphous silica primary particles an order of magnitude smaller. We have performed multi-length-scale simulations of fracture in silica aerogels, in which the interaction b e e n two secondary particles is assumed to be described by a Morse pair potential parameterized such that the potential range is much smaller than the secondary particle size. These Morse parameters are obtained by atomistic simulation of models of the experimentally-observed amorphous silica "bridges," with the fracture behavior of these bridges modeled via molecular statics using a Morse/Coulomb potential for silica. We consider the energetics of the fracture, and compare qualitative features of low-and high-density gel fracture.

  6. Computer simulation of metal-organic materials

    NASA Astrophysics Data System (ADS)

    Stern, Abraham C.

    Computer simulations of metal-organic frameworks are conducted to both investigate the mechanism of hydrogen sorption and to elucidate a detailed, molecular-level understanding of the physical interactions that can lead to successful material design strategies. To this end, important intermolecular interactions are identified and individually parameterized to yield a highly accurate representation of the potential energy landscape. Polarization, one such interaction found to play a significant role in H 2 sorption, is included explicitly for the first time in simulations of metal-organic frameworks. Permanent electrostatics are usually accounted for by means of an approximate fit to model compounds. The application of this method to simulations involving metal-organic frameworks introduces several substantial problems that are characterized in this work. To circumvent this, a method is developed and tested in which atomic point partial charges are computed more directly, fit to the fully periodic electrostatic potential. In this manner, long-range electrostatics are explicitly accounted for via Ewald summation. Grand canonical Monte Carlo simulations are conducted employing the force field parameterization developed here. Several of the major findings of this work are: Polarization is found to play a critical role in determining the overall structure of H2 sorbed in metal-organic frameworks, although not always the determining factor in uptake. The parameterization of atomic point charges by means of a fit to the periodic electrostatic potential is a robust, efficient method and consistently results in a reliable description of Coulombic interactions without introducing ambiguity associated with other procedures. After careful development of both hydrogen and framework potential energy functions, quantitatively accurate results have been obtained. Such predictive accuracy will aid greatly in the rational, iterative design cycle between experimental and theoretical

  7. Computer simulation of solder joint failure

    SciTech Connect

    Burchett, S.N.; Frear, D.R.; Rashid, M.M.

    1997-04-01

    The thermomechanical fatigue failure of solder joints is increasingly becoming an important reliability issue for electronic packages. The purpose of this Laboratory Directed Research and Development (LDRD) project was to develop computational tools for simulating the behavior of solder joints under strain and temperature cycling, taking into account the microstructural heterogeneities that exist in as-solidified near eutectic Sn-Pb joints, as well as subsequent microstructural evolution. The authors present two computational constitutive models, a two-phase model and a single-phase model, that were developed to predict the behavior of near eutectic Sn-Pb solder joints under fatigue conditions. Unique metallurgical tests provide the fundamental input for the constitutive relations. The two-phase model mathematically predicts the heterogeneous coarsening behavior of near eutectic Sn-Pb solder. The finite element simulations with this model agree qualitatively with experimental thermomechanical fatigue tests. The simulations show that the presence of an initial heterogeneity in the solder microstructure could significantly degrade the fatigue lifetime. The single-phase model was developed to predict solder joint behavior using materials data for constitutive relation constants that could be determined through straightforward metallurgical experiments. Special thermomechanical fatigue tests were developed to give fundamental materials input to the models, and an in situ SEM thermomechanical fatigue test system was developed to characterize microstructural evolution and the mechanical behavior of solder joints during the test. A shear/torsion test sample was developed to impose strain in two different orientations. Materials constants were derived from these tests. The simulation results from the two-phase model showed good fit to the experimental test results.

  8. Computer Simulations in Science Education: Implications for Distance Education

    ERIC Educational Resources Information Center

    Sahin, Sami

    2006-01-01

    This paper is a review of literature about the use of computer simulations in science education. This review examines types and examples of computer simulations. The literature review indicated that although computer simulations cannot replace science classroom and laboratory activities completely, they offer various advantages both for classroom…

  9. The Learning Effects of Computer Simulations in Science Education

    ERIC Educational Resources Information Center

    Rutten, Nico; van Joolingen, Wouter R.; van der Veen, Jan T.

    2012-01-01

    This article reviews the (quasi)experimental research of the past decade on the learning effects of computer simulations in science education. The focus is on two questions: how use of computer simulations can enhance traditional education, and how computer simulations are best used in order to improve learning processes and outcomes. We report on…

  10. A Computational Framework for Bioimaging Simulation

    PubMed Central

    Watabe, Masaki; Arjunan, Satya N. V.; Fukushima, Seiya; Iwamoto, Kazunari; Kozuka, Jun; Matsuoka, Satomi; Shindo, Yuki; Ueda, Masahiro; Takahashi, Koichi

    2015-01-01

    Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding how higher level functions emerge from the combined action of biomolecules. However, there still remain formidable challenges in bridging the gap between bioimaging and mathematical modeling. Generally, measurements using fluorescence microscopy systems are influenced by systematic effects that arise from stochastic nature of biological cells, the imaging apparatus, and optical physics. Such systematic effects are always present in all bioimaging systems and hinder quantitative comparison between the cell model and bioimages. Computational tools for such a comparison are still unavailable. Thus, in this work, we present a computational framework for handling the parameters of the cell models and the optical physics governing bioimaging systems. Simulation using this framework can generate digital images of cell simulation results after accounting for the systematic effects. We then demonstrate that such a framework enables comparison at the level of photon-counting units. PMID:26147508

  11. Neural network computer simulation of medical aerosols.

    PubMed

    Richardson, C J; Barlow, D J

    1996-06-01

    Preliminary investigations have been conducted to assess the potential for using artificial neural networks to simulate aerosol behaviour, with a view to employing this type of methodology in the evaluation and design of pulmonary drug-delivery systems. Details are presented of the general purpose software developed for these tasks; it implements a feed-forward back-propagation algorithm with weight decay and connection pruning, the user having complete run-time control of the network architecture and mode of training. A series of exploratory investigations is then reported in which different network structures and training strategies are assessed in terms of their ability to simulate known patterns of fluid flow in simple model systems. The first of these involves simulations of cellular automata-generated data for fluid flow through a partially obstructed two-dimensional pipe. The artificial neural networks are shown to be highly successful in simulating the behaviour of this simple linear system, but with important provisos relating to the information content of the training data and the criteria used to judge when the network is properly trained. A second set of investigations is then reported in which similar networks are used to simulate patterns of fluid flow through aerosol generation devices, using training data furnished through rigorous computational fluid dynamics modelling. These more complex three-dimensional systems are modelled with equal success. It is concluded that carefully tailored, well trained networks could provide valuable tools not just for predicting but also for analysing the spatial dynamics of pharmaceutical aerosols. PMID:8832491

  12. Computational simulation for concurrent engineering of aerospace propulsion systems

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

    Results are summarized for an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulation methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties--fundamental to develop such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering of propulsion systems and systems in general. Benefits and issues needing early attention in the development are outlined.

  13. Computational simulation of concurrent engineering for aerospace propulsion systems

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

    Results are summarized of an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulations methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties - fundamental in developing such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering for propulsion systems and systems in general. Benefits and facets needing early attention in the development are outlined.

  14. Computer simulation of surface and film processes

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  15. Computer simulation of fatigue under diametrical compression

    SciTech Connect

    Carmona, H. A.; Kun, F.; Andrade, J. S. Jr.; Herrmann, H. J.

    2007-04-15

    We study the fatigue fracture of disordered materials by means of computer simulations of a discrete element model. We extend a two-dimensional fracture model to capture the microscopic mechanisms relevant for fatigue and we simulate the diametric compression of a disc shape specimen under a constant external force. The model allows us to follow the development of the fracture process on the macrolevel and microlevel varying the relative influence of the mechanisms of damage accumulation over the load history and healing of microcracks. As a specific example we consider recent experimental results on the fatigue fracture of asphalt. Our numerical simulations show that for intermediate applied loads the lifetime of the specimen presents a power law behavior. Under the effect of healing, more prominent for small loads compared to the tensile strength of the material, the lifetime of the sample increases and a fatigue limit emerges below which no macroscopic failure occurs. The numerical results are in a good qualitative agreement with the experimental findings.

  16. Toward a Coarse Graining/All Atoms Force Field (CG/AA) from a Multiscale Optimization Method: An Application to the MCM-41 Mesoporous Silicates.

    PubMed

    Ghoufi, A; Morineau, D; Lefort, R; Malfreyt, P

    2010-10-12

    Many interesting physical phenomena occur on length and time scales that are not accessible by atomistic molecular simulations. By introducing a coarse graining of the degrees of freedom, coarse-grained (CG) models allow ther study of larger scale systems for longer times. Coarse-grained force fields have been mostly derived for large molecules, including polymeric materials and proteins. By contrast, there exist no satisfactory CG potentials for mesostructured porous solid materials in the literature. This issue has become critical among a growing number of studies on confinement effects on fluid properties, which require both long time and large scale simulations and the conservation of a sufficient level of atomistic description to account for interfacial phenomena. In this paper, we present a general multiscale procedure to derive a hybrid coarse grained/all atoms force field CG/AA model for mesoporous systems. The method is applied to mesostructured MCM-41 molecular sieves, while the parameters of the mesoscopic interaction potentials are obtained and validated from the computation of the adsorption isotherm of methanol by grand canonical molecular dynamic simulation. PMID:26616783

  17. CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-Aldopentofuranosides and Fructofuranose

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields. PMID:19694450

  18. Chip level simulation of fault tolerant computers

    NASA Technical Reports Server (NTRS)

    Armstrong, J. R.

    1983-01-01

    Chip level modeling techniques, functional fault simulation, simulation software development, a more efficient, high level version of GSP, and a parallel architecture for functional simulation are discussed.

  19. Space radiator simulation manual for computer code

    NASA Technical Reports Server (NTRS)

    Black, W. Z.; Wulff, W.

    1972-01-01

    A computer program that simulates the performance of a space radiator is presented. The program basically consists of a rigorous analysis which analyzes a symmetrical fin panel and an approximate analysis that predicts system characteristics for cases of non-symmetrical operation. The rigorous analysis accounts for both transient and steady state performance including aerodynamic and radiant heating of the radiator system. The approximate analysis considers only steady state operation with no aerodynamic heating. A description of the radiator system and instructions to the user for program operation is included. The input required for the execution of all program options is described. Several examples of program output are contained in this section. Sample output includes the radiator performance during ascent, reentry and orbit.

  20. Computational simulation methods for composite fracture mechanics

    NASA Technical Reports Server (NTRS)

    Murthy, Pappu L. N.

    1988-01-01

    Structural integrity, durability, and damage tolerance of advanced composites are assessed by studying damage initiation at various scales (micro, macro, and global) and accumulation and growth leading to global failure, quantitatively and qualitatively. In addition, various fracture toughness parameters associated with a typical damage and its growth must be determined. Computational structural analysis codes to aid the composite design engineer in performing these tasks were developed. CODSTRAN (COmposite Durability STRuctural ANalysis) is used to qualitatively and quantitatively assess the progressive damage occurring in composite structures due to mechanical and environmental loads. Next, methods are covered that are currently being developed and used at Lewis to predict interlaminar fracture toughness and related parameters of fiber composites given a prescribed damage. The general purpose finite element code MSC/NASTRAN was used to simulate the interlaminar fracture and the associated individual as well as mixed-mode strain energy release rates in fiber composites.

  1. Computational simulation of hot composite structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Murthy, P. L. N.; Singhal, S. N.

    1991-01-01

    Three different computer codes developed in-house are described for application to hot composite structures. These codes include capabilities for: (1) laminate behavior (METCAN); (2) thermal/structural analysis of hot structures made from high temperature metal matrix composites (HITCAN); and (3) laminate tailoring (MMLT). Results for select sample cases are described to demonstrate the versatility as well as the application of these codes to specific situations. The sample case results show that METCAN can be used to simulate cyclic life in high temperature metal matrix composites; HITCAN can be used to evaluate the structural performance of curved panels as well as respective sensitivities of various nonlinearities, and MMLT can be used to tailor the fabrication process in order to reduce residual stresses in the matrix upon cool-down.

  2. Computational simulation of hot composites structures

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Murthy, P. L. N.; Singhal, S. N.

    1991-01-01

    Three different computer codes developed in-house are described for application to hot composite structures. These codes include capabilities for: (1) laminate behavior (METCAN); (2) thermal/structural analysis of hot structures made from high temperature metal matrix composites (HITCAN); and (3) laminate tailoring (MMLT). Results for select sample cases are described to demonstrate the versatility as well as the application of these codes to specific situations. The sample case results show that METCAN can be used to simulate cyclic life in high temperature metal matrix composites; HITCAN can be used to evaluate the structural performance of curved panels as well as respective sensitivities of various nonlinearities, and MMLT can be used to tailor the fabrication process in order to reduce residual stresses in the matrix upon cool-down.

  3. Miller experiments in atomistic computer simulations

    PubMed Central

    Saitta, Antonino Marco; Saija, Franz

    2014-01-01

    The celebrated Miller experiments reported on the spontaneous formation of amino acids from a mixture of simple molecules reacting under an electric discharge, giving birth to the research field of prebiotic chemistry. However, the chemical reactions involved in those experiments have never been studied at the atomic level. Here we report on, to our knowledge, the first ab initio computer simulations of Miller-like experiments in the condensed phase. Our study, based on the recent method of treatment of aqueous systems under electric fields and on metadynamics analysis of chemical reactions, shows that glycine spontaneously forms from mixtures of simple molecules once an electric field is switched on and identifies formic acid and formamide as key intermediate products of the early steps of the Miller reactions, and the crucible of formation of complex biological molecules. PMID:25201948

  4. A Mass Spectrometer Simulator in Your Computer

    NASA Astrophysics Data System (ADS)

    Gagnon, Michel

    2012-12-01

    Introduced to study components of ionized gas, the mass spectrometer has evolved into a highly accurate device now used in many undergraduate and research laboratories. Unfortunately, despite their importance in the formation of future scientists, mass spectrometers remain beyond the financial reach of many high schools and colleges. As a result, it is not possible for instructors to take full advantage of this equipment. Therefore, to facilitate accessibility to this tool, we have developed a realistic computer-based simulator. Using this software, students are able to practice their ability to identify the components of the original gas, thereby gaining a better understanding of the underlying physical laws. The software is available as a free download.

  5. Ab initio prediction of protein structure with both all-atom and simplified force fields

    NASA Astrophysics Data System (ADS)

    Scheraga, Harold

    2004-03-01

    Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.

  6. Experiential Learning through Computer-Based Simulations.

    ERIC Educational Resources Information Center

    Maynes, Bill; And Others

    1992-01-01

    Describes experiential learning instructional model and simulation for student principals. Describes interactive laser videodisc simulation. Reports preliminary findings about student principal learning from simulation. Examines learning approaches by unsuccessful and successful students and learning levels of model learners. Simulation's success…

  7. Engineering Fracking Fluids with Computer Simulation

    NASA Astrophysics Data System (ADS)

    Shaqfeh, Eric

    2015-11-01

    There are no comprehensive simulation-based tools for engineering the flows of viscoelastic fluid-particle suspensions in fully three-dimensional geometries. On the other hand, the need for such a tool in engineering applications is immense. Suspensions of rigid particles in viscoelastic fluids play key roles in many energy applications. For example, in oil drilling the ``drilling mud'' is a very viscous, viscoelastic fluid designed to shear-thin during drilling, but thicken at stoppage so that the ``cuttings'' can remain suspended. In a related application known as hydraulic fracturing suspensions of solids called ``proppant'' are used to prop open the fracture by pumping them into the well. It is well-known that particle flow and settling in a viscoelastic fluid can be quite different from that which is observed in Newtonian fluids. First, it is now well known that the ``fluid particle split'' at bifurcation cracks is controlled by fluid rheology in a manner that is not understood. Second, in Newtonian fluids, the presence of an imposed shear flow in the direction perpendicular to gravity (which we term a cross or orthogonal shear flow) has no effect on the settling of a spherical particle in Stokes flow (i.e. at vanishingly small Reynolds number). By contrast, in a non-Newtonian liquid, the complex rheological properties induce a nonlinear coupling between the sedimentation and shear flow. Recent experimental data have shown both the shear thinning and the elasticity of the suspending polymeric solutions significantly affects the fluid-particle split at bifurcations, as well as the settling rate of the solids. In the present work, we use the Immersed Boundary Method to develop computer simulations of viscoelastic flow in suspensions of spheres to study these problems. These simulations allow us to understand the detailed physical mechanisms for the remarkable physical behavior seen in practice, and actually suggest design rules for creating new fluid recipes.

  8. Duality quantum computer and the efficient quantum simulations

    NASA Astrophysics Data System (ADS)

    Wei, Shi-Jie; Long, Gui-Lu

    2016-03-01

    Duality quantum computing is a new mode of a quantum computer to simulate a moving quantum computer passing through a multi-slit. It exploits the particle wave duality property for computing. A quantum computer with n qubits and a qudit simulates a moving quantum computer with n qubits passing through a d-slit. Duality quantum computing can realize an arbitrary sum of unitaries and therefore a general quantum operator, which is called a generalized quantum gate. All linear bounded operators can be realized by the generalized quantum gates, and unitary operators are just the extreme points of the set of generalized quantum gates. Duality quantum computing provides flexibility and a clear physical picture in designing quantum algorithms, and serves as a powerful bridge between quantum and classical algorithms. In this paper, after a brief review of the theory of duality quantum computing, we will concentrate on the applications of duality quantum computing in simulations of Hamiltonian systems. We will show that duality quantum computing can efficiently simulate quantum systems by providing descriptions of the recent efficient quantum simulation algorithm of Childs and Wiebe (Quantum Inf Comput 12(11-12):901-924, 2012) for the fast simulation of quantum systems with a sparse Hamiltonian, and the quantum simulation algorithm by Berry et al. (Phys Rev Lett 114:090502, 2015), which provides exponential improvement in precision for simulating systems with a sparse Hamiltonian.

  9. Using Computational Simulations to Confront Students' Mental Models

    ERIC Educational Resources Information Center

    Rodrigues, R.; Carvalho, P. Simeão

    2014-01-01

    In this paper we show an example of how to use a computational simulation to obtain visual feedback for students' mental models, and compare their predictions with the simulated system's behaviour. Additionally, we use the computational simulation to incrementally modify the students' mental models in order to accommodate new data,…

  10. Computer-aided simulation study of photomultiplier tubes

    NASA Technical Reports Server (NTRS)

    Zaghloul, Mona E.; Rhee, Do Jun

    1989-01-01

    A computer model that simulates the response of photomultiplier tubes (PMTs) and the associated voltage divider circuit is developed. An equivalent circuit that approximates the operation of the device is derived and then used to develop a computer simulation of the PMT. Simulation results are presented and discussed.

  11. Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.

    PubMed

    Genheden, Samuel; Cabedo Martinez, Ana I; Criddle, Michael P; Essex, Jonathan W

    2014-03-01

    We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol(-1) and a Kendall's τ of 0.65 compared with experiment. PMID:24488307

  12. Computer simulation and the features of novel empirical data.

    PubMed

    Lusk, Greg

    2016-04-01

    In an attempt to determine the epistemic status of computer simulation results, philosophers of science have recently explored the similarities and differences between computer simulations and experiments. One question that arises is whether and, if so, when, simulation results constitute novel empirical data. It is often supposed that computer simulation results could never be empirical or novel because simulations never interact with their targets, and cannot go beyond their programming. This paper argues against this position by examining whether, and under what conditions, the features of empiricality and novelty could be displayed by computer simulation data. I show that, to the extent that certain familiar measurement results have these features, so can some computer simulation results. PMID:27083094

  13. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

    PubMed Central

    2015-01-01

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

  14. Computer simulation of FCC riser reactors.

    SciTech Connect

    Chang, S. L.; Golchert, B.; Lottes, S. A.; Petrick, M.; Zhou, C. Q.

    1999-04-20

    A three-dimensional computational fluid dynamics (CFD) code, ICRKFLO, was developed to simulate the multiphase reacting flow system in a fluid catalytic cracking (FCC) riser reactor. The code solve flow properties based on fundamental conservation laws of mass, momentum, and energy for gas, liquid, and solid phases. Useful phenomenological models were developed to represent the controlling FCC processes, including droplet dispersion and evaporation, particle-solid interactions, and interfacial heat transfer between gas, droplets, and particles. Techniques were also developed to facilitate numerical calculations. These techniques include a hybrid flow-kinetic treatment to include detailed kinetic calculations, a time-integral approach to overcome numerical stiffness problems of chemical reactions, and a sectional coupling and blocked-cell technique for handling complex geometry. The copyrighted ICRKFLO software has been validated with experimental data from pilot- and commercial-scale FCC units. The code can be used to evaluate the impacts of design and operating conditions on the production of gasoline and other oil products.

  15. Computational simulation of liquid rocket injector anomalies

    NASA Technical Reports Server (NTRS)

    Przekwas, A. J.; Singhal, A. K.; Tam, L. T.; Davidian, K.

    1986-01-01

    A computer model has been developed to analyze the three-dimensional two-phase reactive flows in liquid fueled rocket combustors. The model is designed to study the influence of liquid propellant injection nonuniformities on the flow pattern, combustion and heat transfer within the combustor. The Eulerian-Lagrangian approach for simulating polidisperse spray flow, evaporation and combustion has been used. Full coupling between the phases is accounted for. A nonorthogonal, body fitted coordinate system along with a conservative control volume formulation is employed. The physical models built into the model include a kappa-epsilon turbulence model, a two-step chemical reaction, and the six-flux radiation model. Semiempirical models are used to describe all interphase coupling terms as well as chemical reaction rates. The purpose of this study was to demonstrate an analytical capability to predict the effects of reactant injection nonuniformities (injection anomalies) on combustion and heat transfer within the rocket combustion chamber. The results show promising application of the model to comprehensive modeling of liquid propellant rocket engines.

  16. Quantitative and Qualitative Simulation in Computer Based Training.

    ERIC Educational Resources Information Center

    Stevens, Albert; Roberts, Burce

    1983-01-01

    Computer-based systems combining quantitative simulation with qualitative tutorial techniques provide learners with sophisticated individualized training. The teaching capabilities and operating procedures of Steamer, a simulated steam plant, are described. (Author/MBR)

  17. Simulating complex intracellular processes using object-oriented computational modelling.

    PubMed

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

    2004-11-01

    The aim of this paper is to give an overview of computer modelling and simulation in cellular biology, in particular as applied to complex biochemical processes within the cell. This is illustrated by the use of the techniques of object-oriented modelling, where the computer is used to construct abstractions of objects in the domain being modelled, and these objects then interact within the computer to simulate the system and allow emergent properties to be observed. The paper also discusses the role of computer simulation in understanding complexity in biological systems, and the kinds of information which can be obtained about biology via simulation. PMID:15302205

  18. Computer Simulation Methods for Defect Configurations and Nanoscale Structures

    SciTech Connect

    Gao, Fei

    2010-01-01

    This chapter will describe general computer simulation methods, including ab initio calculations, molecular dynamics and kinetic Monte-Carlo method, and their applications to the calculations of defect configurations in various materials (metals, ceramics and oxides) and the simulations of nanoscale structures due to ion-solid interactions. The multiscale theory, modeling, and simulation techniques (both time scale and space scale) will be emphasized, and the comparisons between computer simulation results and exprimental observations will be made.

  19. Computer Simulation Studies of CTG Triplet Repeat Sequences

    NASA Astrophysics Data System (ADS)

    Rasaiah, Jayendran. C.; Lynch, Joshua

    1998-03-01

    Long segments of CTG trinucleotide repeats in human DNA are correlated with a class of neurological diseases (myotonic dystrophy, fragile-X syndrome, and Kenndy's disease). These diseases are characterized by genetic anticipation and are thought to arise from replication errors caused by unusual conformations of CTG repeat segments. We have studied the properties of a single short segment of double starnded DNA with CTG repeats in 0.5 M sodium chloride solution with molecular dynamics simulations. The simulations are carried out in the micro canonical ensemble using an all-atom force field with CHARMM parameters. The TIPS3 water model is used to simulate a molecular solvent. Electrostatic interactions are calculated by Ewald summation and the equations of motion integrated using a Verlet algorithm in conjunction with SHAKE constrained dynamics to maintain bond lengths. The simulation of CTG repeat sequence is compared with a control system containing CAG triplet repeats to determine possible differencesin the conformation and elasticity of the two sequences.

  20. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins

    PubMed Central

    2016-01-01

    We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N-acetylglucosamine, N-acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran–cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1–12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide–monosaccharide and protein–glycan linkages are derived

  1. Simulation of reliability in multiserver computer networks

    NASA Astrophysics Data System (ADS)

    Minkevičius, Saulius

    2012-11-01

    The performance in terms of reliability of computer multiserver networks motivates this paper. The probability limit theorem is derived on the extreme queue length in open multiserver queueing networks in heavy traffic and applied to a reliability model for multiserver computer networks where we relate the time of failure of a multiserver computer network to the system parameters.

  2. Computational simulations of vorticity enhanced diffusion

    NASA Astrophysics Data System (ADS)

    Vold, Erik L.

    1999-11-01

    Computer simulations are used to investigate a phenomenon of vorticity enhanced diffusion (VED), a net transport and mixing of a passive scalar across a prescribed vortex flow field driven by a background gradient in the scalar quantity. The central issue under study here is the increase in scalar flux down the gradient and across the vortex field. The numerical scheme uses cylindrical coordinates centered with the vortex flow which allows an exact advective solution and 1D or 2D diffusion using simple numerical methods. In the results, the ratio of transport across a localized vortex region in the presence of the vortex flow over that expected for diffusion alone is evaluated as a measure of VED. This ratio is seen to increase dramatically while the absolute flux across the vortex decreases slowly as the diffusion coefficient is decreased. Similar results are found and compared for varying diffusion coefficient, D, or vortex rotation time, τv, for a constant background gradient in the transported scalar vs an interface in the transported quantity, and for vortex flow fields constant in time vs flow which evolves in time from an initial state and with a Schmidt number of order unity. A simple analysis shows that for a small diffusion coefficient, the flux ratio measure of VED scales as the vortex radius over the thickness for mass diffusion in a viscous shear layer within the vortex characterized by (Dτv)1/2. The phenomenon is linear as investigated here and suggests that a significant enhancement of mixing in fluids may be a relatively simple linear process. Discussion touches on how this vorticity enhanced diffusion may be related to mixing in nonlinear turbulent flows.

  3. Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations

    NASA Astrophysics Data System (ADS)

    Jin, Yu

    2016-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We stay away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while addressing statistical physics modeling approaches along with all-atom molecular dynamics simulation studies. We organize this review around our own modeling and simulation practices on a single subunit T7 RNA polymerase, and summarize commensurate studies on structurally similar DNA polymerases as well. For multi-subunit RNA polymerases that have been actively studied in recent years, we leave systematical reviews of the simulation achievements to latest computational chemistry surveys, while covering only representative studies published very recently, including our own work modeling structure-based elongation kinetic of yeast RNA polymerase II. In the end, we briefly go through physical modeling on elongation pauses and backtracking activities of the multi-subunit RNAPs. We emphasize on the fluctuation and control mechanisms of the polymerase actions, highlight the non-equilibrium nature of the operation system, and try to build some perspectives toward understanding the polymerase impacts from the single molecule level to a genome-wide scale. Project supported by the National Natural Science Foundation (Grant No. 11275022).

  4. Computer simulator for a mobile telephone system

    NASA Technical Reports Server (NTRS)

    Schilling, D. L.; Ziegler, C.

    1983-01-01

    A software simulator to help NASA in the design of the LMSS was developed. The simulator will be used to study the characteristics of implementation requirements of the LMSS's configuration with specifications as outlined by NASA.

  5. Simulation of the stress computation in shells

    NASA Technical Reports Server (NTRS)

    Salama, M.; Utku, S.

    1978-01-01

    A self-teaching computer program is described, whereby the stresses in thin shells can be computed with good accuracy using the best fit approach. The program is designed for use in interactive game mode to allow the structural engineer to learn about (1) the major sources of difficulties and associated errors in the computation of stresses in thin shells, (2) possible ways to reduce the errors, and (3) trade-off between computational cost and accuracy. Included are derivation of the computational approach, program description, and several examples illustrating the program usage.

  6. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX

    SciTech Connect

    Bell, Jeffrey A.; Ho, Kenneth L.; Farid, Ramy

    2012-08-01

    All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close nonbonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects many of these problematic interactions, producing models that are better suited for use in computational chemistry and related applications. All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5–2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R{sub free} values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein–ligand interactions.

  7. Cognitive Effects from Process Learning with Computer-Based Simulations.

    ERIC Educational Resources Information Center

    Breuer, Klaus; Kummer, Ruediger

    1990-01-01

    Discusses content learning versus process learning, describes process learning with computer-based simulations, and highlights an empirical study on the effects of process learning with problem-oriented, computer-managed simulations in technical vocational education classes in West Germany. Process learning within a model of the cognitive system…

  8. Computer Simulation Models of Economic Systems in Higher Education.

    ERIC Educational Resources Information Center

    Smith, Lester Sanford

    The increasing complexity of educational operations make analytical tools, such as computer simulation models, especially desirable for educational administrators. This MA thesis examined the feasibility of developing computer simulation models of economic systems in higher education to assist decision makers in allocating resources. The report…

  9. Explore Effective Use of Computer Simulations for Physics Education

    ERIC Educational Resources Information Center

    Lee, Yu-Fen; Guo, Yuying

    2008-01-01

    The dual purpose of this article is to provide a synthesis of the findings related to the use of computer simulations in physics education and to present implications for teachers and researchers in science education. We try to establish a conceptual framework for the utilization of computer simulations as a tool for learning and instruction in…

  10. The Link between Computer Simulations and Social Studies Learning: Debriefing.

    ERIC Educational Resources Information Center

    Chiodo, John J.; Flaim, Mary L.

    1993-01-01

    Asserts that debriefing is the missing link between learning achievement and simulations in social studies. Maintains that teachers who employ computer-assisted instruction must utilize effective debriefing activities. Provides a four-step debriefing model using the computer simulation, Oregon Trail. (CFR)

  11. The Role of Computer Simulations in Engineering Education.

    ERIC Educational Resources Information Center

    Smith, P. R.; Pollard, D.

    1986-01-01

    Discusses role of computer simulation in complementing and extending conventional components of undergraduate engineering education process in United Kingdom universities and polytechnics. Aspects of computer-based learning are reviewed (laboratory simulation, lecture and tutorial support, inservice teacher education) with reference to programs in…

  12. How Effective Is Instructional Support for Learning with Computer Simulations?

    ERIC Educational Resources Information Center

    Eckhardt, Marc; Urhahne, Detlef; Conrad, Olaf; Harms, Ute

    2013-01-01

    The study examined the effects of two different instructional interventions as support for scientific discovery learning using computer simulations. In two well-known categories of difficulty, data interpretation and self-regulation, instructional interventions for learning with computer simulations on the topic "ecosystem water" were developed…

  13. Evaluation of Computer Simulations for Teaching Apparel Merchandising Concepts.

    ERIC Educational Resources Information Center

    Jolly, Laura D.; Sisler, Grovalynn

    1988-01-01

    The study developed and evaluated computer simulations for teaching apparel merchandising concepts. Evaluation results indicated that teaching method (computer simulation versus case study) does not significantly affect cognitive learning. Student attitudes varied, however, according to topic (profitable merchandising analysis versus retailing…

  14. New Pedagogies on Teaching Science with Computer Simulations

    ERIC Educational Resources Information Center

    Khan, Samia

    2011-01-01

    Teaching science with computer simulations is a complex undertaking. This case study examines how an experienced science teacher taught chemistry using computer simulations and the impact of his teaching on his students. Classroom observations over 3 semesters, teacher interviews, and student surveys were collected. The data was analyzed for (1)…

  15. Computers for real time flight simulation: A market survey

    NASA Technical Reports Server (NTRS)

    Bekey, G. A.; Karplus, W. J.

    1977-01-01

    An extensive computer market survey was made to determine those available systems suitable for current and future flight simulation studies at Ames Research Center. The primary requirement is for the computation of relatively high frequency content (5 Hz) math models representing powered lift flight vehicles. The Rotor Systems Research Aircraft (RSRA) was used as a benchmark vehicle for computation comparison studies. The general nature of helicopter simulations and a description of the benchmark model are presented, and some of the sources of simulation difficulties are examined. A description of various applicable computer architectures is presented, along with detailed discussions of leading candidate systems and comparisons between them.

  16. A thermodynamic study of Abeta(16-21) dissociation from a fibril using computer simulations

    NASA Astrophysics Data System (ADS)

    Dias, Cristiano; Mahmoudinobar, Farbod; Su, Zhaoqian

    Here, I will discuss recent all-atom molecular dynamics simulations with explicit water in which we studied the thermodynamic properties of Abeta(16-21) dissociation from an amyloid fibril. Changes in thermodynamics quantities, e.g., entropy, enthalpy, and volume, are computed from the temperature dependence of the free-energy computed using the umbrella sampling method. We find similarities and differences between the thermodynamics of peptide dissociation and protein unfolding. Similarly to protein unfolding, Abeta(16-21) dissociation is characterized by an unfavorable change in enthalpy, a favorable change in the entropic energy, and an increase in the heat capacity. A main difference is that peptide dissociation is characterized by a weak enthalpy-entropy compensation. We characterize dock and lock states of the peptide based on the solvent accessible surface area. The Lennard-Jones energy of the system is observed to increase continuously in lock and dock states as the peptide dissociates. The electrostatic energy increases in the lock state and it decreases in the dock state as the peptide dissociates. These results will be discussed as well as their implication for fibril growth.

  17. Performance Analysis of Cloud Computing Architectures Using Discrete Event Simulation

    NASA Technical Reports Server (NTRS)

    Stocker, John C.; Golomb, Andrew M.

    2011-01-01

    Cloud computing offers the economic benefit of on-demand resource allocation to meet changing enterprise computing needs. However, the flexibility of cloud computing is disadvantaged when compared to traditional hosting in providing predictable application and service performance. Cloud computing relies on resource scheduling in a virtualized network-centric server environment, which makes static performance analysis infeasible. We developed a discrete event simulation model to evaluate the overall effectiveness of organizations in executing their workflow in traditional and cloud computing architectures. The two part model framework characterizes both the demand using a probability distribution for each type of service request as well as enterprise computing resource constraints. Our simulations provide quantitative analysis to design and provision computing architectures that maximize overall mission effectiveness. We share our analysis of key resource constraints in cloud computing architectures and findings on the appropriateness of cloud computing in various applications.

  18. GPU-accelerated micromagnetic simulations using cloud computing

    NASA Astrophysics Data System (ADS)

    Jermain, C. L.; Rowlands, G. E.; Buhrman, R. A.; Ralph, D. C.

    2016-03-01

    Highly parallel graphics processing units (GPUs) can improve the speed of micromagnetic simulations significantly as compared to conventional computing using central processing units (CPUs). We present a strategy for performing GPU-accelerated micromagnetic simulations by utilizing cost-effective GPU access offered by cloud computing services with an open-source Python-based program for running the MuMax3 micromagnetics code remotely. We analyze the scaling and cost benefits of using cloud computing for micromagnetics.

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

    ERIC Educational Resources Information Center

    Skrein, Dale

    1994-01-01

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

  20. Computational Electromagnetics (CEM) Laboratory: Simulation Planning Guide

    NASA Technical Reports Server (NTRS)

    Khayat, Michael A.

    2011-01-01

    The simulation process, milestones and inputs are unknowns to first-time users of the CEM Laboratory. The Simulation Planning Guide aids in establishing expectations for both NASA and non-NASA facility customers. The potential audience for this guide includes both internal and commercial spaceflight hardware/software developers. It is intended to assist their engineering personnel in simulation planning and execution. Material covered includes a roadmap of the simulation process, roles and responsibilities of facility and user, major milestones, facility capabilities, and inputs required by the facility. Samples of deliverables, facility interfaces, and inputs necessary to define scope, cost, and schedule are included as an appendix to the guide.

  1. Computer simulated plant design for waste minimization/pollution prevention

    SciTech Connect

    Bumble, S.

    2000-07-01

    The book discusses several paths to pollution prevention and waste minimization by using computer simulation programs. It explains new computer technologies used in the field of pollution prevention and waste management; provides information pertaining to overcoming technical, economic, and environmental barriers to waste reduction; gives case-studies from industries; and covers computer aided flow sheet design and analysis for nuclear fuel reprocessing.

  2. Creating Science Simulations through Computational Thinking Patterns

    ERIC Educational Resources Information Center

    Basawapatna, Ashok Ram

    2012-01-01

    Computational thinking aims to outline fundamental skills from computer science that everyone should learn. As currently defined, with help from the National Science Foundation (NSF), these skills include problem formulation, logically organizing data, automating solutions through algorithmic thinking, and representing data through abstraction.…

  3. Computer Simulations as an Integral Part of Intermediate Macroeconomics.

    ERIC Educational Resources Information Center

    Millerd, Frank W.; Robertson, Alastair R.

    1987-01-01

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

  4. Genetic Crossing vs Cloning by Computer Simulation

    NASA Astrophysics Data System (ADS)

    Dasgupta, Subinay

    We perform Monte Carlo simulation using Penna's bit string model, and compare the process of asexual reproduction by cloning with that by genetic crossover. We find them to be comparable as regards survival of a species, and also if a natural disaster is simulated.

  5. Genetic crossing vs cloning by computer simulation

    SciTech Connect

    Dasgupta, S.

    1997-06-01

    We perform Monte Carlo simulation using Penna`s bit string model, and compare the process of asexual reproduction by cloning with that by genetic crossover. We find them to be comparable as regards survival of a species, and also if a natural disaster is simulated.

  6. Spatial Learning and Computer Simulations in Science

    ERIC Educational Resources Information Center

    Lindgren, Robb; Schwartz, Daniel L.

    2009-01-01

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

  7. High Fidelity Simulation of a Computer Room

    NASA Technical Reports Server (NTRS)

    Ahmad, Jasim; Chan, William; Chaderjian, Neal; Pandya, Shishir

    2005-01-01

    This viewgraph presentation reviews NASA's Columbia supercomputer and the mesh technology used to test the adequacy of the fluid and cooling of a computer room. A technical description of the Columbia supercomputer is also presented along with its performance capability.

  8. Some theoretical issues on computer simulations

    SciTech Connect

    Barrett, C.L.; Reidys, C.M.

    1998-02-01

    The subject of this paper is the development of mathematical foundations for a theory of simulation. Sequentially updated cellular automata (sCA) over arbitrary graphs are employed as a paradigmatic framework. In the development of the theory, the authors focus on the properties of causal dependencies among local mappings in a simulation. The main object of and study is the mapping between a graph representing the dependencies among entities of a simulation and a representing the equivalence classes of systems obtained by all possible updates.

  9. Use of advanced computers for aerodynamic flow simulation

    NASA Technical Reports Server (NTRS)

    Bailey, F. R.; Ballhaus, W. F.

    1980-01-01

    The current and projected use of advanced computers for large-scale aerodynamic flow simulation applied to engineering design and research is discussed. The design use of mature codes run on conventional, serial computers is compared with the fluid research use of new codes run on parallel and vector computers. The role of flow simulations in design is illustrated by the application of a three dimensional, inviscid, transonic code to the Sabreliner 60 wing redesign. Research computations that include a more complete description of the fluid physics by use of Reynolds averaged Navier-Stokes and large-eddy simulation formulations are also presented. Results of studies for a numerical aerodynamic simulation facility are used to project the feasibility of design applications employing these more advanced three dimensional viscous flow simulations.

  10. Parallel Computing Environments and Methods for Power Distribution System Simulation

    SciTech Connect

    Lu, Ning; Taylor, Zachary T.; Chassin, David P.; Guttromson, Ross T.; Studham, Scott S.

    2005-11-10

    The development of cost-effective high-performance parallel computing on multi-processor super computers makes it attractive to port excessively time consuming simulation software from personal computers (PC) to super computes. The power distribution system simulator (PDSS) takes a bottom-up approach and simulates load at appliance level, where detailed thermal models for appliances are used. This approach works well for a small power distribution system consisting of a few thousand appliances. When the number of appliances increases, the simulation uses up the PC memory and its run time increases to a point where the approach is no longer feasible to model a practical large power distribution system. This paper presents an effort made to port a PC-based power distribution system simulator (PDSS) to a 128-processor shared-memory super computer. The paper offers an overview of the parallel computing environment and a description of the modification made to the PDSS model. The performances of the PDSS running on a standalone PC and on the super computer are compared. Future research direction of utilizing parallel computing in the power distribution system simulation is also addressed.

  11. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

    PubMed Central

    Mohammadiarani, Hossein; Vashisth, Harish

    2016-01-01

    The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID

  12. Computational field simulation of temporally deforming geometries

    SciTech Connect

    Boyalakuntla, K.; Soni, B.K.; Thornburg, H.J.

    1996-12-31

    A NURBS based moving grid generation technique is presented to simulate temporally deforming geometries. Grid generation for a complex configuration can be a time consuming process and temporally varying geometries necessitate the regeneration of such a grid for every time step. The Non Uniform Rational B Spline (NURBS) based control point information is used for geometry description. The parametric definition of the NURBS is utilized in the development of the methodology to generate well distributed grid in a timely manner. The numerical simulation involving temporally deforming geometry is accomplished by appropriately linking to a unsteady, multi-block, thin layer Navier-Stokes solver. The present method greatly reduces CPU requirements for time dependent remeshing, facilitating the simulation of more complex unsteady problems. This current effort is the first step towards multidisciplinary design optimization, which involves coupling aerodynamic heat transfer and structural analysis. Applications include simulation of temporally deforming bodies.

  13. Computer simulation of water reclamation processors

    NASA Technical Reports Server (NTRS)

    Fisher, John W.; Hightower, T. M.; Flynn, Michael T.

    1991-01-01

    The development of detailed simulation models of water reclamation processors based on the ASPEN PLUS simulation program is discussed. Individual models have been developed for vapor compression distillation, vapor phase catalytic ammonia removal, and supercritical water oxidation. These models are used for predicting the process behavior. Particular attention is given to methodology which is used to complete this work, and the insights which are gained by this type of model development.

  14. Estimating computer communication network performance using network simulations

    SciTech Connect

    Garcia, A.B.

    1985-01-01

    A generalized queuing model simulation of store-and-forward computer communication networks is developed and implemented using Simulation Language for Alternative Modeling (SLAM). A baseline simulation model is validated by comparison with published analytic models. The baseline model is expanded to include an ACK/NAK data link protocol, four-level message precedence, finite queues, and a response traffic scenario. Network performance, as indicated by average message delay and message throughput, is estimated using the simulation model.

  15. Computer simulation results of attitude estimation of earth orbiting satellites

    NASA Technical Reports Server (NTRS)

    Kou, S. R.

    1976-01-01

    Computer simulation results of attitude estimation of Earth-orbiting satellites (including Space Telescope) subjected to environmental disturbances and noises are presented. Decomposed linear recursive filter and Kalman filter were used as estimation tools. Six programs were developed for this simulation, and all were written in the basic language and were run on HP 9830A and HP 9866A computers. Simulation results show that a decomposed linear recursive filter is accurate in estimation and fast in response time. Furthermore, for higher order systems, this filter has computational advantages (i.e., less integration errors and roundoff errors) over a Kalman filter.

  16. Computer Simulation Performed for Columbia Project Cooling System

    NASA Technical Reports Server (NTRS)

    Ahmad, Jasim

    2005-01-01

    This demo shows a high-fidelity simulation of the air flow in the main computer room housing the Columbia (10,024 intel titanium processors) system. The simulation asseses the performance of the cooling system and identified deficiencies, and recommended modifications to eliminate them. It used two in house software packages on NAS supercomputers: Chimera Grid tools to generate a geometric model of the computer room, OVERFLOW-2 code for fluid and thermal simulation. This state-of-the-art technology can be easily extended to provide a general capability for air flow analyses on any modern computer room. Columbia_CFD_black.tiff

  17. Avoiding pitfalls in simulating real-time computer systems

    NASA Technical Reports Server (NTRS)

    Smith, R. S.

    1984-01-01

    The software simulation of a computer target system on a computer host system, known as an interpretive computer simulator (ICS), functionally models and implements the action of the target hardware. For an ICS to function as efficiently as possible and to avoid certain pitfalls in designing an ICS, it is important that the details of the hardware architectural design of both the target and the host computers be known. This paper discusses both host selection considerations and ICS design features that, without proper consideration, could make the resulting ICS too slow to use or too costly to maintain and expand.

  18. Icing simulation: A survey of computer models and experimental facilities

    NASA Technical Reports Server (NTRS)

    Potapczuk, M. G.; Reinmann, J. J.

    1991-01-01

    A survey of the current methods for simulation of the response of an aircraft or aircraft subsystem to an icing encounter is presented. The topics discussed include a computer code modeling of aircraft icing and performance degradation, an evaluation of experimental facility simulation capabilities, and ice protection system evaluation tests in simulated icing conditions. Current research focussed on upgrading simulation fidelity of both experimental and computational methods is discussed. The need for increased understanding of the physical processes governing ice accretion, ice shedding, and iced airfoil aerodynamics is examined.

  19. Two inviscid computational simulations of separated flow about airfoils

    NASA Technical Reports Server (NTRS)

    Barnwell, R. W.

    1976-01-01

    Two inviscid computational simulations of separated flow about airfoils are described. The basic computational method is the line relaxation finite-difference method. Viscous separation is approximated with inviscid free-streamline separation. The point of separation is specified, and the pressure in the separation region is calculated. In the first simulation, the empiricism of constant pressure in the separation region is employed. This empiricism is easier to implement with the present method than with singularity methods. In the second simulation, acoustic theory is used to determine the pressure in the separation region. The results of both simulations are compared with experiment.

  20. Computer simulator for a mobile telephone system

    NASA Technical Reports Server (NTRS)

    Schilling, D. L.

    1981-01-01

    A software simulator was developed to assist NASA in the design of the land mobile satellite service. Structured programming techniques were used by developing the algorithm using an ALCOL-like pseudo language and then encoding the algorithm into FORTRAN 4. The basic input data to the system is a sine wave signal although future plans call for actual sampled voice as the input signal. The simulator is capable of studying all the possible combinations of types and modes of calls through the use of five communication scenarios: single hop systems; double hop, signal gateway system; double hop, double gateway system; mobile to wireline system; and wireline to mobile system. The transmitter, fading channel, and interference source simulation are also discussed.

  1. Biocellion: accelerating computer simulation of multicellular biological system models

    PubMed Central

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

    2014-01-01

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

  2. Computer simulation of bounded plasma systems

    SciTech Connect

    Lawson, W.S.

    1987-03-05

    The physical and numerical problems of kinetic simulation of a bounded electrostatic plasma system in one planar dimension are examined, and solutions to them are presented. These problems include particle absorption, reflection and emission at boundaries, the solution of Poisson's equation under non-periodic boundary conditions, and the treatment of an external circuit connecting the boundaries. Some comments are also made regarding the problems of higher dimensions. The methods which are described here are implemented in a code named PDW1, which is available from Professor C.K. Birdsall, Plasma Theory and Simulation Group, Cory Hall, University of California, Berkeley, CA 94720.

  3. Computer Simulations in the Science Classroom.

    ERIC Educational Resources Information Center

    Richards, John; And Others

    1992-01-01

    Explorer is an interactive environment based on a constructivist epistemology of learning that integrates animated computer models with analytic capabilities for learning science. The system includes graphs, a spreadsheet, scripting, and interactive tools. Two examples involving the dynamics of colliding objects and electric circuits illustrate…

  4. Computer Simulation of Electric Field Lines.

    ERIC Educational Resources Information Center

    Kirkup, L.

    1985-01-01

    Describes a computer program which plots electric field line plots. Includes program listing, sample diagrams produced on a BBC model B microcomputer (which could be produced on other microcomputers by modifying the program), and a discussion of the properties of field lines. (JN)

  5. Using Computer Simulations to Integrate Learning.

    ERIC Educational Resources Information Center

    Liao, Thomas T.

    1983-01-01

    Describes the primary design criteria and the classroom activities involved in "The Yellow Light Problem," a minicourse on decision making in the secondary school Mathematics, Engineering and Science Achievement (MESA) program in California. Activities include lectures, discussions, science and math labs, computer labs, and development of…

  6. Numerical simulation of supersonic wake flow with parallel computers

    SciTech Connect

    Wong, C.C.; Soetrisno, M.

    1995-07-01

    Simulating a supersonic wake flow field behind a conical body is a computing intensive task. It requires a large number of computational cells to capture the dominant flow physics and a robust numerical algorithm to obtain a reliable solution. High performance parallel computers with unique distributed processing and data storage capability can provide this need. They have larger computational memory and faster computing time than conventional vector computers. We apply the PINCA Navier-Stokes code to simulate a wind-tunnel supersonic wake experiment on Intel Gamma, Intel Paragon, and IBM SP2 parallel computers. These simulations are performed to study the mean flow in the near wake region of a sharp, 7-degree half-angle, adiabatic cone at Mach number 4.3 and freestream Reynolds number of 40,600. Overall the numerical solutions capture the general features of the hypersonic laminar wake flow and compare favorably with the wind tunnel data. With a refined and clustering grid distribution in the recirculation zone, the calculated location of the rear stagnation point is consistent with the 2D axisymmetric and 3D experiments. In this study, we also demonstrate the importance of having a large local memory capacity within a computer node and the effective utilization of the number of computer nodes to achieve good parallel performance when simulating a complex, large-scale wake flow problem.

  7. Computer simulation of on-orbit manned maneuvering unit operations

    NASA Technical Reports Server (NTRS)

    Stuart, G. M.; Garcia, K. D.

    1986-01-01

    Simulation of spacecraft on-orbit operations is discussed in reference to Martin Marietta's Space Operations Simulation laboratory's use of computer software models to drive a six-degree-of-freedom moving base carriage and two target gimbal systems. In particular, key simulation issues and related computer software models associated with providing real-time, man-in-the-loop simulations of the Manned Maneuvering Unit (MMU) are addressed with special attention given to how effectively these models and motion systems simulate the MMU's actual on-orbit operations. The weightless effects of the space environment require the development of entirely new devices for locomotion. Since the access to space is very limited, it is necessary to design, build, and test these new devices within the physical constraints of earth using simulators. The simulation method that is discussed here is the technique of using computer software models to drive a Moving Base Carriage (MBC) that is capable of providing simultaneous six-degree-of-freedom motions. This method, utilized at Martin Marietta's Space Operations Simulation (SOS) laboratory, provides the ability to simulate the operation of manned spacecraft, provides the pilot with proper three-dimensional visual cues, and allows training of on-orbit operations. The purpose here is to discuss significant MMU simulation issues, the related models that were developed in response to these issues and how effectively these models simulate the MMU's actual on-orbiter operations.

  8. Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations.

    PubMed

    Ghaemi, Zhaleh; Alberga, Domenico; Carloni, Paolo; Laio, Alessandro; Lattanzi, Gianluca

    2016-08-01

    The ability of a drug to cross the intestine-blood barrier is a key quantity for drug design and employment and is normally quantified by the permeability coefficient P, often evaluated in the so-called Caco-2 assay. This assay is based on measuring the initial growth rate of the concentration of the drug beyond the cellular barrier but not its steady-state flux through the membrane. This might lead to confusion since, in the case of lipophilic drugs, the initial slope is strongly affected by the retention of the drug in the membrane. This effect is well known but seldom considered in the assay. Here, we exploit all-atoms molecular dynamics and bias exchange metadynamics to calculate the concentration of two lipophilic drugs across a model membrane as a function of time. This allows estimating both the steady-state flux and the initial slope of the concentration growth and comparing Caco-2 and steady-state estimates of P. We show that our computational procedure is able to reproduce the experimental values, although these may differ from the permeability coefficients by orders of magnitude. Our findings are generalized by a simplified one-dimensional model of the permeation process that may act as a roadmap to assess which measure of membrane permeability would be more appropriate and, consequently, whether retention corrections should be included in estimates based on Caco-2 assays. PMID:27392273

  9. Advanced Simulation and Computing Business Plan

    SciTech Connect

    Rummel, E.

    2015-07-09

    To maintain a credible nuclear weapons program, the National Nuclear Security Administration’s (NNSA’s) Office of Defense Programs (DP) needs to make certain that the capabilities, tools, and expert staff are in place and are able to deliver validated assessments. This requires a complete and robust simulation environment backed by an experimental program to test ASC Program models. This ASC Business Plan document encapsulates a complex set of elements, each of which is essential to the success of the simulation component of the Nuclear Security Enterprise. The ASC Business Plan addresses the hiring, mentoring, and retaining of programmatic technical staff responsible for building the simulation tools of the nuclear security complex. The ASC Business Plan describes how the ASC Program engages with industry partners—partners upon whom the ASC Program relies on for today’s and tomorrow’s high performance architectures. Each piece in this chain is essential to assure policymakers, who must make decisions based on the results of simulations, that they are receiving all the actionable information they need.

  10. Multidimensional computer simulation of Stirling cycle engines

    NASA Astrophysics Data System (ADS)

    Hall, Charles A.; Porsching, Thomas A.

    1992-07-01

    This report summarizes the activities performed under NASA-Grant NAG3-1097 during 1991. During that period, work centered on the following tasks: (1) to investigate more effective solvers for ALGAE; (2) to modify the plotting package for ALGAE; and (3) to validate ALGAE by simulating oscillating flow problems similar to those studied by Kurzweg and Ibrahim.

  11. Multidimensional computer simulation of Stirling cycle engines

    NASA Technical Reports Server (NTRS)

    Hall, Charles A.; Porsching, Thomas A.

    1992-01-01

    This report summarizes the activities performed under NASA-Grant NAG3-1097 during 1991. During that period, work centered on the following tasks: (1) to investigate more effective solvers for ALGAE; (2) to modify the plotting package for ALGAE; and (3) to validate ALGAE by simulating oscillating flow problems similar to those studied by Kurzweg and Ibrahim.

  12. Student Ecosystems Problem Solving Using Computer Simulation.

    ERIC Educational Resources Information Center

    Howse, Melissa A.

    The purpose of this study was to determine the procedural knowledge brought to, and created within, a pond ecology simulation by students. Environmental Decision Making (EDM) is an ecosystems modeling tool that allows users to pose their own problems and seek satisfying solutions. Of specific interest was the performance of biology majors who had…

  13. Process Training Derived from a Computer Simulation Theory

    ERIC Educational Resources Information Center

    Holzman, Thomas G.; And Others

    1976-01-01

    Discusses a study which investigated whether a computer simulation model could suggest subroutines that were instructable and whether instruction on these subroutines could facilitate subjects' solutions to the problem task. (JM)

  14. Development and Formative Evaluation of Computer Simulated College Chemistry Experiments.

    ERIC Educational Resources Information Center

    Cavin, Claudia S.; Cavin, E. D.

    1978-01-01

    This article describes the design, preparation, and initial evaluation of a set of computer-simulated chemistry experiments. The experiments entailed the use of an atomic emission spectroscope and a single-beam visible absorption spectrophometer. (Author/IRT)

  15. Computer Simulations as a Teaching Tool in Community Colleges

    ERIC Educational Resources Information Center

    Grimm, Floyd M., III

    1978-01-01

    Describes the implementation of a computer assisted instruction program at Harford Community College. Eight different biology simulation programs are used covering topics in ecology, genetics, biochemistry, and sociobiology. (MA)

  16. MINEXP, A Computer-Simulated Mineral Exploration Program

    ERIC Educational Resources Information Center

    Smith, Michael J.; And Others

    1978-01-01

    This computer simulation is designed to put students into a realistic decision making situation in mineral exploration. This program can be used with different exploration situations such as ore deposits, petroleum, ground water, etc. (MR)

  17. Issues in Computer Simulation in Military Maintenance Training

    ERIC Educational Resources Information Center

    Brock, John F.

    1978-01-01

    This article discusses the state of computer-based simulation, reviews the early phases of ISD, suggests that current ISD approaches are missing critical inputs, and proposes a research and development program. (Author)

  18. An Exercise in Biometrical Genetics Based on a Computer Simulation.

    ERIC Educational Resources Information Center

    Murphy, P. J.

    1983-01-01

    Describes an exercise in biometrical genetics based on the noninteractive use of a computer simulation of a wheat hydridization program. Advantages of using the material in this way are also discussed. (Author/JN)

  19. Understanding Islamist political violence through computational social simulation

    SciTech Connect

    Watkins, Jennifer H; Mackerrow, Edward P; Patelli, Paolo G; Eberhardt, Ariane; Stradling, Seth G

    2008-01-01

    Understanding the process that enables political violence is of great value in reducing the future demand for and support of violent opposition groups. Methods are needed that allow alternative scenarios and counterfactuals to be scientifically researched. Computational social simulation shows promise in developing 'computer experiments' that would be unfeasible or unethical in the real world. Additionally, the process of modeling and simulation reveals and challenges assumptions that may not be noted in theories, exposes areas where data is not available, and provides a rigorous, repeatable, and transparent framework for analyzing the complex dynamics of political violence. This paper demonstrates the computational modeling process using two simulation techniques: system dynamics and agent-based modeling. The benefits and drawbacks of both techniques are discussed. In developing these social simulations, we discovered that the social science concepts and theories needed to accurately simulate the associated psychological and social phenomena were lacking.

  20. GATE Monte Carlo simulation in a cloud computing environment

    NASA Astrophysics Data System (ADS)

    Rowedder, Blake Austin

    The GEANT4-based GATE is a unique and powerful Monte Carlo (MC) platform, which provides a single code library allowing the simulation of specific medical physics applications, e.g. PET, SPECT, CT, radiotherapy, and hadron therapy. However, this rigorous yet flexible platform is used only sparingly in the clinic due to its lengthy calculation time. By accessing the powerful computational resources of a cloud computing environment, GATE's runtime can be significantly reduced to clinically feasible levels without the sizable investment of a local high performance cluster. This study investigated a reliable and efficient execution of GATE MC simulations using a commercial cloud computing services. Amazon's Elastic Compute Cloud was used to launch several nodes equipped with GATE. Job data was initially broken up on the local computer, then uploaded to the worker nodes on the cloud. The results were automatically downloaded and aggregated on the local computer for display and analysis. Five simulations were repeated for every cluster size between 1 and 20 nodes. Ultimately, increasing cluster size resulted in a decrease in calculation time that could be expressed with an inverse power model. Comparing the benchmark results to the published values and error margins indicated that the simulation results were not affected by the cluster size and thus that integrity of a calculation is preserved in a cloud computing environment. The runtime of a 53 minute long simulation was decreased to 3.11 minutes when run on a 20-node cluster. The ability to improve the speed of simulation suggests that fast MC simulations are viable for imaging and radiotherapy applications. With high power computing continuing to lower in price and accessibility, implementing Monte Carlo techniques with cloud computing for clinical applications will continue to become more attractive.

  1. Launch Site Computer Simulation and its Application to Processes

    NASA Technical Reports Server (NTRS)

    Sham, Michael D.

    1995-01-01

    This paper provides an overview of computer simulation, the Lockheed developed STS Processing Model, and the application of computer simulation to a wide range of processes. The STS Processing Model is an icon driven model that uses commercial off the shelf software and a Macintosh personal computer. While it usually takes one year to process and launch 8 space shuttles, with the STS Processing Model this process is computer simulated in about 5 minutes. Facilities, orbiters, or ground support equipment can be added or deleted and the impact on launch rate, facility utilization, or other factors measured as desired. This same computer simulation technology can be used to simulate manufacturing, engineering, commercial, or business processes. The technology does not require an 'army' of software engineers to develop and operate, but instead can be used by the layman with only a minimal amount of training. Instead of making changes to a process and realizing the results after the fact, with computer simulation, changes can be made and processes perfected before they are implemented.

  2. Computer Simulated Growth of Icosahedral Glass

    NASA Astrophysics Data System (ADS)

    Leino, Y. A. J.; Salomaa, M. M.

    1990-01-01

    One possible model for materials displaying classically forbidden symmetry properties (apart from perfect quasicrystals) is the icosahedral glass model. We simulate the random growth of two types of two-dimensional icosahedral glasses consisting of the Penrose tiles, First we restrict the growth with the arrow rules, then we let the structure develop totally freely. The diffraction patterns have a clear five-fold symmetry in both cases. The diffraction peak intensities do not differ, but shapes of the central peaks vary depending on whether the arrow rules are imposed or not. Finally, we show that the half-width of the central peak decreases when the size of the simulation increases until a finite disorder-limited value is achieved. This phenomenon is in agreement with the behaviour of physical quasicrystallites and in contradiction with perfect mathematical quasicrystals which have Bragg peaks of zero width.

  3. Computational Aerothermodynamic Simulation Issues on Unstructured Grids

    NASA Technical Reports Server (NTRS)

    Gnoffo, Peter A.; White, Jeffery A.

    2004-01-01

    The synthesis of physical models for gas chemistry and turbulence from the structured grid codes LAURA and VULCAN into the unstructured grid code FUN3D is described. A directionally Symmetric, Total Variation Diminishing (STVD) algorithm and an entropy fix (eigenvalue limiter) keyed to local cell Reynolds number are introduced to improve solution quality for hypersonic aeroheating applications. A simple grid-adaptation procedure is incorporated within the flow solver. Simulations of flow over an ellipsoid (perfect gas, inviscid), Shuttle Orbiter (viscous, chemical nonequilibrium) and comparisons to the structured grid solvers LAURA (cylinder, Shuttle Orbiter) and VULCAN (flat plate) are presented to show current capabilities. The quality of heating in 3D stagnation regions is very sensitive to algorithm options in general, high aspect ratio tetrahedral elements complicate the simulation of high Reynolds number, viscous flow as compared to locally structured meshes aligned with the flow.

  4. Computer simulation of a geomagnetic substorm

    NASA Technical Reports Server (NTRS)

    Lyon, J. G.; Brecht, S. H.; Huba, J. D.; Fedder, J. A.; Palmadesso, P. J.

    1981-01-01

    A global two-dimensional simulation of a substormlike process occurring in earth's magnetosphere is presented. The results are consistent with an empirical substorm model - the neutral-line model. Specifically, the introduction of a southward interplanetary magnetic field forms an open magnetosphere. Subsequently, a substorm neutral line forms at about 15 earth radii or closer in the magnetotail, and plasma sheet thinning and plasma acceleration occur. Eventually the substorm neutral line moves tailward toward its presubstorm position.

  5. Computer simulation of surface and film processes

    NASA Technical Reports Server (NTRS)

    Tiller, W. A.

    1981-01-01

    A molecular dynamics technique based upon Lennard-Jones type pair interactions is used to investigate time-dependent as well as equilibrium properties. The case study deals with systems containing Si and O atoms. In this case a more involved potential energy function (PEF) is employed and the system is simulated via a Monte-Carlo procedure. This furnishes the equilibrium properties of the system at its interfaces and surfaces as well as in the bulk.

  6. Evaluation of a Computer Simulation in a Therapeutics Case Discussion.

    ERIC Educational Resources Information Center

    Kinkade, Raenel E.; And Others

    1995-01-01

    A computer program was used to simulate a case presentation in pharmacotherapeutics. Students (n=24) used their knowledge of the disease (glaucoma) and various topical agents on the computer program's formulary to "treat" the patient. Comparison of results with a control group found the method as effective as traditional case presentation on…

  7. Use of Computer Simulations in Microbial and Molecular Genetics.

    ERIC Educational Resources Information Center

    Wood, Peter

    1984-01-01

    Describes five computer programs: four simulations of genetic and physical mapping experiments and one interactive learning program on the genetic coding mechanism. The programs were originally written in BASIC for the VAX-11/750 V.3. mainframe computer and have been translated into Applesoft BASIC for Apple IIe microcomputers. (JN)

  8. COFLO: A Computer Aid for Teaching Ecological Simulation.

    ERIC Educational Resources Information Center

    Le vow, Roy B.

    A computer-assisted course was designed to provide students with an understanding of modeling and simulation techniques in quantitiative ecology. It deals with continuous systems and has two segments. One develops mathematical and computer tools, beginning with abstract systems and their relation to physical systems. Modeling principles are next…

  9. Coached, Interactive Computer Simulations: A New Technology for Training.

    ERIC Educational Resources Information Center

    Hummel, Thomas J.

    This paper provides an overview of a prototype simulation-centered intelligent computer-based training (CBT) system--implemented using expert system technology--which provides: (1) an environment in which trainees can learn and practice complex skills; (2) a computer-based coach or mentor to critique performance, suggest improvements, and provide…

  10. Frontiers in the Teaching of Physiology. Computer Literacy and Simulation.

    ERIC Educational Resources Information Center

    Tidball, Charles S., Ed.; Shelesnyak, M. C., Ed.

    Provided is a collection of papers on computer literacy and simulation originally published in The Physiology Teacher, supplemented by additional papers and a glossary of terms relevant to the field. The 12 papers are presented in five sections. An affirmation of conventional physiology laboratory exercises, coping with computer terminology, and…

  11. Generating dynamic simulations of movement using computed muscle control.

    PubMed

    Thelen, Darryl G; Anderson, Frank C; Delp, Scott L

    2003-03-01

    Computation of muscle excitation patterns that produce coordinated movements of muscle-actuated dynamic models is an important and challenging problem. Using dynamic optimization to compute excitation patterns comes at a large computational cost, which has limited the use of muscle-actuated simulations. This paper introduces a new algorithm, which we call computed muscle control, that uses static optimization along with feedforward and feedback controls to drive the kinematic trajectory of a musculoskeletal model toward a set of desired kinematics. We illustrate the algorithm by computing a set of muscle excitations that drive a 30-muscle, 3-degree-of-freedom model of pedaling to track measured pedaling kinematics and forces. Only 10 min of computer time were required to compute muscle excitations that reproduced the measured pedaling dynamics, which is over two orders of magnitude faster than conventional dynamic optimization techniques. Simulated kinematics were within 1 degrees of experimental values, simulated pedal forces were within one standard deviation of measured pedal forces for nearly all of the crank cycle, and computed muscle excitations were similar in timing to measured electromyographic patterns. The speed and accuracy of this new algorithm improves the feasibility of using detailed musculoskeletal models to simulate and analyze movement. PMID:12594980

  12. Teaching Macroeconomics with a Computer Simulation. Final Report.

    ERIC Educational Resources Information Center

    Dolbear, F. Trenery, Jr.

    The study of macroeconomics--the determination and control of aggregative variables such as gross national product, unemployment and inflation--may be facilitated by the use of a computer simulation policy game. An aggregative model of the economy was constructed and programed for a computer and (hypothetical) historical data were generated. The…

  13. The Use of Computer Simulations in High School Curricula.

    ERIC Educational Resources Information Center

    Visich, Marian, Jr.; Braun, Ludwig

    The Huntington Computer Project has developed 17 simulation games which can be used for instructional purposes in high schools. These games were designed to run on digital computers and to deal with material from either biology, physics, or social studies. Distribution was achieved through the Digital Equipment Corporation, which disseminated…

  14. A computer simulator for development of engineering system design methodologies

    NASA Technical Reports Server (NTRS)

    Padula, S. L.; Sobieszczanski-Sobieski, J.

    1987-01-01

    A computer program designed to simulate and improve engineering system design methodology is described. The simulator mimics the qualitative behavior and data couplings occurring among the subsystems of a complex engineering system. It eliminates the engineering analyses in the subsystems by replacing them with judiciously chosen analytical functions. With the cost of analysis eliminated, the simulator is used for experimentation with a large variety of candidate algorithms for multilevel design optimization to choose the best ones for the actual application. Thus, the simulator serves as a development tool for multilevel design optimization strategy. The simulator concept, implementation, and status are described and illustrated with examples.

  15. A New Boundary Condition for Computer Simulations of Interfacial Systems

    SciTech Connect

    Wong, Ka-Yiu; Pettitt, Bernard M.; Montgomery, B.

    2000-08-18

    A new boundary condition for computer simulations of interfacial systems is presented. The simulation box used in this boundary condition is the asymmetric unit of space group Pb, and it contains only one interface. Compared to the simulation box using common periodic boundary conditions which contains two interfaces, the number of particles in the simulation is reduced by half. This boundary condition was tested against common periodic boundary conditions in molecular dynamic simulations of liquid water interacting with hydroxylated silica surfaces. It yielded results essentially identical to periodic boundary condition and consumed less CPU time for comparable statistics.

  16. A new boundary condition for computer simulations of interfacial systems

    NASA Astrophysics Data System (ADS)

    Wong, Ka-Yiu; Pettitt, B. Montgomery

    2000-08-01

    A new boundary condition for computer simulations of interfacial systems is presented. The simulation box used in this boundary condition is the asymmetric unit of space group Pb, and it contains only one interface. Compared to the simulation box using common periodic boundary conditions which contains two interfaces, the number of particles in the simulation is reduced by half. This boundary condition was tested against common periodic boundary conditions in molecular dynamic simulations of liquid water interacting with hydroxylated silica surfaces. It yielded results essentially identical to periodic boundary condition and consumed less CPU time for comparable statistics.

  17. Developing Computer-Based Interactive Video Simulations on Questioning Strategies.

    ERIC Educational Resources Information Center

    Rogers, Randall; Rieff, Judith

    1989-01-01

    This article presents a rationale for development and implementation of computer based interactive videotape (CBIV) in preservice teacher education; identifies advantages of CBIV simulations over other practice exercises; describes economical production procedures; discusses implications and importance of these simulations; and makes…

  18. Computer Simulation of Incomplete-Data Interpretation Exercise.

    ERIC Educational Resources Information Center

    Robertson, Douglas Frederick

    1987-01-01

    Described is a computer simulation that was used to help general education students enrolled in a large introductory geology course. The purpose of the simulation is to learn to interpret incomplete data. Students design a plan to collect bathymetric data for an area of the ocean. Procedures used by the students and instructor are included.…

  19. Learner Perceptions of Realism and Magic in Computer Simulations.

    ERIC Educational Resources Information Center

    Hennessy, Sara; O'Shea, Tim

    1993-01-01

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

  20. Preliminary Evaluation of a Computer Simulation of Long Cane Use.

    ERIC Educational Resources Information Center

    Chubon, Robert A.; Keith, Ashley D.

    1989-01-01

    Developed and evaluated long cane mobility computer simulation as visual rehabilitation training device and research tool in graduate students assigned to instruction (BI) (N=10) or enhanced instruction (EI) (N=9). Found higher percentage of EI students completed simulation task. Concluded that students registered positive understanding changes,…

  1. Enhancing Computer Science Education with a Wireless Intelligent Simulation Environment

    ERIC Educational Resources Information Center

    Cook, Diane J.; Huber, Manfred; Yerraballi, Ramesh; Holder, Lawrence B.

    2004-01-01

    The goal of this project is to develop a unique simulation environment that can be used to increase students' interest and expertise in Computer Science curriculum. Hands-on experience with physical or simulated equipment is an essential ingredient for learning, but many approaches to training develop a separate piece of equipment or software for…

  2. Plant Closings and Capital Flight: A Computer-Assisted Simulation.

    ERIC Educational Resources Information Center

    Warner, Stanley; Breitbart, Myrna M.

    1989-01-01

    A course at Hampshire College was designed to simulate the decision-making environment in which constituencies in a medium-sized city would respond to the closing and relocation of a major corporate plant. The project, constructed as a role simulation with a computer component, is described. (MLW)

  3. Computer Simulation of Laboratory Experiments: An Unrealized Potential.

    ERIC Educational Resources Information Center

    Magin, D. J.; Reizes, J. A.

    1990-01-01

    Discussion of the use of computer simulation for laboratory experiments in undergraduate engineering education focuses on work at the University of New South Wales in the instructional design and software development of a package simulating a heat exchange device. The importance of integrating theory, design, and experimentation is also discussed.…

  4. Design Model for Learner-Centered, Computer-Based Simulations.

    ERIC Educational Resources Information Center

    Hawley, Chandra L.; Duffy, Thomas M.

    This paper presents a model for designing computer-based simulation environments within a constructivist framework for the K-12 school setting. The following primary criteria for the development of simulations are proposed: (1) the problem needs to be authentic; (2) the cognitive demand in learning should be authentic; (3) scaffolding supports a…

  5. Effectiveness of an Endodontic Diagnosis Computer Simulation Program.

    ERIC Educational Resources Information Center

    Fouad, Ashraf F.; Burleson, Joseph A.

    1997-01-01

    Effectiveness of a computer simulation to teach endodontic diagnosis was assessed using three groups (n=34,32,24) of dental students. All were lectured on diagnosis, pathology, and radiographic interpretation. One group then used the simulation, another had a seminar on the same material, and the third group had no further instruction. Results…

  6. The Design, Development, and Evaluation of an Evaluative Computer Simulation.

    ERIC Educational Resources Information Center

    Ehrlich, Lisa R.

    This paper discusses evaluation design considerations for a computer based evaluation simulation developed at the University of Iowa College of Medicine in Cardiology to assess the diagnostic skills of primary care physicians and medical students. The simulation developed allows for the assessment of diagnostic skills of physicians in the…

  7. Computer Simulation of the Population Growth (Schizosaccharomyces Pombe) Experiment.

    ERIC Educational Resources Information Center

    Daley, Michael; Hillier, Douglas

    1981-01-01

    Describes a computer program (available from authors) developed to simulate "Growth of a Population (Yeast) Experiment." Students actively revise the counting techniques with realistically simulated haemocytometer or eye-piece grid and are reminded of the necessary dilution technique. Program can be modified to introduce such variables as…

  8. Computer simulation program is adaptable to industrial processes

    NASA Technical Reports Server (NTRS)

    Schultz, F. E.

    1966-01-01

    The Reaction kinetics ablation program /REKAP/, developed to simulate ablation of various materials, provides mathematical formulations for computer programs which can simulate certain industrial processes. The programs are based on the use of nonsymmetrical difference equations that are employed to solve complex partial differential equation systems.

  9. Investigating the Effectiveness of Computer Simulations for Chemistry Learning

    ERIC Educational Resources Information Center

    Plass, Jan L.; Milne, Catherine; Homer, Bruce D.; Schwartz, Ruth N.; Hayward, Elizabeth O.; Jordan, Trace; Verkuilen, Jay; Ng, Florrie; Wang, Yan; Barrientos, Juan

    2012-01-01

    Are well-designed computer simulations an effective tool to support student understanding of complex concepts in chemistry when integrated into high school science classrooms? We investigated scaling up the use of a sequence of simulations of kinetic molecular theory and associated topics of diffusion, gas laws, and phase change, which we designed…

  10. Simulation of Robot Kinematics Using Interactive Computer Graphics.

    ERIC Educational Resources Information Center

    Leu, M. C.; Mahajan, R.

    1984-01-01

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

  11. Computer Models Simulate Fine Particle Dispersion

    NASA Technical Reports Server (NTRS)

    2010-01-01

    Through a NASA Seed Fund partnership with DEM Solutions Inc., of Lebanon, New Hampshire, scientists at Kennedy Space Center refined existing software to study the electrostatic phenomena of granular and bulk materials as they apply to planetary surfaces. The software, EDEM, allows users to import particles and obtain accurate representations of their shapes for modeling purposes, such as simulating bulk solids behavior, and was enhanced to be able to more accurately model fine, abrasive, cohesive particles. These new EDEM capabilities can be applied in many industries unrelated to space exploration and have been adopted by several prominent U.S. companies, including John Deere, Pfizer, and Procter & Gamble.

  12. Computer simulator for training operators of thermal cameras

    NASA Astrophysics Data System (ADS)

    Chrzanowski, Krzysztof; Krupski, Marcin

    2004-08-01

    A PC-based image generator SIMTERM developed for training operators of non-airborne military thermal imaging systems is presented in this paper. SIMTERM allows its users to generate images closely resembling thermal images of many military type targets at different scenarios obtained with the simulated thermal camera. High fidelity of simulation was achieved due to use of measurable parameters of thermal camera as input data. Two modified versions of this computer simulator developed for designers and test teams are presented, too.

  13. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    PubMed Central

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  14. All-atom homology model of the Escherichia coli 30S ribosomal subunit.

    PubMed

    Tung, Chang-Shung; Joseph, Simpson; Sanbonmatsu, Kevin Y

    2002-10-01

    Understanding the structural basis of ribosomal function requires close comparison between biochemical and structural data. Although a large amount of biochemical data are available for the Escherichia coli ribosome, the structure has not been solved to atomic resolution. Using a new RNA homology procedure, we have modeled the all-atom structure of the E. coli 30S ribosomal subunit. We find that the tertiary structure of the ribosome core, including the A-, P- and E-sites, is highly conserved. The hypervariable regions in our structure, which differ from the structure of the 30S ribosomal subunit from Thermus thermophilus, are consistent with the cryo-EM map of the E. coli ribosome. PMID:12244297

  15. All-atomic generation and noise-quadrature filtering of squeezed vacuum in hot Rb vapor

    NASA Astrophysics Data System (ADS)

    Horrom, Travis; Romanov, Gleb; Novikova, Irina; Mikhailov, Eugeniy E.

    2013-01-01

    With our all-atomic squeezing and filtering setup, we demonstrate control over the noise amplitudes and manipulation of the frequency-dependent squeezing angle of a squeezed vacuum quantum state by passing it through an atomic medium with electromagnetically induced transparency (EIT). We generate low sideband frequency squeezed vacuum using the polarization self-rotation effect in a hot Rb vapor cell, and direct it through a second atomic vapor subject to EIT conditions. We use the frequency-dependent absorption of the EIT window to demonstrate an example of squeeze amplitude attenuation and squeeze angle rotation of the quantum noise quadratures of the squeezed probe. These studies have implications for quantum memory and storage as well as gravitational wave interferometric detectors.

  16. Computer simulation of vasectomy for wolf control

    USGS Publications Warehouse

    Haight, R.G.; Mech, L.D.

    1997-01-01

    Recovering gray wolf (Canis lupus) populations in the Lake Superior region of the United States are prompting state management agencies to consider strategies to control population growth. In addition to wolf removal, vasectomy has been proposed. To predict the population effects of different sterilization and removal strategies, we developed a simulation model of wolf dynamics using simple rules for demography and dispersal. Simulations suggested that the effects of vasectomy and removal in a disjunct population depend largely on the degree of annual immigration. With low immigration, periodic sterilization reduced pup production and resulted in lower rates of territory recolonization. Consequently, average pack size, number of packs, and population size were significantly less than those for an untreated population. Periodically removing a proportion of the population produced roughly the same trends as did sterilization; however, more than twice as many wolves had to be removed than sterilized. With high immigration, periodic sterilization reduced pup production but not territory recolonization and produced only moderate reductions in population size relative to an untreated population. Similar reductions in population size were obtained by periodically removing large numbers of wolves. Our analysis does not address the possible effects of vasectomy on larger wolf populations, but it suggests that the subject should be considered through modeling or field testing.

  17. Advanced computer graphic techniques for laser range finder (LRF) simulation

    NASA Astrophysics Data System (ADS)

    Bedkowski, Janusz; Jankowski, Stanislaw

    2008-11-01

    This paper show an advanced computer graphic techniques for laser range finder (LRF) simulation. The LRF is the common sensor for unmanned ground vehicle, autonomous mobile robot and security applications. The cost of the measurement system is extremely high, therefore the simulation tool is designed. The simulation gives an opportunity to execute algorithm such as the obstacle avoidance[1], slam for robot localization[2], detection of vegetation and water obstacles in surroundings of the robot chassis[3], LRF measurement in crowd of people[1]. The Axis Aligned Bounding Box (AABB) and alternative technique based on CUDA (NVIDIA Compute Unified Device Architecture) is presented.

  18. Computer Simulations of Supercooled Liquids and Glasses

    NASA Astrophysics Data System (ADS)

    Kob, Walter

    Glasses are materials that are ubiquitous in our daily life. We find them in such diverse items as window pans, optical fibers, computer chips, ceramics, all of which are oxide glasses, as well as in food, foams, polymers, gels, which are mainly of organic nature. Roughly speaking glasses are solid materials that have no translational or orientational order on the scale beyond O(10) diameters of the constituent particles (atoms, colloids, …) [1]. Note that these materials are not necessarily homogeneous since, e.g., alkali-glasses such as Na2O-SiO2 show (disordered!) structural features on the length scale of 6-10 Å (compare to the interatomic distance of 1-2 Å) and gels can have structural inhomogeneities that extend up to macroscopic length scales.

  19. Computer simulation of digital signal modulation techniques in satellite communications

    NASA Astrophysics Data System (ADS)

    Carlson, C. D.

    1985-09-01

    Tutorial on digital signal modulation techniques used in satellite communications is presented and includes computer simulation of those digital signal modulation techniques introduced. The purpose is to introduce digital signal modulation techniques and through the use of computer simulation, generate statistics which represent the characteristics of the FFT for the respective signal type. Further, an analysis of the statistics of the FFT's is conducted to determine if there is any relationship between the components of the FFT of the different signals. The statistic used to investigate this possible relationship is the F-distribution. The computer simulation is written and conducted in the FORTRAN programming language. A copy of the program, results of the simulation and the statistical analysis conducted are included in the appendices.

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

    SciTech Connect

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

    2000-04-01

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

  1. Computational Simulations and the Scientific Method

    NASA Technical Reports Server (NTRS)

    Kleb, Bil; Wood, Bill

    2005-01-01

    As scientific simulation software becomes more complicated, the scientific-software implementor's need for component tests from new model developers becomes more crucial. The community's ability to follow the basic premise of the Scientific Method requires independently repeatable experiments, and model innovators are in the best position to create these test fixtures. Scientific software developers also need to quickly judge the value of the new model, i.e., its cost-to-benefit ratio in terms of gains provided by the new model and implementation risks such as cost, time, and quality. This paper asks two questions. The first is whether other scientific software developers would find published component tests useful, and the second is whether model innovators think publishing test fixtures is a feasible approach.

  2. Computer simulations of adsorbed liquid crystal films

    NASA Astrophysics Data System (ADS)

    Wall, Greg D.; Cleaver, Douglas J.

    2003-01-01

    The structures adopted by adsorbed thin films of Gay-Berne particles in the presence of a coexisting vapour phase are investigated by molecular dynamics simulation. The films are adsorbed at a flat substrate which favours planar anchoring, whereas the nematic-vapour interface favours normal alignment. On cooling, a system with a high molecule-substrate interaction strength exhibits substrate-induced planar orientational ordering and considerable stratification is observed in the density profiles. In contrast, a system with weak molecule-substrate coupling adopts a director orientation orthogonal to the substrate plane, owing to the increased influence of the nematic-vapour interface. There are significant differences between the structures adopted at the two interfaces, in contrast with the predictions of density functional treatments of such systems.

  3. Computing abstraction hierarchies by numerical simulation

    SciTech Connect

    Bundy, A.; Giunchiglia, F.; Sebastiani, R.; Walsh, T.

    1996-12-31

    We present a novel method for building ABSTRIPS-style abstraction hierarchies in planning. The aim of this method is to minimize the amount of backtracking between abstraction levels. Previous approaches have determined the criticality of operator preconditions by reasoning about plans directly. Here, we adopt a simpler and faster approach where we use numerical simulation of the planning process. We demonstrate the theoretical advantages of our approach by identifying some simple properties lacking in previous approaches but possessed by our method. We demonstrate the empirical advantages of our approach by a set of four benchmark experiments using the ABTWEAK system. We compare the quality of the abstraction hierarchies generated with those built by the ALPINE and HIGHPOINT algorithms.

  4. Osmosis : a molecular dynamics computer simulation study

    NASA Astrophysics Data System (ADS)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  5. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

    PubMed

    Bell, Jeffrey A; Ho, Kenneth L; Farid, Ramy

    2012-08-01

    All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions. PMID:22868759

  6. The computer scene generation for star simulator hardware-in-the-loop simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Ying; Yu, Hong; Du, Huijie; Lei, Jie

    2011-08-01

    The star sensor simulation system is used to test the star sensor performance on the ground, which is designed for star identification and spacecraft attitude determination of the spacecraft. The computer star scene based on the astronomical star chat is generated for hardware-in-the-loop simulation of the star sensor simulation system using by OpenGL.

  7. Computation simulation of the nonlinear response of suspension bridges

    SciTech Connect

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

    1997-10-01

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

  8. Traffic simulations on parallel computers using domain decomposition techniques

    SciTech Connect

    Hanebutte, U.R.; Tentner, A.M.

    1995-12-31

    Large scale simulations of Intelligent Transportation Systems (ITS) can only be achieved by using the computing resources offered by parallel computing architectures. Domain decomposition techniques are proposed which allow the performance of traffic simulations with the standard simulation package TRAF-NETSIM on a 128 nodes IBM SPx parallel supercomputer as well as on a cluster of SUN workstations. Whilst this particular parallel implementation is based on NETSIM, a microscopic traffic simulation model, the presented strategy is applicable to a broad class of traffic simulations. An outer iteration loop must be introduced in order to converge to a global solution. A performance study that utilizes a scalable test network that consist of square-grids is presented, which addresses the performance penalty introduced by the additional iteration loop.

  9. Numerical simulation of polymer flows: A parallel computing approach

    SciTech Connect

    Aggarwal, R.; Keunings, R.; Roux, F.X.

    1993-12-31

    We present a parallel algorithm for the numerical simulation of viscoelastic fluids on distributed memory computers. The algorithm has been implemented within a general-purpose commercial finite element package used in polymer processing applications. Results obtained on the Intel iPSC/860 computer demonstrate high parallel efficiency in complex flow problems. However, since the computational load is unknown a priori, load balancing is a challenging issue. We have developed an adaptive allocation strategy which dynamically reallocates the work load to the processors based upon the history of the computational procedure. We compare the results obtained with the adaptive and static scheduling schemes.

  10. Large Scale Computer Simulation of Erthocyte Membranes

    NASA Astrophysics Data System (ADS)

    Harvey, Cameron; Revalee, Joel; Laradji, Mohamed

    2007-11-01

    The cell membrane is crucial to the life of the cell. Apart from partitioning the inner and outer environment of the cell, they also act as a support of complex and specialized molecular machinery, important for both the mechanical integrity of the cell, and its multitude of physiological functions. Due to its relative simplicity, the red blood cell has been a favorite experimental prototype for investigations of the structural and functional properties of the cell membrane. The erythrocyte membrane is a composite quasi two-dimensional structure composed essentially of a self-assembled fluid lipid bilayer and a polymerized protein meshwork, referred to as the cytoskeleton or membrane skeleton. In the case of the erythrocyte, the polymer meshwork is mainly composed of spectrin, anchored to the bilayer through specialized proteins. Using a coarse-grained model, recently developed by us, of self-assembled lipid membranes with implicit solvent and using soft-core potentials, we simulated large scale red-blood-cells bilayers with dimensions ˜ 10-1 μm^2, with explicit cytoskeleton. Our aim is to investigate the renormalization of the elastic properties of the bilayer due to the underlying spectrin meshwork.

  11. New Pedagogies on Teaching Science with Computer Simulations

    NASA Astrophysics Data System (ADS)

    Khan, Samia

    2011-06-01

    Teaching science with computer simulations is a complex undertaking. This case study examines how an experienced science teacher taught chemistry using computer simulations and the impact of his teaching on his students. Classroom observations over 3 semesters, teacher interviews, and student surveys were collected. The data was analyzed for (1) patterns in teacher-student-computer interactions, and (2) the outcome of these interactions on student learning. Using Technological Pedagogical Content Knowledge (TPCK) as a theoretical framework, analysis of the data indicates that computer simulations were employed in a unique instructional cycle across 11 topics in the science curriculum and that several teacher-developed heuristics were important to guiding the pedagogical approach. The teacher followed a pattern of "generate-evaluate-modify" (GEM) to teach chemistry, and simulation technology (T) was integrated in every stage of GEM (or T-GEM). Analysis of the student survey suggested that engagement with T-GEM enhanced conceptual understanding of chemistry. The author postulates the affordances of computer simulations and suggests T-GEM and its heuristics as an effective and viable pedagogy for teaching science with technology.

  12. Computer simulation tests of optimized neutron powder diffractometer configurations

    NASA Astrophysics Data System (ADS)

    Cussen, L. D.; Lieutenant, K.

    2016-06-01

    Recent work has developed a new mathematical approach to optimally choose beam elements for constant wavelength neutron powder diffractometers. This article compares Monte Carlo computer simulations of existing instruments with simulations of instruments using configurations chosen using the new approach. The simulations show that large performance improvements over current best practice are possible. The tests here are limited to instruments optimized for samples with a cubic structure which differs from the optimization for triclinic structure samples. A novel primary spectrometer design is discussed and simulation tests show that it performs as expected and allows a single instrument to operate flexibly over a wide range of measurement resolution.

  13. A computer-based simulator of the atmospheric turbulence

    NASA Astrophysics Data System (ADS)

    Konyaev, Petr A.

    2015-11-01

    Computer software for modeling the atmospheric turbulence is developed on the basis of a time-varying random medium simulation algorithm and a split-step Fourier transform method for solving a wave propagation equation. A judicious choice of the simulator parameters, like the velocity of the evolution and motion of the medium, turbulence spectrum and scales, enables different effects of a random medium on the optical wavefront to be simulated. The implementation of the simulation software is shown to be simple and efficient due to parallel programming functions from the MKL Intel ® Parallel Studio libraries.

  14. Executive Summary: Special Section on Credible Computational Fluid Dynamics Simulations

    NASA Technical Reports Server (NTRS)

    Mehta, Unmeel B.

    1998-01-01

    This summary presents the motivation for the Special Section on the credibility of computational fluid dynamics (CFD) simulations, its objective, its background and context, its content, and its major conclusions. Verification and validation (V&V) are the processes for establishing the credibility of CFD simulations. Validation assesses whether correct things are performed and verification assesses whether they are performed correctly. Various aspects of V&V are discussed. Progress is made in verification of simulation models. Considerable effort is still needed for developing a systematic validation method that can assess the credibility of simulated reality.

  15. Usage of a reconfigurable computer to simulate multiparticle systems

    NASA Astrophysics Data System (ADS)

    Fragner, Heinrich

    2007-03-01

    In this article we focus on the implementation of a Lattice Monte Carlo simulation for a generic pair potential within a reconfigurable computing platform. The approach presented was used to simulate a specific soft matter system. We found the performed simulations to be in excellent accordance with previous theoretical and simulation studies. By taking advantage of the shortened processing time, we were also able to find new micro- and macroscopic properties of this system. Furthermore we analyzed analytically the effects of the spatial discretization introduced by the Lattice Monte Carlo algorithm.

  16. Advanced ERS design using computer simulation

    SciTech Connect

    Melhem, G.A.

    1995-12-31

    There are two schools of thought regarding pressure relief design, shortcut/simplified methods and detailed methods. The shortcut/simplified methods are mostly applicable to non-reactive systems. These methods use direct scale-up techniques to obtain a vent size. Little useful information can be obtained for reaction data such as onset temperatures, activation energy, decompositon stoichiometry, etc. In addition, this approach does not readily provide the ability to perform what-if and sensitivity analysis or data that can be used for post-release mitigation design. The detailed approach advocates a more fundamental approach to pressure relief design, especially for reactive systems. First, the reaction chemistry is qualified using small scale experiments and then this data is coupled with fluid dynamics to design the emergency relief system. In addition to vent sizing information, this approach provides insights into process modification and refinement as well as the establishment of a safe operating envelope. This approach provides necessary flow data for vent containment design (if required), structural support, etc. This approach also allows the direct evaluation of design sensitivity to variables such as temperature, pressure, composition, fill level, etc. on vent sizing while the shortcut approach requires an additional experiment per what-if scenario. This approach meets DIERS technology requirements for two-phase flow and vapor/liquid disengagement and exceeds it in many key areas for reacting systems such as stoichiometry estimation for decomposition reactions, non-ideal solutions effects, continuing reactions in piping and vent containment systems, etc. This paper provides an overview of our proposed equation of state based modeling approach and its computer code implementation. Numerous examples and model validations are also described. 42 refs., 23 figs., 9 tabs.

  17. Combining high performance simulation, data acquisition, and graphics display computers

    NASA Technical Reports Server (NTRS)

    Hickman, Robert J.

    1989-01-01

    Issues involved in the continuing development of an advanced simulation complex are discussed. This approach provides the capability to perform the majority of tests on advanced systems, non-destructively. The controlled test environments can be replicated to examine the response of the systems under test to alternative treatments of the system control design, or test the function and qualification of specific hardware. Field tests verify that the elements simulated in the laboratories are sufficient. The digital computer is hosted by a Digital Equipment Corp. MicroVAX computer with an Aptec Computer Systems Model 24 I/O computer performing the communication function. An Applied Dynamics International AD100 performs the high speed simulation computing and an Evans and Sutherland PS350 performs on-line graphics display. A Scientific Computer Systems SCS40 acts as a high performance FORTRAN program processor to support the complex, by generating numerous large files from programs coded in FORTRAN that are required for the real time processing. Four programming languages are involved in the process, FORTRAN, ADSIM, ADRIO, and STAPLE. FORTRAN is employed on the MicroVAX host to initialize and terminate the simulation runs on the system. The generation of the data files on the SCS40 also is performed with FORTRAN programs. ADSIM and ADIRO are used to program the processing elements of the AD100 and its IOCP processor. STAPLE is used to program the Aptec DIP and DIA processors.

  18. Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo

    SciTech Connect

    Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.

    2000-10-10

    Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.

  19. Computers vs. wind tunnels for aerodynamic flow simulations

    NASA Technical Reports Server (NTRS)

    Chapman, D. R.; Mark, H.; Pirtle, M. W.

    1975-01-01

    It is pointed out that in other fields of computational physics, such as ballistics, celestial mechanics, and neutronics, computations have already displaced experiments as the principal means of obtaining dynamic simulations. In the case of aerodynamic investigations, the complexity of the computational work involved in solving the Navier-Stokes equations is the reason that such investigations rely currently mainly on wind-tunnel testing. However, because of inherent limitations of the wind-tunnel approach and economic considerations, it appears that at some time in the future aerodynamic studies will chiefly rely on computational flow data provided by the computer. Taking into account projected development trends, it is estimated that computers with the required capabilities for a solution of the complete viscous, time-dependent Navier-Stokes equations will be available in the mid-1980s.

  20. A computer simulation of aircraft evacuation with fire

    NASA Technical Reports Server (NTRS)

    Middleton, V. E.

    1983-01-01

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

  1. Computer simulation of two-phase flow in nuclear reactors

    SciTech Connect

    Wulff, W.

    1992-09-01

    Two-phase flow models dominate the economic resource requirements for development and use of computer codes for analyzing thermohydraulic transients in nuclear power plants. Six principles are presented on mathematical modeling and selection of numerical methods, along with suggestions on programming and machine selection, all aimed at reducing the cost of analysis. Computer simulation is contrasted with traditional computer calculation. The advantages of run-time interactive access operation in a simulation environment are demonstrated. It is explained that the drift-flux model is better suited for two-phase flow analysis in nuclear reactors than the two-fluid model, because of the latter`s closure problem. The advantage of analytical over numerical integration is demonstrated. Modeling and programming techniques are presented which minimize the number of needed arithmetical and logical operations and thereby increase the simulation speed, while decreasing the cost.

  2. Understanding amyloid fibril nucleation and aβ oligomer/drug interactions from computer simulations.

    PubMed

    Nguyen, Phuong; Derreumaux, Philippe

    2014-02-18

    the critical nucleus size might be on the order of 20 chains under physiological conditions. The transition state might be characterized by a simultaneous change from mixed antiparallel/parallel β-strands with random side-chain packing to the final antiparallel or parallel states with the steric zipper packing of the side chains. Second, we review our current computer-based knowledge of the 3D structures of inhibitors with Aβ42 monomer and oligomers, a prerequisite for developing new drugs against AD. Recent extensive all-atom simulations of Aβ42 dimers with known inhibitors such as the green tea compound epigallocatechin-3-gallate and 1,4-naphthoquinon-2-yl-l-tryptophan provide a spectrum of initial Aβ42/inhibitor structures useful for screening and drug design. We conclude by discussing future directions that may offer opportunities to fully understand nucleation and further AD drug development. PMID:24368046

  3. High performance computing for domestic petroleum reservoir simulation

    SciTech Connect

    Zyvoloski, G.; Auer, L.; Dendy, J.

    1996-06-01

    This is the final report of a two-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory. High-performance computing offers the prospect of greatly increasing the resolution at which petroleum reservoirs can be represented in simulation models. The increases in resolution can be achieved through large increases in computational speed and memory, if machine architecture and numerical methods for solution of the multiphase flow equations can be used to advantage. Perhaps more importantly, the increased speed and size of today`s computers make it possible to add physical processes to simulation codes that heretofore were too expensive in terms of computer time and memory to be practical. These factors combine to allow the development of new, more accurate methods for optimizing petroleum reservoir production.

  4. KU-Band rendezvous radar performance computer simulation model

    NASA Technical Reports Server (NTRS)

    Griffin, J. W.

    1980-01-01

    The preparation of a real time computer simulation model of the KU band rendezvous radar to be integrated into the shuttle mission simulator (SMS), the shuttle engineering simulator (SES), and the shuttle avionics integration laboratory (SAIL) simulator is described. To meet crew training requirements a radar tracking performance model, and a target modeling method were developed. The parent simulation/radar simulation interface requirements, and the method selected to model target scattering properties, including an application of this method to the SPAS spacecraft are described. The radar search and acquisition mode performance model and the radar track mode signal processor model are examined and analyzed. The angle, angle rate, range, and range rate tracking loops are also discussed.

  5. A Real-Time All-Atom Structural Search Engine for Proteins

    PubMed Central

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

  6. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates

    PubMed Central

    Mallajosyula, Sairam S.; Guvench, Olgun; Hatcher, Elizabeth; MacKerell, Alexander D.

    2012-01-01

    Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems both the mono- and di-anionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d) model compound conformational energies which, supplemented with QM geometries, were the main target data for the parametrization. Parameters were validated against crystals of relevant monosaccharide derivatives obtained from the Cambridge Structural Database (CSD) and larger systems, namely inositol-(tri/tetra/penta) phosphates non-covalently bound to the pleckstrin homology (PH) domain and oligomeric chondroitin sulfate in solution and in complex with cathepsin K protein. PMID:22685386

  7. Dataflow computing approach in high-speed digital simulation

    NASA Technical Reports Server (NTRS)

    Ercegovac, M. D.; Karplus, W. J.

    1984-01-01

    New computational tools and methodologies for the digital simulation of continuous systems were explored. Programmability, and cost effective performance in multiprocessor organizations for real time simulation was investigated. Approach is based on functional style languages and data flow computing principles, which allow for the natural representation of parallelism in algorithms and provides a suitable basis for the design of cost effective high performance distributed systems. The objectives of this research are to: (1) perform comparative evaluation of several existing data flow languages and develop an experimental data flow language suitable for real time simulation using multiprocessor systems; (2) investigate the main issues that arise in the architecture and organization of data flow multiprocessors for real time simulation; and (3) develop and apply performance evaluation models in typical applications.

  8. Computational simulation of high temperature metal matrix composite behavior

    NASA Technical Reports Server (NTRS)

    Murthy, Pappu L. N.; Chamis, Christos C.

    1991-01-01

    Computational procedures are described to simulate the thermal and mechanical behavior of high temperature metal matrix composite (HT MMC) in the following four broad areas: (1) behavior of HT MMC from micromechanics to laminate; (2) HT MMC structural response for simple and complex structural components; (3) HT MMC microfracture; and (4) tailoring of HT MMC behavior for optimum specific performance. Representative results from each area are presented to illustrate the effectiveness of the computational simulation procedures. Relevant reports are referenced for extended discussion regarding the specific area.

  9. n-body simulations using message passing parallel computers.

    NASA Astrophysics Data System (ADS)

    Grama, A. Y.; Kumar, V.; Sameh, A.

    The authors present new parallel formulations of the Barnes-Hut method for n-body simulations on message passing computers. These parallel formulations partition the domain efficiently incurring minimal communication overhead. This is in contrast to existing schemes that are based on sorting a large number of keys or on the use of global data structures. The new formulations are augmented by alternate communication strategies which serve to minimize communication overhead. The impact of these communication strategies is experimentally studied. The authors report on experimental results obtained from an astrophysical simulation on an nCUBE2 parallel computer.

  10. Computer simulations of the explosive consolidation of powders

    SciTech Connect

    Reaugh, J.E.

    1987-07-01

    We have used computer simulations to study the explosive consolidation of powders in various experimental configurations. The objectives of these studies are (1) to help design experimental geometries that permit recovery of dense, consolidated powders, and (2) to help understand why failures occur in other geometries. We present results of our computer simulations of the geometries used by various experimenters for the consolidation of tungsten powder into rods, aluminum nitride powder into tubes and diamond powder into disks. We show that the stress histories experienced by the powders in these geometries are qualitatively different.

  11. Urban earthquake simulation of Tokyo metropolis using full K computer

    NASA Astrophysics Data System (ADS)

    Fujita, Kohei; Ichimura, Tsuyoshi; Hori, Muneo

    2016-04-01

    Reflecting detailed urban geographic information data to earthquake simulation of cities is expected to improve the reliability of damage estimates for future earthquakes. Such simulations require high resolution computation of large and complex domains and thus fast and scalable finite element solver capable of utilizing supercomputers are needed. Targeting massively parallel scalar supercomputers, we have been developing a fast low-ordered unstructured finite element solver by combining multi-precision arithmetic, multi-grid method, predictors, and techniques for utilizing multi-cores and SIMD units of CPUs. In this talk, I will show the developed method and its scalability/performance on the K computer. Together, I will show some small scale measurement results on Intel Haswell CPU servers for checking performance portability. As an application example, I will show an urban earthquake simulation targeted on a 10 km by 9 km area of central Tokyo with 320 thousand structures. Here the surface ground is modeled by 33 billion elements and 133 billion degrees-of-freedom, and its seismic response is computed using the whole K computer with 82944 compute nodes. The fast and scalable finite element method can be applied to earthquake wave propagation problems through earth crust or elastic/viscoelastic crustal deformation analyses and is expected to be useful for improving resolution of such simulations in the future.

  12. Energy Efficient Biomolecular Simulations with FPGA-based Reconfigurable Computing

    SciTech Connect

    Hampton, Scott S; Agarwal, Pratul K

    2010-05-01

    Reconfigurable computing (RC) is being investigated as a hardware solution for improving time-to-solution for biomolecular simulations. A number of popular molecular dynamics (MD) codes are used to study various aspects of biomolecules. These codes are now capable of simulating nanosecond time-scale trajectories per day on conventional microprocessor-based hardware, but biomolecular processes often occur at the microsecond time-scale or longer. A wide gap exists between the desired and achievable simulation capability; therefore, there is considerable interest in alternative algorithms and hardware for improving the time-to-solution of MD codes. The fine-grain parallelism provided by Field Programmable Gate Arrays (FPGA) combined with their low power consumption make them an attractive solution for improving the performance of MD simulations. In this work, we use an FPGA-based coprocessor to accelerate the compute-intensive calculations of LAMMPS, a popular MD code, achieving up to 5.5 fold speed-up on the non-bonded force computations of the particle mesh Ewald method and up to 2.2 fold speed-up in overall time-to-solution, and potentially an increase by a factor of 9 in power-performance efficiencies for the pair-wise computations. The results presented here provide an example of the multi-faceted benefits to an application in a heterogeneous computing environment.

  13. Computer simulation of hypersonic flow over the Space Shuttle Orbiter

    NASA Technical Reports Server (NTRS)

    Inouye, M.

    1977-01-01

    Computer simulations of the flow field around the Space Shuttle Orbiter are described. Results of inviscid calculations are presented for the shock wave pattern and bottom centerline pressure distribution at 30 deg angle of attack. Results of viscous calculations are presented for wall pressure and heat transfer distributions for simple configurations representative of regions where shock wave-boundary layer interactions occur. The computer codes are verified by comparisons with wind-tunnel data and can be applied to flight conditions.

  14. Computer simulations of ions in radio-frequency traps

    NASA Technical Reports Server (NTRS)

    Williams, A.; Prestage, J. D.; Maleki, L.; Djomehri, J.; Harabetian, E.

    1990-01-01

    The motion of ions in a trapped-ion frequency standard affects the stability of the standard. In order to study the motion and structures of large ion clouds in a radio-frequency (RF) trap, a computer simulation of the system that incorporates the effect of thermal excitation of the ions was developed. Results are presented from the simulation for cloud sizes up to 512 ions, emphasizing cloud structures in the low-temperature regime.

  15. [Computer simulated images of radiopharmaceutical distributions in anthropomorphic phantoms

    SciTech Connect

    Not Available

    1991-05-17

    We have constructed an anatomically correct human geometry, which can be used to store radioisotope concentrations in 51 various internal organs. Each organ is associated with an index number which references to its attenuating characteristics (composition and density). The initial development of Computer Simulated Images of Radiopharmaceuticals in Anthropomorphic Phantoms (CSIRDAP) over the first 3 years has been very successful. All components of the simulation have been coded, made operational and debugged.

  16. A Generic Scheduling Simulator for High Performance Parallel Computers

    SciTech Connect

    Yoo, B S; Choi, G S; Jette, M A

    2001-08-01

    It is well known that efficient job scheduling plays a crucial role in achieving high system utilization in large-scale high performance computing environments. A good scheduling algorithm should schedule jobs to achieve high system utilization while satisfying various user demands in an equitable fashion. Designing such a scheduling algorithm is a non-trivial task even in a static environment. In practice, the computing environment and workload are constantly changing. There are several reasons for this. First, the computing platforms constantly evolve as the technology advances. For example, the availability of relatively powerful commodity off-the-shelf (COTS) components at steadily diminishing prices have made it feasible to construct ever larger massively parallel computers in recent years [1, 4]. Second, the workload imposed on the system also changes constantly. The rapidly increasing compute resources have provided many applications developers with the opportunity to radically alter program characteristics and take advantage of these additional resources. New developments in software technology may also trigger changes in user applications. Finally, political climate change may alter user priorities or the mission of the organization. System designers in such dynamic environments must be able to accurately forecast the effect of changes in the hardware, software, and/or policies under consideration. If the environmental changes are significant, one must also reassess scheduling algorithms. Simulation has frequently been relied upon for this analysis, because other methods such as analytical modeling or actual measurements are usually too difficult or costly. A drawback of the simulation approach, however, is that developing a simulator is a time-consuming process. Furthermore, an existing simulator cannot be easily adapted to a new environment. In this research, we attempt to develop a generic job-scheduling simulator, which facilitates the evaluation of

  17. Quantum computer simulation using the CUDA programming model

    NASA Astrophysics Data System (ADS)

    Gutiérrez, Eladio; Romero, Sergio; Trenas, María A.; Zapata, Emilio L.

    2010-02-01

    Quantum computing emerges as a field that captures a great theoretical interest. Its simulation represents a problem with high memory and computational requirements which makes advisable the use of parallel platforms. In this work we deal with the simulation of an ideal quantum computer on the Compute Unified Device Architecture (CUDA), as such a problem can benefit from the high computational capacities of Graphics Processing Units (GPU). After all, modern GPUs are becoming very powerful computational architectures which is causing a growing interest in their application for general purpose. CUDA provides an execution model oriented towards a more general exploitation of the GPU allowing to use it as a massively parallel SIMT (Single-Instruction Multiple-Thread) multiprocessor. A simulator that takes into account memory reference locality issues is proposed, showing that the challenge of achieving a high performance depends strongly on the explicit exploitation of memory hierarchy. Several strategies have been experimentally evaluated obtaining good performance results in comparison with conventional platforms.

  18. A Computer Simulation of Community Pharmacy Practice for Educational Use

    PubMed Central

    Ling, Tristan; Bereznicki, Luke; Westbury, Juanita; Chalmers, Leanne; Peterson, Gregory; Ollington, Robert

    2014-01-01

    Objective. To provide a computer-based learning method for pharmacy practice that is as effective as paper-based scenarios, but more engaging and less labor-intensive. Design. We developed a flexible and customizable computer simulation of community pharmacy. Using it, the students would be able to work through scenarios which encapsulate the entirety of a patient presentation. We compared the traditional paper-based teaching method to our computer-based approach using equivalent scenarios. The paper-based group had 2 tutors while the computer group had none. Both groups were given a prescenario and postscenario clinical knowledge quiz and survey. Assessment. Students in the computer-based group had generally greater improvements in their clinical knowledge score, and third-year students using the computer-based method also showed more improvements in history taking and counseling competencies. Third-year students also found the simulation fun and engaging. Conclusion. Our simulation of community pharmacy provided an educational experience as effective as the paper-based alternative, despite the lack of a human tutor. PMID:26056406

  19. Computer model to simulate testing at the National Transonic Facility

    NASA Technical Reports Server (NTRS)

    Mineck, Raymond E.; Owens, Lewis R., Jr.; Wahls, Richard A.; Hannon, Judith A.

    1995-01-01

    A computer model has been developed to simulate the processes involved in the operation of the National Transonic Facility (NTF), a large cryogenic wind tunnel at the Langley Research Center. The simulation was verified by comparing the simulated results with previously acquired data from three experimental wind tunnel test programs in the NTF. The comparisons suggest that the computer model simulates reasonably well the processes that determine the liquid nitrogen (LN2) consumption, electrical consumption, fan-on time, and the test time required to complete a test plan at the NTF. From these limited comparisons, it appears that the results from the simulation model are generally within about 10 percent of the actual NTF test results. The use of actual data acquisition times in the simulation produced better estimates of the LN2 usage, as expected. Additional comparisons are needed to refine the model constants. The model will typically produce optimistic results since the times and rates included in the model are typically the optimum values. Any deviation from the optimum values will lead to longer times or increased LN2 and electrical consumption for the proposed test plan. Computer code operating instructions and listings of sample input and output files have been included.

  20. All-atom force field for the prediction of vapor-liquid equilibria and interfacial properties of HFA134a.

    PubMed

    Peguin, Robson P S; Kamath, Ganesh; Potoff, Jeffrey J; da Rocha, Sandro R P

    2009-01-01

    A new all-atom force field capable of accurately predicting the bulk and interfacial properties of 1,1,1,2-tetrafluoroethane (HFA134a) is reported. Parameterization of several force fields with different initial charge configurations from ab initio calculations was performed using the histogram reweighting method and Monte Carlo simulations in the grand canonical ensemble. The 12-6 Lennard-Jones well depth and diameter for the different HFA134a models were determined by fitting the simulation results to pure-component vapor-equilibrium data. Initial screening of the force fields was achieved by comparing the calculated and experimental bulk properties. The surface tension of pure HFA134a served as an additional screening property to help discriminate an optimum model. The proposed model reproduces the experimental saturated liquid and vapor densities, and the vapor pressure for HFA134a within average errors of 0.7%, 4.4%, and 3.1%, respectively. Critical density, temperature, vapor pressure, normal boiling point, and heat of vaporization at 298 K are also in good agreement with experimental data with errors of 0.2%, 0.1%, 6.2%, 0%, 2.2%, respectively. The calculated surface tension is found to be within the experimental range of 7.7-8.1 mN.m(-1). The dipole moment of the different models was found to significantly affect the prediction of the vapor pressure and surface tension. The ability of the HFA134a models in predicting the interfacial tension against water is also discussed. The results presented here are relevant in the development of technologies where the more environmentally friendly HFA134a is utilized as a substitute to the ozone depleting chlorofluorocarbon propellants. PMID:19086791

  1. The advanced computational testing and simulation toolkit (ACTS)

    SciTech Connect

    Drummond, L.A.; Marques, O.

    2002-05-21

    During the past decades there has been a continuous growth in the number of physical and societal problems that have been successfully studied and solved by means of computational modeling and simulation. Distinctively, a number of these are important scientific problems ranging in scale from the atomic to the cosmic. For example, ionization is a phenomenon as ubiquitous in modern society as the glow of fluorescent lights and the etching on silicon computer chips; but it was not until 1999 that researchers finally achieved a complete numerical solution to the simplest example of ionization, the collision of a hydrogen atom with an electron. On the opposite scale, cosmologists have long wondered whether the expansion of the Universe, which began with the Big Bang, would ever reverse itself, ending the Universe in a Big Crunch. In 2000, analysis of new measurements of the cosmic microwave background radiation showed that the geometry of the Universe is flat, and thus the Universe will continue expanding forever. Both of these discoveries depended on high performance computer simulations that utilized computational tools included in the Advanced Computational Testing and Simulation (ACTS) Toolkit. The ACTS Toolkit is an umbrella project that brought together a number of general purpose computational tool development projects funded and supported by the U.S. Department of Energy (DOE). These tools, which have been developed independently, mainly at DOE laboratories, make it easier for scientific code developers to write high performance applications for parallel computers. They tackle a number of computational issues that are common to a large number of scientific applications, mainly implementation of numerical algorithms, and support for code development, execution and optimization. The ACTS Toolkit Project enables the use of these tools by a much wider community of computational scientists, and promotes code portability, reusability, reduction of duplicate efforts

  2. AKSATINT - SATELLITE INTERFERENCE ANALYSIS AND SIMULATION USING PERSONAL COMPUTERS

    NASA Technical Reports Server (NTRS)

    Kantak, A.

    1994-01-01

    In the late seventies, the number of communication satellites in service increased, and interference has become an increasingly important consideration in designing satellite/ground station communications systems. Satellite Interference Analysis and Simulation Using Personal Computers, AKSATINT, models the interference experienced by a generic satellite communications receiving station due to an interfering satellite. Both the desired and the interfering satellites are considered to be in elliptical orbits. The simulation contains computation of orbital positions of both satellites using classical orbital elements, calculation of the satellite antennae look angles for both satellites and elevation angles at the desired-satellite ground-station antenna, and computation of Doppler effect due to the motions of the satellites and the Earth's rotation. AKSATINT also computes the interference-tosignal-power ratio, taking into account losses suffered by the links. After computing the interference-to-signal-power ratio, the program computes the statistical quantities. The statistical formulation of the interference effect is presented in the form of a histogram of the interference to the desired signal power ratio. The program includes a flowchart, a sample run, and results of that run. AKSATINT is expected to be of general use to system designers and frequency managers in selecting the proper frequency under an interference scenario. The AKSATINT program is written in BASIC. It was designed to operate on the IBM Personal Computer AT or compatibles, and has been implemented under MS DOS 3.2. AKSATINT was developed in 1987.

  3. Computer simulation of plasma and N-body problems

    NASA Technical Reports Server (NTRS)

    Harries, W. L.; Miller, J. B.

    1975-01-01

    The following FORTRAN language computer codes are presented: (1) efficient two- and three-dimensional central force potential solvers; (2) a three-dimensional simulator of an isolated galaxy which incorporates the potential solver; (3) a two-dimensional particle-in-cell simulator of the Jeans instability in an infinite self-gravitating compressible gas; and (4) a two-dimensional particle-in-cell simulator of a rotating self-gravitating compressible gaseous system of which rectangular coordinate and superior polar coordinate versions were written.

  4. Computer simulation of Aphis gossypii insects using Penna aging model

    NASA Astrophysics Data System (ADS)

    Giarola, L. T. P.; Martins, S. G. F.; Toledo Costa, M. C. P.

    2006-08-01

    A computer simulation was made for the population dynamics of Aphis gossypii in laboratory and field conditions. The age structure was inserted in the dynamics through bit string model for biological aging, proposed by Penna in 1995. The influence of different host plants and of climatic factors such as temperature and precipitation was considered in the simulation starting from experimental data. The results obtained indicate that the simulation is an appropriate instrument for understanding of the population dynamics of these species and for the establishment of biological control strategies.

  5. Computer simulation of multigrid body dynamics and control

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

  6. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  7. Computational simulation of periodic thermal processes in the roof deck

    NASA Astrophysics Data System (ADS)

    Stastnik, S.

    2016-06-01

    The climate changes in the Central Europe highlight the importance of protection of buildings against overheating during summer season, with the crucial thermal insulation and accumulation role of the roof deck. This paper demonstrates the possibility of computational simulation of such periodic thermal processes, applying the evaluation of thermal attenuation using complex arithmetics, in confrontation with real experimental data.

  8. Time Advice and Learning Questions in Computer Simulations

    ERIC Educational Resources Information Center

    Rey, Gunter Daniel

    2011-01-01

    Students (N = 101) used an introductory text and a computer simulation to learn fundamental concepts about statistical analyses (e.g., analysis of variance, regression analysis and General Linear Model). Each learner was randomly assigned to one cell of a 2 (with or without time advice) x 3 (with learning questions and corrective feedback, with…

  9. Role of Computer Graphics in Simulations for Teaching Physiology.

    ERIC Educational Resources Information Center

    Modell, H. I.; And Others

    1983-01-01

    Discusses a revision of existing respiratory physiology simulations to promote active learning experiences for individual students. Computer graphics were added to aid student's conceptualization of the physiological system. Specific examples are provided, including those dealing with alveolar gas equations and effects of anatomic shunt flow on…

  10. Effectiveness of Computer Simulation for Enhancing Higher Order Thinking.

    ERIC Educational Resources Information Center

    Gokhale, Anu A.

    1996-01-01

    Electronics students (16 controls, 16 experimentals) designed, built, and tested an amplifier. The experimentals did so after it was designed through computer simulation (using Electronics Workbench software). The experimental group performed significantly better on problem-solving tests; both groups did the same on drill and practice tests. (SK)

  11. Faster quantum chemistry simulation on fault-tolerant quantum computers

    NASA Astrophysics Data System (ADS)

    Cody Jones, N.; Whitfield, James D.; McMahon, Peter L.; Yung, Man-Hong; Van Meter, Rodney; Aspuru-Guzik, Alán; Yamamoto, Yoshihisa

    2012-11-01

    Quantum computers can in principle simulate quantum physics exponentially faster than their classical counterparts, but some technical hurdles remain. We propose methods which substantially improve the performance of a particular form of simulation, ab initio quantum chemistry, on fault-tolerant quantum computers; these methods generalize readily to other quantum simulation problems. Quantum teleportation plays a key role in these improvements and is used extensively as a computing resource. To improve execution time, we examine techniques for constructing arbitrary gates which perform substantially faster than circuits based on the conventional Solovay-Kitaev algorithm (Dawson and Nielsen 2006 Quantum Inform. Comput. 6 81). For a given approximation error ɛ, arbitrary single-qubit gates can be produced fault-tolerantly and using a restricted set of gates in time which is O(log ɛ) or O(log log ɛ) with sufficient parallel preparation of ancillas, constant average depth is possible using a method we call programmable ancilla rotations. Moreover, we construct and analyze efficient implementations of first- and second-quantized simulation algorithms using the fault-tolerant arbitrary gates and other techniques, such as implementing various subroutines in constant time. A specific example we analyze is the ground-state energy calculation for lithium hydride.

  12. Simulations Using a Computer/Videodisc System: Instructional Design Considerations.

    ERIC Educational Resources Information Center

    Ehrlich, Lisa R.

    Instructional design considerations involved in using level four videodisc systems when designing simulations are explored. Discussion of the hardware and software system characteristics notes that computer based training offers the features of text, graphics, color, animation, and highlighting techniques, while a videodisc player offers all of…

  13. Social Choice in a Computer-Assisted Simulation

    ERIC Educational Resources Information Center

    Thavikulwat, Precha

    2009-01-01

    Pursuing a line of inquiry suggested by Crookall, Martin, Saunders, and Coote, the author applied, within the framework of design science, an optimal-design approach to incorporate into a computer-assisted simulation two innovative social choice processes: the multiple period double auction and continuous voting. Expectations that the…

  14. Integrating Computer Simulations into High School Physics Teaching.

    ERIC Educational Resources Information Center

    Ronen, Miky; And Others

    1992-01-01

    Describes a project aimed at examining the problems involved in a large scale integration of computerized simulations into the present structure of physics teaching in Israeli high schools. Assessment by students, teachers, and the project team indicated general satisfaction with the project. Discusses difficulties of implementing computer-based…

  15. A Computer Simulated Experiment in Complex Order Kinetics

    ERIC Educational Resources Information Center

    Merrill, J. C.; And Others

    1975-01-01

    Describes a computer simulation experiment in which physical chemistry students can determine all of the kinetic parameters of a reaction, such as order of the reaction with respect to each reagent, forward and reverse rate constants for the overall reaction, and forward and reverse activation energies. (MLH)

  16. Instructional Advice, Time Advice and Learning Questions in Computer Simulations

    ERIC Educational Resources Information Center

    Rey, Gunter Daniel

    2010-01-01

    Undergraduate students (N = 97) used an introductory text and a computer simulation to learn fundamental concepts about statistical analyses (e.g., analysis of variance, regression analysis and General Linear Model). Each learner was randomly assigned to one cell of a 2 (with or without instructional advice) x 2 (with or without time advice) x 2…

  17. Biology Students Building Computer Simulations Using StarLogo TNG

    ERIC Educational Resources Information Center

    Smith, V. Anne; Duncan, Ishbel

    2011-01-01

    Confidence is an important issue for biology students in handling computational concepts. This paper describes a practical in which honours-level bioscience students simulate complex animal behaviour using StarLogo TNG, a freely-available graphical programming environment. The practical consists of two sessions, the first of which guides students…

  18. Accelerating sino-atrium computer simulations with graphic processing units.

    PubMed

    Zhang, Hong; Xiao, Zheng; Lin, Shien-fong

    2015-01-01

    Sino-atrial node cells (SANCs) play a significant role in rhythmic firing. To investigate their role in arrhythmia and interactions with the atrium, computer simulations based on cellular dynamic mathematical models are generally used. However, the large-scale computation usually makes research difficult, given the limited computational power of Central Processing Units (CPUs). In this paper, an accelerating approach with Graphic Processing Units (GPUs) is proposed in a simulation consisting of the SAN tissue and the adjoining atrium. By using the operator splitting method, the computational task was made parallel. Three parallelization strategies were then put forward. The strategy with the shortest running time was further optimized by considering block size, data transfer and partition. The results showed that for a simulation with 500 SANCs and 30 atrial cells, the execution time taken by the non-optimized program decreased 62% with respect to a serial program running on CPU. The execution time decreased by 80% after the program was optimized. The larger the tissue was, the more significant the acceleration became. The results demonstrated the effectiveness of the proposed GPU-accelerating methods and their promising applications in more complicated biological simulations. PMID:26406070

  19. Interview and Interrogation Training using a Computer-Simulated Subject.

    ERIC Educational Resources Information Center

    Olsen, Dale E.

    Interactive, multimedia software involving a simulated subject has been created to help trainees develop interview and interrogation techniques using personal computers, because practice interviews are not always realistic and are too expensive. New and experienced law enforcement agents, among others, need such extensive training in techniques…

  20. Interaction of Intuitive Physics with Computer-Simulated Physics.

    ERIC Educational Resources Information Center

    Flick, Lawrence B.

    1990-01-01

    The question of how children solve force and motion problems in computer simulations without explicit knowledge of the underlying physics was investigated. Keystroke sequences made by children were saved and analyzed, and children were interviewed to understand their perception of the relationship between keyboard input and on-screen action. (CW)

  1. Advanced Simulation and Computing Co-Design Strategy

    SciTech Connect

    Ang, James A.; Hoang, Thuc T.; Kelly, Suzanne M.; McPherson, Allen; Neely, Rob

    2015-11-01

    This ASC Co-design Strategy lays out the full continuum and components of the co-design process, based on what we have experienced thus far and what we wish to do more in the future to meet the program’s mission of providing high performance computing (HPC) and simulation capabilities for NNSA to carry out its stockpile stewardship responsibility.

  2. Improving a Computer Networks Course Using the Partov Simulation Engine

    ERIC Educational Resources Information Center

    Momeni, B.; Kharrazi, M.

    2012-01-01

    Computer networks courses are hard to teach as there are many details in the protocols and techniques involved that are difficult to grasp. Employing programming assignments as part of the course helps students to obtain a better understanding and gain further insight into the theoretical lectures. In this paper, the Partov simulation engine and…

  3. Computational Modelling and Simulation Fostering New Approaches in Learning Probability

    ERIC Educational Resources Information Center

    Kuhn, Markus; Hoppe, Ulrich; Lingnau, Andreas; Wichmann, Astrid

    2006-01-01

    Discovery learning in mathematics in the domain of probability based on hands-on experiments is normally limited because of the difficulty in providing sufficient materials and data volume in terms of repetitions of the experiments. Our cooperative, computational modelling and simulation environment engages students and teachers in composing and…

  4. Interaction of intuitive physics with computer-simulated physics

    NASA Astrophysics Data System (ADS)

    Flick, Lawrence B.

    How do children solve force and motion problems in computer simulations without explicit knowledge of the underlying physics? This question was addressed by saving the keystroke input of 19 sixth-grade children in computer memory as each interacted with a simulated, frictionless object using Logo turtle-graphics. The keystroke sequences were first used to determine subject performance on the gamelike features of the simulation. A second analysis used the Newtonian structure of the program to investigate alternative methods for controlling turtle velocity. Five boys and five girls were interviewed during the simulation concerning the perceived relationship between keyboard input and turtle behavior. Subjects who could clearly state some keyboard effects did not score high on either computer analysis, yet achieved the most general solutions of the computer problem. They did so by exploring turtle behavior under a greater variety of conditions than the subjects who achieved partial solutions. For the successful subjects, the turtle was related by analogy to useful information from existing conceptions of motion.

  5. Teaching Physics (and Some Computation) Using Intentionally Incorrect Simulations

    ERIC Educational Resources Information Center

    Cox, Anne J.; Junkin, William F., III; Christian, Wolfgang; Belloni, Mario; Esquembre, Francisco

    2011-01-01

    Computer simulations are widely used in physics instruction because they can aid student visualization of abstract concepts, they can provide multiple representations of concepts (graphical, trajectories, charts), they can approximate real-world examples, and they can engage students interactively, all of which can enhance student understanding of…

  6. Computation techniques for the simulation of turbomachinery compressible flows

    NASA Astrophysics Data System (ADS)

    Veuillot, J. P.; Cambier, L.

    Computation techniques for the simulation of turbomachinery compressible flows via the numerical solution of Euler and Navier-Stokes equations are described. In a discussion of the Euler and Navier-Stokes equations for turbomachinery flow calculations, attention is given to equations for a rotating system, quasi-three-dimensional formulation, and turbulence modeling. Examples of Navier-Stokes calculations are presented.

  7. A Computer Simulation for the Study of Waves.

    ERIC Educational Resources Information Center

    Bork, Alfred M.; Robson, John

    A computer program, designed for use in the second quarter of the beginning course for science and engineering majors at the University of California, Irvine, simulates an experimental investigation of a pulse in a rope. A full trial run is given, in which the student's problem is to discover enough about the disturbance of the rope to answer…

  8. Computers With Wings: Flight Simulation and Personalized Landscapes

    NASA Astrophysics Data System (ADS)

    Oss, Stefano

    2005-03-01

    We propose, as a special way to explore the physics of flying objects, to use a flight simulator with a personalized scenery to reproduce the territory where students live. This approach increases the participation and attention of students to physics classes but also creates several opportunities for addressing side activities and arguments of various nature, from history to geography, computer science, and much more.

  9. Robotics, Artificial Intelligence, Computer Simulation: Future Applications in Special Education.

    ERIC Educational Resources Information Center

    Moore, Gwendolyn B.; And Others

    1986-01-01

    Describes possible applications of new technologies to special education. Discusses results of a study designed to explore the use of robotics, artificial intelligence, and computer simulations to aid people with handicapping conditions. Presents several scenarios in which specific technological advances may contribute to special education…

  10. Robotics, Artificial Intelligence, Computer Simulation: Future Applications in Special Education.

    ERIC Educational Resources Information Center

    Moore, Gwendolyn B.; And Others

    The report describes three advanced technologies--robotics, artificial intelligence, and computer simulation--and identifies the ways in which they might contribute to special education. A hybrid methodology was employed to identify existing technology and forecast future needs. Following this framework, each of the technologies is defined,…

  11. Computational Simulation of a Water-Cooled Heat Pump

    NASA Technical Reports Server (NTRS)

    Bozarth, Duane

    2008-01-01

    A Fortran-language computer program for simulating the operation of a water-cooled vapor-compression heat pump in any orientation with respect to gravity has been developed by modifying a prior general-purpose heat-pump design code used at Oak Ridge National Laboratory (ORNL).

  12. Computer Simulation and Laboratory Work in the Teaching of Mechanics.

    ERIC Educational Resources Information Center

    Borghi, L.; And Others

    1987-01-01

    Describes a teaching strategy designed to help high school students learn mechanics by involving them in simple experimental work, observing didactic films, running computer simulations, and executing more complex laboratory experiments. Provides an example of the strategy as it is applied to the topic of projectile motion. (TW)

  13. Symbolic Quantum Computation Simulation in SymPy

    NASA Astrophysics Data System (ADS)

    Cugini, Addison; Curry, Matt; Granger, Brian

    2010-10-01

    Quantum computing is an emerging field which aims to use quantum mechanics to solve difficult computational problems with greater efficiency than on a classical computer. There is a need to create software that i) helps newcomers to learn the field, ii) enables practitioners to design and simulate quantum circuits and iii) provides an open foundation for further research in the field. Towards these ends we have created a package, in the open-source symbolic computation library SymPy, that simulates the quantum circuit model of quantum computation using Dirac notation. This framework builds on the extant powerful symbolic capabilities of SymPy to preform its simulations in a fully symbolic manner. We use object oriented design to abstract circuits as ordered collections of quantum gate and qbit objects. The gate objects can either be applied directly to the qbit objects or be represented as matrices in different bases. The package is also capable of performing the quantum Fourier transform and Shor's algorithm. A notion of measurement is made possible through the use of a non-commutative gate object. In this talk, we describe the software and show examples of quantum circuits on single and multi qbit states that involve common algorithms, gates and measurements.

  14. Computer Simulation Of Radiographic Screen-Film Images

    NASA Astrophysics Data System (ADS)

    Metter, Richard V.; Dillon, Peter L.; Huff, Kenneth E.; Rabbani, Majid

    1986-06-01

    A method is described for computer simulation of radiographic screen-film images. This method is based on a previously published model of the screen-film imaging process.l The x-ray transmittance of a test object is sampled at a pitch of 50 μm by scanning a high-resolution, low-noise direct-exposure radiograph. This transmittance is then used, along with the x-ray exposure incident upon the object, to determine the expected number of quanta per pixel incident upon the screen. The random nature of x-ray arrival and absorption, x-ray quantum to light photon conversion, and photon absorption by the film is simulated by appropriate random number generation. Standard FFT techniques are used for computing the effects of scattering. Finally, the computed film density for each pixel is produced on a high-resolution, low-noise output film by a scanning printer. The simulation allows independent specification of x-ray exposure, x-ray quantum absorption, light conversion statistics, light scattering, and film characteristics (sensitometry and gran-ularity). Each of these parameters is independently measured for radiographic systems of interest. The simulator is tested by comparing actual radiographic images with simulated images resulting from the independently measured parameters. Images are also shown illustrating the effects of changes in these parameters on image quality. Finally, comparison is made with a "perfect" imaging system where information content is only limited by the finite number of x-rays.

  15. Bibliography for Verification and Validation in Computational Simulations

    SciTech Connect

    Oberkampf, W.L.

    1998-10-01

    A bibliography has been compiled dealing with the verification and validation of computational simulations. The references listed in this bibliography are concentrated in the field of computational fluid dynamics (CFD). However, references from the following fields are also included: operations research, heat transfer, solid dynamics, software quality assurance, software accreditation, military systems, and nuclear reactor safety. This bibliography, containing 221 references, is not meant to be comprehensive. It was compiled during the last ten years in response to the author's interest and research in the methodology for verification and validation. The emphasis in the bibliography is in the following areas: philosophy of science underpinnings, development of terminology and methodology, high accuracy solutions for CFD verification, experimental datasets for CFD validation, and the statistical quantification of model validation. This bibliography should provide a starting point for individual researchers in many fields of computational simulation in science and engineering.

  16. Optimizing Quantum Simulation for Heterogeneous Computing: a Hadamard Transformation Study

    NASA Astrophysics Data System (ADS)

    de Avila, Anderson B.; Schumalfuss, Murilo F.; Reiser, Renata H. S.; Pilla, Mauricio L.; Maron, Adriano K.

    2015-10-01

    The D-GM execution environment improves distributed simulation of quantum algorithms in heterogeneous computing environments comprising both multi-core CPUs and GPUs. The main contribution of this work consists in the optimization of the environment VirD-GM, conceived in three steps: (i) the theoretical studies and implementation of the abstractions of the Mixed Partial Process defined in the qGM model, focusing on the reduction of the memory consumption regarding multidimensional QTs; (ii) the distributed/parallel implementation of such abstractions allowing its execution on clusters of GPUs; (iii) and optimizations that predict multiplications by zero-value of the quantum states/transformations, implying reduction in the number of computations. The results obtained in this work embrace the distribute/parallel simulation of Hadamard gates up to 21 qubits, showing scalability with the increase in the number of computing nodes.

  17. Computational Simulation of the Formation and Material Behavior of Ice

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  18. Adaptive scapula bone remodeling computational simulation: Relevance to regenerative medicine

    NASA Astrophysics Data System (ADS)

    Sharma, Gulshan B.; Robertson, Douglas D.

    2013-07-01

    Shoulder arthroplasty success has been attributed to many factors including, bone quality, soft tissue balancing, surgeon experience, and implant design. Improved long-term success is primarily limited by glenoid implant loosening. Prosthesis design examines materials and shape and determines whether the design should withstand a lifetime of use. Finite element (FE) analyses have been extensively used to study stresses and strains produced in implants and bone. However, these static analyses only measure a moment in time and not the adaptive response to the altered environment produced by the therapeutic intervention. Computational analyses that integrate remodeling rules predict how bone will respond over time. Recent work has shown that subject-specific two- and three dimensional adaptive bone remodeling models are feasible and valid. Feasibility and validation were achieved computationally, simulating bone remodeling using an intact human scapula, initially resetting the scapular bone material properties to be uniform, numerically simulating sequential loading, and comparing the bone remodeling simulation results to the actual scapula's material properties. Three-dimensional scapula FE bone model was created using volumetric computed tomography images. Muscle and joint load and boundary conditions were applied based on values reported in the literature. Internal bone remodeling was based on element strain-energy density. Initially, all bone elements were assigned a homogeneous density. All loads were applied for 10 iterations. After every iteration, each bone element's remodeling stimulus was compared to its corresponding reference stimulus and its material properties modified. The simulation achieved convergence. At the end of the simulation the predicted and actual specimen bone apparent density were plotted and compared. Location of high and low predicted bone density was comparable to the actual specimen. High predicted bone density was greater than actual

  19. Adaptive scapula bone remodeling computational simulation: Relevance to regenerative medicine

    SciTech Connect

    Sharma, Gulshan B.; Robertson, Douglas D.

    2013-07-01

    Shoulder arthroplasty success has been attributed to many factors including, bone quality, soft tissue balancing, surgeon experience, and implant design. Improved long-term success is primarily limited by glenoid implant loosening. Prosthesis design examines materials and shape and determines whether the design should withstand a lifetime of use. Finite element (FE) analyses have been extensively used to study stresses and strains produced in implants and bone. However, these static analyses only measure a moment in time and not the adaptive response to the altered environment produced by the therapeutic intervention. Computational analyses that integrate remodeling rules predict how bone will respond over time. Recent work has shown that subject-specific two- and three dimensional adaptive bone remodeling models are feasible and valid. Feasibility and validation were achieved computationally, simulating bone remodeling using an intact human scapula, initially resetting the scapular bone material properties to be uniform, numerically simulating sequential loading, and comparing the bone remodeling simulation results to the actual scapula’s material properties. Three-dimensional scapula FE bone model was created using volumetric computed tomography images. Muscle and joint load and boundary conditions were applied based on values reported in the literature. Internal bone remodeling was based on element strain-energy density. Initially, all bone elements were assigned a homogeneous density. All loads were applied for 10 iterations. After every iteration, each bone element’s remodeling stimulus was compared to its corresponding reference stimulus and its material properties modified. The simulation achieved convergence. At the end of the simulation the predicted and actual specimen bone apparent density were plotted and compared. Location of high and low predicted bone density was comparable to the actual specimen. High predicted bone density was greater than

  20. Computational performance of a smoothed particle hydrodynamics simulation for shared-memory parallel computing

    NASA Astrophysics Data System (ADS)

    Nishiura, Daisuke; Furuichi, Mikito; Sakaguchi, Hide

    2015-09-01

    The computational performance of a smoothed particle hydrodynamics (SPH) simulation is investigated for three types of current shared-memory parallel computer devices: many integrated core (MIC) processors, graphics processing units (GPUs), and multi-core CPUs. We are especially interested in efficient shared-memory allocation methods for each chipset, because the efficient data access patterns differ between compute unified device architecture (CUDA) programming for GPUs and OpenMP programming for MIC processors and multi-core CPUs. We first introduce several parallel implementation techniques for the SPH code, and then examine these on our target computer architectures to determine the most effective algorithms for each processor unit. In addition, we evaluate the effective computing performance and power efficiency of the SPH simulation on each architecture, as these are critical metrics for overall performance in a multi-device environment. In our benchmark test, the GPU is found to produce the best arithmetic performance as a standalone device unit, and gives the most efficient power consumption. The multi-core CPU obtains the most effective computing performance. The computational speed of the MIC processor on Xeon Phi approached that of two Xeon CPUs. This indicates that using MICs is an attractive choice for existing SPH codes on multi-core CPUs parallelized by OpenMP, as it gains computational acceleration without the need for significant changes to the source code.

  1. Computational simulation for analysis and synthesis of impact resilient structure

    NASA Astrophysics Data System (ADS)

    Djojodihardjo, Harijono

    2013-10-01

    Impact resilient structures are of great interest in many engineering applications varying from civil, land vehicle, aircraft and space structures, to mention a few examples. To design such structure, one has to resort fundamental principles and take into account progress in analytical and computational approaches as well as in material science and technology. With such perspectives, this work looks at a generic beam and plate structure subject to impact loading and carry out analysis and numerical simulation. The first objective of the work is to develop a computational algorithm to analyze flat plate as a generic structure subjected to impact loading for numerical simulation and parametric study. The analysis will be based on dynamic response analysis. Consideration is given to the elastic-plastic region. The second objective is to utilize the computational algorithm for direct numerical simulation, and as a parallel scheme, commercial off-the shelf numerical code is utilized for parametric study, optimization and synthesis. Through such analysis and numerical simulation, effort is devoted to arrive at an optimum configuration in terms of loading, structural dimensions, material properties and composite lay-up, among others. Results will be discussed in view of practical applications.

  2. Cosmic reionization on computers. I. Design and calibration of simulations

    SciTech Connect

    Gnedin, Nickolay Y.

    2014-09-20

    Cosmic Reionization On Computers is a long-term program of numerical simulations of cosmic reionization. Its goal is to model fully self-consistently (albeit not necessarily from the first principles) all relevant physics, from radiative transfer to gas dynamics and star formation, in simulation volumes of up to 100 comoving Mpc, and with spatial resolution approaching 100 pc in physical units. In this method paper, we describe our numerical method, the design of simulations, and the calibration of numerical parameters. Using several sets (ensembles) of simulations in 20 h {sup –1} Mpc and 40 h {sup –1} Mpc boxes with spatial resolution reaching 125 pc at z = 6, we are able to match the observed galaxy UV luminosity functions at all redshifts between 6 and 10, as well as obtain reasonable agreement with the observational measurements of the Gunn-Peterson optical depth at z < 6.

  3. Computation of surface tensions using expanded ensemble simulations.

    PubMed

    de Miguel, Enrique

    2008-04-17

    A method for the direct simulation of the surface tension is examined. The technique is based on the thermodynamic route to the interfacial tension and makes use of the expanded ensemble simulation method for the calculation of the free energy difference between two inhomogeneous systems with the same number of particles, temperature, and volume, but different interfacial area. The method is completely general and suitable for systems with either continuous or discontinuous interactions. The adequacy of the expanded ensemble method is assessed by computing the interfacial tension of the planar vapor-liquid interface of Lennard-Jones, Lennard-Jones dimers, Gay-Berne, and square-well model fluids; in the latter, the interactions are discontinuous and the present method does not exhibit the asymmetry of other related methods, such as the test area. The expanded ensemble simulation results are compared with simulation data obtained from other techniques (mechanical and test area) with overall good agreement. PMID:18358023

  4. CAD-based graphical computer simulation in endoscopic surgery.

    PubMed

    Kuehnapfel, U G; Neisius, B

    1993-06-01

    This article presents new techniques for three-dimensional, kinematic realtime simulation of dextrous endoscopic instruments. The integrated simulation package KISMET is used for engineering design verification and evaluation. Geometric and kinematic computer models of the mechanisms and the laparoscopic workspace were created. Using the advanced capabilities of high-performance graphical workstations combined with state-of-the-art simulation software, it is possible to generate displays of the surgical instruments acting realistically on the organs of the digestive system. The organ geometry is modelled in a high degree of detail. Apart from discussing the use of KISMET for the development of MFM-II (Modular Flexible MIS Instrument, Release II), the paper indicates further applications of realtime 3D graphical simulation methods in endoscopic surgery. PMID:8055320

  5. Computational Fluid Dynamics (CFD) simulation of the Madison Dynamo Experiment.

    NASA Astrophysics Data System (ADS)

    Haehn, N. S.; Forest, C. B.; Weber, C. R.; Kendrick, R. D.; Taylor, N. Z.; Oakley, J. G.; Bonazza, R.; Spence, Erik

    2007-11-01

    The Madison Dynamo Experiment is designed to study a self-generated magnetic field called a dynamo. The flow characteristics of a water experiment that is dimensionally similar to the liquid sodium experiment has been modeled using the Computational Fluid Dynamics (CFD) software Fluent. Results from the CFD simulations are used to confirm flow characteristics measured experimentally by both Laser Doppler Velocimetry (LDV) and Particle Imaging Velocimetry (PIV). Simulations can also give insight into the flow characteristics in regions of the experiment which are not accessible via the LDV and PIV systems. The results from the simulations are also used as input for a MHD code to predict the threshold for Dynamo onset. The CFD simulations -- in conjunction with the MHD dynamo prediction code -- can be used to design modifications to the experiment to minimize costly changes. The CFD code has shown that the addition of an equatorial baffle along with several poloidal baffles can lower the threshold for Dynamo onset.

  6. Computer simulations of realistic microstructures: Implications for simulation-based materials design

    NASA Astrophysics Data System (ADS)

    Singh, Harpreet

    The conventional route of materials development typically involves fabrication of numerous batches of specimens having a range of different microstructures generated via variations of process parameters and measurements of relevant properties of these microstructures to identify the combination of processing conditions that yield the material having desired properties. Clearly, such a trial and error based materials development methodology is expensive, time consuming, and inefficient. Consequently, it is of interest to explore alternate strategies that can lead to a decrease in the cost and time required for development of advanced materials such as composites. Availability of powerful and inexpensive computational power and progress in computational materials science permits advancement of modeling and simulations assisted materials design methodology that may require fewer experiments, and therefore, lower cost and time for materials development. The key facets of such a technology would be computational tools for (i) creating models to generate computer simulated realistic microstructures; (ii) capturing the process-microstructure relationship using these models; and (iii) implementation of simulated microstructures in the computational models for materials behavior. Therefore, development of a general and flexible methodology for simulations of realistic microstructures is crucial for the development of simulations based materials design and development technology. Accordingly, this research concerns development of such a methodology for simulations of realistic microstructures based on experimental quantitative stereological data on few microstructures that can capture relevant details of microstructural geometry (including spatial clustering and second phase particle orientations) and its variations with process parameters in terms of a set of simulation parameters. The interpolation and extrapolation of the simulation parameters can then permit generation

  7. COMPUTER MODEL AND SIMULATION OF A GLOVE BOX PROCESS

    SciTech Connect

    C. FOSTER; ET AL

    2001-01-01

    The development of facilities to deal with the disposition of nuclear materials at an acceptable level of Occupational Radiation Exposure (ORE) is a significant issue facing the nuclear community. One solution is to minimize the worker's exposure though the use of automated systems. However, the adoption of automated systems for these tasks is hampered by the challenging requirements that these systems must meet in order to be cost effective solutions in the hazardous nuclear materials processing environment. Retrofitting current glove box technologies with automation systems represents potential near-term technology that can be applied to reduce worker ORE associated with work in nuclear materials processing facilities. Successful deployment of automation systems for these applications requires the development of testing and deployment strategies to ensure the highest level of safety and effectiveness. Historically, safety tests are conducted with glove box mock-ups around the finished design. This late detection of problems leads to expensive redesigns and costly deployment delays. With wide spread availability of computers and cost effective simulation software it is possible to discover and fix problems early in the design stages. Computer simulators can easily create a complete model of the system allowing a safe medium for testing potential failures and design shortcomings. The majority of design specification is now done on computer and moving that information to a model is relatively straightforward. With a complete model and results from a Failure Mode Effect Analysis (FMEA), redesigns can be worked early. Additional issues such as user accessibility, component replacement, and alignment problems can be tackled early in the virtual environment provided by computer simulation. In this case, a commercial simulation package is used to simulate a lathe process operation at the Los Alamos National Laboratory (LANL). The Lathe process operation is indicative of

  8. Computational Aerodynamic Simulations of a Spacecraft Cabin Ventilation Fan Design

    NASA Technical Reports Server (NTRS)

    Tweedt, Daniel L.

    2010-01-01

    Quieter working environments for astronauts are needed if future long-duration space exploration missions are to be safe and productive. Ventilation and payload cooling fans are known to be dominant sources of noise, with the International Space Station being a good case in point. To address this issue cost effectively, early attention to fan design, selection, and installation has been recommended, leading to an effort by NASA to examine the potential for small-fan noise reduction by improving fan aerodynamic design. As a preliminary part of that effort, the aerodynamics of a cabin ventilation fan designed by Hamilton Sundstrand has been simulated using computational fluid dynamics codes, and the computed solutions analyzed to quantify various aspects of the fan aerodynamics and performance. Four simulations were performed at the design rotational speed: two at the design flow rate and two at off-design flow rates. Following a brief discussion of the computational codes, various aerodynamic- and performance-related quantities derived from the computed flow fields are presented along with relevant flow field details. The results show that the computed fan performance is in generally good agreement with stated design goals.

  9. QDENSITY/QCWAVE: A Mathematica quantum computer simulation update

    NASA Astrophysics Data System (ADS)

    Tabakin, Frank

    2016-04-01

    The Mathematica quantum computer simulation packages QDENSITY and QCWAVE are updated for Mathematica 9-10.3. An overview is given of the new QDensity, QCWave, BTSystem and Circuits packages, which includes: (1) improved treatment of tensor products of states and density matrices, (2) major extension to include qutrit (triplet), as well as qubit (binary) and hybrid qubit/qutrit systems in the associated BTSystem package, (3) updated sample quantum computation algorithms, (4) entanglement studies, including Schmidt decomposition, entropy, mutual information, partial transposition, and calculation of the quantum discord. Examples of Bell's theorem and concurrence are also included. This update will hopefully aid in studies of QC dynamics.

  10. Computational simulations and experimental validation of a furnace brazing process

    SciTech Connect

    Hosking, F.M.; Gianoulakis, S.E.; Malizia, L.A.

    1998-12-31

    Modeling of a furnace brazing process is described. The computational tools predict the thermal response of loaded hardware in a hydrogen brazing furnace to programmed furnace profiles. Experiments were conducted to validate the model and resolve computational uncertainties. Critical boundary conditions that affect materials and processing response to the furnace environment were determined. {open_quotes}Global{close_quotes} and local issues (i.e., at the furnace/hardware and joint levels, respectively) are discussed. The ability to accurately simulate and control furnace conditions is examined.

  11. The very local Hubble flow: Computer simulations of dynamical history

    NASA Astrophysics Data System (ADS)

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

    2004-02-01

    The phenomenon of the very local (≤3 Mpc) Hubble flow is studied on the basis of the data of recent precision observations. A set of computer simulations is performed to trace the trajectories of the flow galaxies back in time to the epoch of the formation of the Local Group. It is found that the ``initial conditions'' of the flow are drastically different from the linear velocity-distance relation. The simulations enable one also to recognize the major trends of the flow evolution and identify the dynamical role of universal antigravity produced by the cosmic vacuum.

  12. Methodology for characterizing modeling and discretization uncertainties in computational simulation

    SciTech Connect

    ALVIN,KENNETH F.; OBERKAMPF,WILLIAM L.; RUTHERFORD,BRIAN M.; DIEGERT,KATHLEEN V.

    2000-03-01

    This research effort focuses on methodology for quantifying the effects of model uncertainty and discretization error on computational modeling and simulation. The work is directed towards developing methodologies which treat model form assumptions within an overall framework for uncertainty quantification, for the purpose of developing estimates of total prediction uncertainty. The present effort consists of work in three areas: framework development for sources of uncertainty and error in the modeling and simulation process which impact model structure; model uncertainty assessment and propagation through Bayesian inference methods; and discretization error estimation within the context of non-deterministic analysis.

  13. Computer simulations of the motion and decay of global strings

    SciTech Connect

    Hagmann, C.; Sikivie, P.

    1990-01-01

    Computer simulations have been carried out of the motion and decay of global strings, including spectrum analysis of the energy stored in the scalar field which describes the global string and the radiated Nambu-Goldstone bosons. We simulated relaxing pieces of bent string and collapsing loops. We find, for the string sizes investigated, that the spectrum of field energy hardens rather than softens while the string decays into Nambu-Goldstone radiation. We argue on theoretical grounds that is indeed the most plausible general behaviour. 19 refs., 12 figs.

  14. A computer simulation approach to measurement of human control strategy

    NASA Technical Reports Server (NTRS)

    Green, J.; Davenport, E. L.; Engler, H. F.; Sears, W. E., III

    1982-01-01

    Human control strategy is measured through use of a psychologically-based computer simulation which reflects a broader theory of control behavior. The simulation is called the human operator performance emulator, or HOPE. HOPE was designed to emulate control learning in a one-dimensional preview tracking task and to measure control strategy in that setting. When given a numerical representation of a track and information about current position in relation to that track, HOPE generates positions for a stick controlling the cursor to be moved along the track. In other words, HOPE generates control stick behavior corresponding to that which might be used by a person learning preview tracking.

  15. A computer program for scanning transmission ion microscopy simulation

    NASA Astrophysics Data System (ADS)

    Wu, R.; Shen, H.; Mi, Y.; Sun, M. D.; Yang, M. J.

    2005-04-01

    With the installation of the Scanning Proton Microprobe system at Fudan University, we are in the process of developing a three-dimension reconstruction technique based on scanning transmission ion microscopy-computed tomography (STIM-CT). As the first step, a related computer program of STIM simulation has been established. This program is written in the Visual C++®, using the technique of OOP (Object Oriented Programming) and it is a standard multiple-document Windows® program. It can be run with all MS Windows® operating systems. The operating mode is the menu mode, using a multiple process technique. The stopping power theory is based on the Bethe-Bloch formula. In order to simplify the calculation, the improved cylindrical coordinate model was introduced in the program instead of a usual spherical or cylindrical coordinate model. The simulated results of a sample at several rotation angles are presented.

  16. Using Computer Simulation for Neurolab 2 Mission Planning

    NASA Technical Reports Server (NTRS)

    Sanders, Betty M.

    1997-01-01

    This paper presents an overview of the procedure used in the creation of a computer simulation video generated by the Graphics Research and Analysis Facility at NASA/Johnson Space Center. The simulation was preceded by an analysis of anthropometric characteristics of crew members and workspace requirements for 13 experiments to be conducted on Neurolab 2 which is dedicated to neuroscience and behavioral research. Neurolab 2 is being carried out as a partnership among national domestic research institutes and international space agencies. The video is a tour of the Spacelab module as it will be configured for STS-90, scheduled for launch in the spring of 1998, and identifies experiments that can be conducted in parallel during that mission. Therefore, this paper will also address methods for using computer modeling to facilitate the mission planning activity.

  17. Development of computer simulations for landfill methane recovery

    SciTech Connect

    Massmann, J.W.; Moore, C.A.; Sykes, R.M.

    1981-12-01

    Two- and three-dimensional finite-difference computer programs simulating methane recovery systems in landfills have been developed. These computer programs model multicomponent combined pressure and diffusional flow in porous media. Each program and the processes it models are described in this report. Examples of the capabilities of each program are also presented. The two-dimensional program was used to simulate methane recovery systems in a cylindrically shaped landfill. The effects of various pump locations, geometries, and extraction rates were determined. The three-dimensional program was used to model the Puente Hills landfill, a field test site in southern California. The biochemical and microbiological details of methane generation in landfills are also given. Effects of environmental factors, such as moisture, oxygen, temperature, and nutrients on methane generation are discussed and an analytical representation of the gas generation rate is developed.

  18. Computer Simulation for Air-coupled Ultrasonic Testing

    NASA Astrophysics Data System (ADS)

    Yamawaki, H.

    2014-06-01

    Air-coupled ultrasound is used as non-contact ultrasonic testing method. For wider application of air-coupled ultrasonic technique, it is required to know situation of ultrasonic propagation between air and solid. Transmittance of the ultrasonic waves from air to solids is extremely small with 10-5 however it was revealed that, by using computer simulation methods based on the two-stage elastic wave equation in which two independent variables of stress and particle velocity are used, visualization calculation of ultrasonic propagation between air and solid was possible. In this report, the calculation of air-coupled ultrasound using the new Improved-FDM for computer simulation of ultrasonic propagation in solids is shown. Waveforms obtained by 1-dimensional calculation are discussed for principle and performance of the calculation. Visualization of ultrasonic incidence to cylindrical steel pipe is demonstrated as an example to show availability for ultrasonic testing.

  19. Computational aeroacoustics and numerical simulation of supersonic jets

    NASA Technical Reports Server (NTRS)

    Morris, Philip J.; Long, Lyle N.

    1996-01-01

    The research project has been a computational study of computational aeroacoustics algorithms and numerical simulations of the flow and noise of supersonic jets. During this study a new method for the implementation of solid wall boundary conditions for complex geometries in three dimensions has been developed. In addition, a detailed study of the simulation of the flow in and noise from supersonic circular and rectangular jets has been conducted. Extensive comparisons have been made with experimental measurements. A summary of the results of the research program are attached as the main body of this report in the form of two publications. Also, the report lists the names of the students who were supported by this grant, their degrees, and the titles of their dissertations. In addition, a list of presentations and publications made by the Principal Investigators and the research students is also included.

  20. Lessons from computer simulations of ablation of atrial fibrillation.

    PubMed

    Jacquemet, Vincent

    2016-05-01

    This paper reviews the simulations of catheter ablation in computer models of the atria, from the first attempts to the most recent anatomical models. It describes how postulated substrates of atrial fibrillation can be incorporated into mathematical models, how modelling studies can be designed to test ablation strategies, what their current trade-offs and limitations are, and what clinically relevant lessons can be learnt from these simulations. Drawing a parallel between clinical and modelling studies, six ablation targets are considered: pulmonary vein isolation, linear ablation, ectopic foci, complex fractionated atrial electrogram, rotors and ganglionated plexi. The examples presented for each ablation target illustrate a major advantage of computer models, the ability to identify why a therapy is successful or not in a given atrial fibrillation substrate. The integration of pathophysiological data to create detailed models of arrhythmogenic substrates is expected to solidify the understanding of ablation mechanisms and to provide theoretical arguments supporting substrate-specific ablation strategies. PMID:26846178

  1. Computational simulation of flows in an entire centrifugal heart pump.

    PubMed

    Nakamura, S; Yano, K

    1999-06-01

    A prototype computational code to numerically simulate the blood flows in an entire centrifugal heart pump has been developed. The unsteady incompressible Navier-Stokes equations are solved on a parallel computer, the Cray T3E. By domain decomposition, the whole flow space is decomposed to a number of subdomains for each of which a structured algebraic grid is assigned. The grids for the inlet eye and blade regions are on the rotating frame while grids for other regions are on the nonrotating frame, and the edge of the rotating grids slides over the edge of the nonrotating frame, and the edge of the rotating grids slides over the edge of the nonrotating grids. The code is able to simulate the flows in the rotor, volute, and diffuser as well as to find pump performance indicators. The present paper presents an overview of the code and describes a study on the effect of volute width. PMID:10392287

  2. A Computational Approach for Probabilistic Analysis of Water Impact Simulations

    NASA Technical Reports Server (NTRS)

    Horta, Lucas G.; Mason, Brian H.; Lyle, Karen H.

    2009-01-01

    NASA's development of new concepts for the Crew Exploration Vehicle Orion presents many similar challenges to those worked in the sixties during the Apollo program. However, with improved modeling capabilities, new challenges arise. For example, the use of the commercial code LS-DYNA, although widely used and accepted in the technical community, often involves high-dimensional, time consuming, and computationally intensive simulations. The challenge is to capture what is learned from a limited number of LS-DYNA simulations to develop models that allow users to conduct interpolation of solutions at a fraction of the computational time. This paper presents a description of the LS-DYNA model, a brief summary of the response surface techniques, the analysis of variance approach used in the sensitivity studies, equations used to estimate impact parameters, results showing conditions that might cause injuries, and concluding remarks.

  3. Flexing computational muscle: modeling and simulation of musculotendon dynamics.

    PubMed

    Millard, Matthew; Uchida, Thomas; Seth, Ajay; Delp, Scott L

    2013-02-01

    Muscle-driven simulations of human and animal motion are widely used to complement physical experiments for studying movement dynamics. Musculotendon models are an essential component of muscle-driven simulations, yet neither the computational speed nor the biological accuracy of the simulated forces has been adequately evaluated. Here we compare the speed and accuracy of three musculotendon models: two with an elastic tendon (an equilibrium model and a damped equilibrium model) and one with a rigid tendon. Our simulation benchmarks demonstrate that the equilibrium and damped equilibrium models produce similar force profiles but have different computational speeds. At low activation, the damped equilibrium model is 29 times faster than the equilibrium model when using an explicit integrator and 3 times faster when using an implicit integrator; at high activation, the two models have similar simulation speeds. In the special case of simulating a muscle with a short tendon, the rigid-tendon model produces forces that match those generated by the elastic-tendon models, but simulates 2-54 times faster when an explicit integrator is used and 6-31 times faster when an implicit integrator is used. The equilibrium, damped equilibrium, and rigid-tendon models reproduce forces generated by maximally-activated biological muscle with mean absolute errors less than 8.9%, 8.9%, and 20.9% of the maximum isometric muscle force, respectively. When compared to forces generated by submaximally-activated biological muscle, the forces produced by the equilibrium, damped equilibrium, and rigid-tendon models have mean absolute errors less than 16.2%, 16.4%, and 18.5%, respectively. To encourage further development of musculotendon models, we provide implementations of each of these models in OpenSim version 3.1 and benchmark data online, enabling others to reproduce our results and test their models of musculotendon dynamics. PMID:23445050

  4. pV3-Gold Visualization Environment for Computer Simulations

    NASA Technical Reports Server (NTRS)

    Babrauckas, Theresa L.

    1997-01-01

    A new visualization environment, pV3-Gold, can be used during and after a computer simulation to extract and visualize the physical features in the results. This environment, which is an extension of the pV3 visualization environment developed at the Massachusetts Institute of Technology with guidance and support by researchers at the NASA Lewis Research Center, features many tools that allow users to display data in various ways.

  5. Ku-Band rendezvous radar performance computer simulation model

    NASA Technical Reports Server (NTRS)

    Magnusson, H. G.; Goff, M. F.

    1984-01-01

    All work performed on the Ku-band rendezvous radar performance computer simulation model program since the release of the preliminary final report is summarized. Developments on the program fall into three distinct categories: (1) modifications to the existing Ku-band radar tracking performance computer model; (2) the addition of a highly accurate, nonrealtime search and acquisition performance computer model to the total software package developed on this program; and (3) development of radar cross section (RCS) computation models for three additional satellites. All changes in the tracking model involved improvements in the automatic gain control (AGC) and the radar signal strength (RSS) computer models. Although the search and acquisition computer models were developed under the auspices of the Hughes Aircraft Company Ku-Band Integrated Radar and Communications Subsystem program office, they have been supplied to NASA as part of the Ku-band radar performance comuter model package. Their purpose is to predict Ku-band acquisition performance for specific satellite targets on specific missions. The RCS models were developed for three satellites: the Long Duration Exposure Facility (LDEF) spacecraft, the Solar Maximum Mission (SMM) spacecraft, and the Space Telescopes.

  6. IMPROVING TACONITE PROCESSING PLANT EFFICIENCY BY COMPUTER SIMULATION, Final Report

    SciTech Connect

    William M. Bond; Salih Ersayin

    2007-03-30

    This project involved industrial scale testing of a mineral processing simulator to improve the efficiency of a taconite processing plant, namely the Minorca mine. The Concentrator Modeling Center at the Coleraine Minerals Research Laboratory, University of Minnesota Duluth, enhanced the capabilities of available software, Usim Pac, by developing mathematical models needed for accurate simulation of taconite plants. This project provided funding for this technology to prove itself in the industrial environment. As the first step, data representing existing plant conditions were collected by sampling and sample analysis. Data were then balanced and provided a basis for assessing the efficiency of individual devices and the plant, and also for performing simulations aimed at improving plant efficiency. Performance evaluation served as a guide in developing alternative process strategies for more efficient production. A large number of computer simulations were then performed to quantify the benefits and effects of implementing these alternative schemes. Modification of makeup ball size was selected as the most feasible option for the target performance improvement. This was combined with replacement of existing hydrocyclones with more efficient ones. After plant implementation of these modifications, plant sampling surveys were carried out to validate findings of the simulation-based study. Plant data showed very good agreement with the simulated data, confirming results of simulation. After the implementation of modifications in the plant, several upstream bottlenecks became visible. Despite these bottlenecks limiting full capacity, concentrator energy improvement of 7% was obtained. Further improvements in energy efficiency are expected in the near future. The success of this project demonstrated the feasibility of a simulation-based approach. Currently, the Center provides simulation-based service to all the iron ore mining companies operating in northern

  7. Numerical simulations of the thermoacoustic computed tomography breast imaging system

    NASA Astrophysics Data System (ADS)

    Kiser, William Lester, Jr.

    A thermoacoustic wave is produced when an object absorbs energy and experiences a subsequent thermal expansion. We have developed a Thermoacoustic Computed Tomography (TACT) breast imaging system to exploit the thermoacoustic phenomena as a method of soft tissue imaging. By exposing the breast to short pulses of 434 MHz microwaves, ultrasonic pulses are generated and detected with a hemispherical transducer array submersed in a water bath. Filtering and back projecting the transducer signals generates a 3-D image that maps the localized microwave absorption properties of the breast. In an effort to understand the factors limiting image quality, the TACT system was numerically simulated. The simulations were used to generate the transducer signals that would be collected by the TACT system during a scan of an object. These simulated data streams were then fed into the system image reconstruction software to provide images of simulated phantoms. The effects of transducer diameter, transducer response, transducer array geometry and stimulating pulse width on the spatial and contrast resolution of the system were quantified using the simulations. The spatial resolution was highly dependent upon location in the imaging volume. This was due to the off axis response of transducers of finite aperture. Simulated data were compared with experimental data, obtained by imaging a parallel-piped resolution phantom, to verify the accuracy of the simulation code. A contrast-detail phantom was numerically simulated to determine the ability of the system to image spheres of diameters <1 cm with absorption values on the order of physiologic saline, when located in a background of noise. The results of the contrast-detail analysis were dependent on the location of the spheres in the imaging volume and the diameter of the simulated transducers. This work sets the foundation for the initial image quality studies of the TACT system. Improvements to the current imaging system, based on

  8. Cane Toad or Computer Mouse? Real and Computer-Simulated Laboratory Exercises in Physiology Classes

    ERIC Educational Resources Information Center

    West, Jan; Veenstra, Anneke

    2012-01-01

    Traditional practical classes in many countries are being rationalised to reduce costs. The challenge for university educators is to provide students with the opportunity to reinforce theoretical concepts by running something other than a traditional practical program. One alternative is to replace wet labs with comparable computer simulations.…

  9. Some computer simulations based on the linear relative risk model

    SciTech Connect

    Gilbert, E.S.

    1991-10-01

    This report presents the results of computer simulations designed to evaluate and compare the performance of the likelihood ratio statistic and the score statistic for making inferences about the linear relative risk mode. The work was motivated by data on workers exposed to low doses of radiation, and the report includes illustration of several procedures for obtaining confidence limits for the excess relative risk coefficient based on data from three studies of nuclear workers. The computer simulations indicate that with small sample sizes and highly skewed dose distributions, asymptotic approximations to the score statistic or to the likelihood ratio statistic may not be adequate. For testing the null hypothesis that the excess relative risk is equal to zero, the asymptotic approximation to the likelihood ratio statistic was adequate, but use of the asymptotic approximation to the score statistic rejected the null hypothesis too often. Frequently the likelihood was maximized at the lower constraint, and when this occurred, the asymptotic approximations for the likelihood ratio and score statistics did not perform well in obtaining upper confidence limits. The score statistic and likelihood ratio statistics were found to perform comparably in terms of power and width of the confidence limits. It is recommended that with modest sample sizes, confidence limits be obtained using computer simulations based on the score statistic. Although nuclear worker studies are emphasized in this report, its results are relevant for any study investigating linear dose-response functions with highly skewed exposure distributions. 22 refs., 14 tabs.

  10. Improving computational efficiency of Monte Carlo simulations with variance reduction

    SciTech Connect

    Turner, A.

    2013-07-01

    CCFE perform Monte-Carlo transport simulations on large and complex tokamak models such as ITER. Such simulations are challenging since streaming and deep penetration effects are equally important. In order to make such simulations tractable, both variance reduction (VR) techniques and parallel computing are used. It has been found that the application of VR techniques in such models significantly reduces the efficiency of parallel computation due to 'long histories'. VR in MCNP can be accomplished using energy-dependent weight windows. The weight window represents an 'average behaviour' of particles, and large deviations in the arriving weight of a particle give rise to extreme amounts of splitting being performed and a long history. When running on parallel clusters, a long history can have a detrimental effect on the parallel efficiency - if one process is computing the long history, the other CPUs complete their batch of histories and wait idle. Furthermore some long histories have been found to be effectively intractable. To combat this effect, CCFE has developed an adaptation of MCNP which dynamically adjusts the WW where a large weight deviation is encountered. The method effectively 'de-optimises' the WW, reducing the VR performance but this is offset by a significant increase in parallel efficiency. Testing with a simple geometry has shown the method does not bias the result. This 'long history method' has enabled CCFE to significantly improve the performance of MCNP calculations for ITER on parallel clusters, and will be beneficial for any geometry combining streaming and deep penetration effects. (authors)

  11. Scalable High Performance Computing: Direct and Large-Eddy Turbulent Flow Simulations Using Massively Parallel Computers

    NASA Technical Reports Server (NTRS)

    Morgan, Philip E.

    2004-01-01

    This final report contains reports of research related to the tasks "Scalable High Performance Computing: Direct and Lark-Eddy Turbulent FLow Simulations Using Massively Parallel Computers" and "Devleop High-Performance Time-Domain Computational Electromagnetics Capability for RCS Prediction, Wave Propagation in Dispersive Media, and Dual-Use Applications. The discussion of Scalable High Performance Computing reports on three objectives: validate, access scalability, and apply two parallel flow solvers for three-dimensional Navier-Stokes flows; develop and validate a high-order parallel solver for Direct Numerical Simulations (DNS) and Large Eddy Simulation (LES) problems; and Investigate and develop a high-order Reynolds averaged Navier-Stokes turbulence model. The discussion of High-Performance Time-Domain Computational Electromagnetics reports on five objectives: enhancement of an electromagnetics code (CHARGE) to be able to effectively model antenna problems; utilize lessons learned in high-order/spectral solution of swirling 3D jets to apply to solving electromagnetics project; transition a high-order fluids code, FDL3DI, to be able to solve Maxwell's Equations using compact-differencing; develop and demonstrate improved radiation absorbing boundary conditions for high-order CEM; and extend high-order CEM solver to address variable material properties. The report also contains a review of work done by the systems engineer.

  12. The smart vapor retarder: An innovation inspired by computer simulations

    SciTech Connect

    Kuenzel, H.M.

    1998-12-31

    Water management is the new trend in civil engineering. Since it is difficult to ensure perfect vapor- and watertightness of building components, a limited moisture ingress is acceptable as long as the drying process is effective enough to avoid moisture damage. Recent computer models for the simulation of heat and moisture transport are valuable tools for the risk assessment of structures and their repair or retrofit. Unventilated, insulated assemblies with a vapor-resistant exterior layer can accumulate water because winter condensation and summer drying are not balanced. The balance can be reestablished if the vapor retarder is more permeable in summer than in winter. Parametric computer studies have defined the required properties of such a vapor retarder. Developed according to the computed specifications, the smart vapor retarder shows a seasonal variation in vapor permeability of a factor of ten. The secret of this behavior lies in the humidity-dependent vapor diffusion resistance of the film material.

  13. An FPGA computing demo core for space charge simulation

    SciTech Connect

    Wu, Jinyuan; Huang, Yifei; /Fermilab

    2009-01-01

    In accelerator physics, space charge simulation requires large amount of computing power. In a particle system, each calculation requires time/resource consuming operations such as multiplications, divisions, and square roots. Because of the flexibility of field programmable gate arrays (FPGAs), we implemented this task with efficient use of the available computing resources and completely eliminated non-calculating operations that are indispensable in regular micro-processors (e.g. instruction fetch, instruction decoding, etc.). We designed and tested a 16-bit demo core for computing Coulomb's force in an Altera Cyclone II FPGA device. To save resources, the inverse square-root cube operation in our design is computed using a memory look-up table addressed with nine to ten most significant non-zero bits. At 200 MHz internal clock, our demo core reaches a throughput of 200 M pairs/s/core, faster than a typical 2 GHz micro-processor by about a factor of 10. Temperature and power consumption of FPGAs were also lower than those of micro-processors. Fast and convenient, FPGAs can serve as alternatives to time-consuming micro-processors for space charge simulation.

  14. Precision Constraints from Computational Cosmology and Type Ia Supernova Simulations

    NASA Astrophysics Data System (ADS)

    Bernstein, Joseph P.; Kuhlmann, S. E.; Norris, B.; Biswas, R.

    2011-01-01

    The evidence for dark energy represents one of the greatest mysteries of modern science. The research undertaken probes the implications of dark energy via analysis of large scale structure and detonation-based Type Ia supernova light curve simulations. It is presently an exciting time to be involved in cosmology because planned astronomical surveys will effectively result in dark sector probes becoming systematics-limited, making numerical simulations crucial to the formulation of precision constraints. This work aims to assist in reaching the community goal of 1% constraints on the dark energy equation of state parameter. Reaching this goal will require 1) hydrodynamic+N-body simulations with a minimum of a 1 Gpc box size, 20483 hydrodynamic cells, and 1011 dark matter particles, which push the limits of existing codes, and 2) a better understanding of the explosion mechanism(s) for Type Ia supernovae, together with larger, high-quality data sets from present and upcoming supernova surveys. Initial results are discussed from two projects. The first is computational cosmology studies aimed at enabling the large simulations discussed above. The second is radiative transfer calculations drawn from Type Ia supernova explosion simulations aimed at bridging the gap between simulated light curves and those observed from, e.g., the Sloan Digital Sky Survey II and, eventually, the Dark Energy Survey.

  15. Numerical simulation of landfill aeration using computational fluid dynamics.

    PubMed

    Fytanidis, Dimitrios K; Voudrias, Evangelos A

    2014-04-01

    The present study is an application of Computational Fluid Dynamics (CFD) to the numerical simulation of landfill aeration systems. Specifically, the CFD algorithms provided by the commercial solver ANSYS Fluent 14.0, combined with an in-house source code developed to modify the main solver, were used. The unsaturated multiphase flow of air and liquid phases and the biochemical processes for aerobic biodegradation of the organic fraction of municipal solid waste were simulated taking into consideration their temporal and spatial evolution, as well as complex effects, such as oxygen mass transfer across phases, unsaturated flow effects (capillary suction and unsaturated hydraulic conductivity), temperature variations due to biochemical processes and environmental correction factors for the applied kinetics (Monod and 1st order kinetics). The developed model results were compared with literature experimental data. Also, pilot scale simulations and sensitivity analysis were implemented. Moreover, simulation results of a hypothetical single aeration well were shown, while its zone of influence was estimated using both the pressure and oxygen distribution. Finally, a case study was simulated for a hypothetical landfill aeration system. Both a static (steadily positive or negative relative pressure with time) and a hybrid (following a square wave pattern of positive and negative values of relative pressure with time) scenarios for the aeration wells were examined. The results showed that the present model is capable of simulating landfill aeration and the obtained results were in good agreement with corresponding previous experimental and numerical investigations. PMID:24525420

  16. Effective computer simulation of equilibrium adsorption with limited solubility

    NASA Astrophysics Data System (ADS)

    Zedek, Lukáš; Šembera, Jan

    2014-12-01

    Radioactive waste repositories are discussed to be built in compact granite rock massif somewhere in the Czech Republic. To support the decision-making, various computer simulations are performed. These simulations help to evaluate risks connected with potential isolation failures, followed by transport of released radionuclides in the groundwater. Transport of radionuclides is affected by many natural processes. In this paper we focus on two important processes: adsorption and limited solubility (surface precipitation) of radionuclides in groundwater. Presented approach is based on interpolation instead of time demanding solution of nonlinear equations arising from mathematical description of the problem. The effectiveness of the proposed approach consists in creation of an interpolation table of points lying on an isotherm and transformed to mass balance maintaining system of coordinates. This kind of table is used to project data from transport part of simulation on the isotherm. The interpolation table points are computed using free derivative, nonlinear equation solver which avoids some of numerical solution difficulties. Results achieved with the use of our approach are comparable to Newton-Raphson method achieved solutions, but the simulation times are shorter.

  17. Computer simulations of a tumor surface octapeptide epitope.

    PubMed

    Reid, R H; Hooper, C A; Brooks, B R

    1989-01-01

    Molecular dynamics using CHARMM and GEMM programs with the Star Technologies ST 100 array processor functioning at the speed of super computers was used as a searching algorithm for conformational exploration of the octapeptide Gly-Asn-Thr-Ile-Val-Ala-Glu. This poorly soluble octapeptide is the N-terminal epitope of an 11 KD glycoprotein antigen residing on human ductal carcinoma (breast) cells. Very long (nanoseconds) simulations were required. Both an alpha-helix and the N-acetyl-N1-methylamide derived minimized starting structures gave the same lowest potential energy conformation with simulations at 600 K. The same conformation was found only when using the latter starting conformation with simulations at 300 K. The lowest potential energy conformation was stabilized by 4 hydrophobic contacts and 13 H bonds completing one turn of a left-handed helix. PMID:2470439

  18. Basic plasma and fusion theory and computer simulations survey

    SciTech Connect

    Kawakami, I.; Nishikawa, K.

    1983-12-01

    The College of Science and Technology at Nihon University and the Institute for Fusion Theory at Hiroshima University discuss the history of the role of theory and simulation in fusion-oriented research. Recent activities include a one-dimensional tokamak transport code at Nagoya University and three-dimensional resistive MHD simulation studies of spheromaks. Other recent activities discussed include the tokamak computer code system TRITON, transport flux in currentless ECH-produced plasma in Heliotron-E, and thermal electron transport in the presence of a steep temperature gradient. The Japan-U.S. Joint Institute for Fusion Theory's present activities are discussed, including subject areas in three-dimensional simulation studies, nonequilibrium statistical physics, anaomalous transport and drift wave turbulence and hot-electron physics.

  19. Simulation of Tailrace Hydrodynamics Using Computational Fluid Dynamics Models

    SciTech Connect

    Cook, Christopher B.; Richmond, Marshall C.

    2001-05-01

    This report investigates the feasibility of using computational fluid dynamics (CFD) tools to investigate hydrodynamic flow fields surrounding the tailrace zone below large hydraulic structures. Previous and ongoing studies using CFD tools to simulate gradually varied flow with multiple constituents and forebay/intake hydrodynamics have shown that CFD tools can provide valuable information for hydraulic and biological evaluation of fish passage near hydraulic structures. These studies however are incapable of simulating the rapidly varying flow fields that involving breakup of the free-surface, such as those through and below high flow outfalls and spillways. Although the use of CFD tools for these types of flow are still an active area of research, initial applications discussed in this report show that these tools are capable of simulating the primary features of these highly transient flow fields.

  20. Lightweight computational steering of very large scale molecular dynamics simulations

    SciTech Connect

    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 how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.

  1. Computer-based simulator for catheter insertion training.

    PubMed

    Aloisio, Giovanni; Barone, Luigi; Bergamasco, Massimo; Avizzano, Carlo Alberto; De Paolis, Lucio Tommaso; Franceschini, Marco; Mongelli, Antonio; Pantile, Gianluca; Provenzano, Luciana; Raspolli, Mirko

    2004-01-01

    Minimally invasive surgery procedures are getting common in surgical practice; however the new interventional procedure requires different skills compared to the conventional surgical techniques. The need for training process is very important in order to successfully and safely execute a surgical procedure. Computer-based simulators, with appropriate tactile feedback device, can be an efficient method for facilitating the education and training process. In addition, virtual reality surgical simulators can reduce costs of education and provide realism with regard to tissues behaviour and real-time interaction. This work take into account the results of the HERMES Project (HEmatology Research virtual MEdical System), conceived and managed by Consorzio CETMA-Research Centre; the aim of this project is to build an integrate system in order to simulate a coronary angioplasty intervention. PMID:15544228

  2. Advanced manned space flight simulation and training: An investigation of simulation host computer system concepts

    NASA Technical Reports Server (NTRS)

    Montag, Bruce C.; Bishop, Alfred M.; Redfield, Joe B.

    1989-01-01

    The findings of a preliminary investigation by Southwest Research Institute (SwRI) in simulation host computer concepts is presented. It is designed to aid NASA in evaluating simulation technologies for use in spaceflight training. The focus of the investigation is on the next generation of space simulation systems that will be utilized in training personnel for Space Station Freedom operations. SwRI concludes that NASA should pursue a distributed simulation host computer system architecture for the Space Station Training Facility (SSTF) rather than a centralized mainframe based arrangement. A distributed system offers many advantages and is seen by SwRI as the only architecture that will allow NASA to achieve established functional goals and operational objectives over the life of the Space Station Freedom program. Several distributed, parallel computing systems are available today that offer real-time capabilities for time critical, man-in-the-loop simulation. These systems are flexible in terms of connectivity and configurability, and are easily scaled to meet increasing demands for more computing power.

  3. Animats: computer-simulated animals in behavioral research.

    PubMed

    Watts, J M

    1998-10-01

    The term animat refers to a class of simulated animals. This article is intended as a nontechnical introduction to animat research. Animats can be robots interacting with the real world or computer simulations. In this article, the use of computer-generated animats is emphasized. The scientific use of animats has been pioneered by artificial intelligence and artificial life researchers. Behavior-based artificial intelligence uses animats capable of autonomous and adaptive activity as conceptual tools in the design of usefully intelligent systems. Artificial life proponents view some human artifacts, including informational structures that show adaptive behavior and self-replication, as animats may do, as analogous to biological organisms. Animat simulations may be used for rapid and inexpensive evaluation of new livestock environments or management techniques. The animat approach is a powerful heuristic for understanding the mechanisms that underlie behavior. The simple rules and capabilities of animat models generate emergent and sometimes unpredictable behavior. Adaptive variability in animat behavior may be exploited using artificial neural networks. These have computational properties similar to natural neurons and are capable of learning. Artificial neural networks can control behavior at all levels of an animat's functional organization. Improving the performance of animats often requires genetic programming. Genetic algorithms are computer programs that are capable of self-replication, simulating biological reproduction. Animats may thus evolve over generations. Selective forces may be provided by a human overseer or be part of the simulated environment. Animat techniques allow researchers to culture behavior outside the organism that usually produces it. This approach could contribute new insights in theoretical ethology on questions including the origins of social behavior and cooperation, adaptation, and the emergent nature of complex behavior. Animat

  4. Analysis of solvation structure and thermodynamics of ethane and propane in water by reference interaction site model theory using all-atom models

    NASA Astrophysics Data System (ADS)

    Cui, Qizhi; Smith, Vedene H.

    2001-08-01

    Following our previous paper on methane [Cui and Smith, J. Chem. Phys. 113, 10240 (2000)], we study the solvation structures and thermodynamics of ethane and propane in water at the infinite dilution limit by using the hypernetted chain closure reference interaction site model (HNC-RISM) theory with all-atom representations for solute molecules. At four thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3, all the atomic solute-solvent radial distribution functions are obtained, and the corresponding running coordination numbers and the hydration free energies, energies, enthalpies, and entropies are calculated with the radial distribution functions as input. The hydration structures of ethane and propane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes [Yin and Mackerell, J. Comput. Chem. 19, 334 (1998)], the ethane and propane hydration thermodynamic properties predicted by the HNC-RISM theory are improved in the specified temperature range (10-55 °C).

  5. Accelerating Climate and Weather Simulations through Hybrid Computing

    NASA Technical Reports Server (NTRS)

    Zhou, Shujia; Cruz, Carlos; Duffy, Daniel; Tucker, Robert; Purcell, Mark

    2011-01-01

    Unconventional multi- and many-core processors (e.g. IBM (R) Cell B.E.(TM) and NVIDIA (R) GPU) have emerged as effective accelerators in trial climate and weather simulations. Yet these climate and weather models typically run on parallel computers with conventional processors (e.g. Intel, AMD, and IBM) using Message Passing Interface. To address challenges involved in efficiently and easily connecting accelerators to parallel computers, we investigated using IBM's Dynamic Application Virtualization (TM) (IBM DAV) software in a prototype hybrid computing system with representative climate and weather model components. The hybrid system comprises two Intel blades and two IBM QS22 Cell B.E. blades, connected with both InfiniBand(R) (IB) and 1-Gigabit Ethernet. The system significantly accelerates a solar radiation model component by offloading compute-intensive calculations to the Cell blades. Systematic tests show that IBM DAV can seamlessly offload compute-intensive calculations from Intel blades to Cell B.E. blades in a scalable, load-balanced manner. However, noticeable communication overhead was observed, mainly due to IP over the IB protocol. Full utilization of IB Sockets Direct Protocol and the lower latency production version of IBM DAV will reduce this overhead.

  6. Further developments in cloud statistics for computer simulations

    NASA Technical Reports Server (NTRS)

    Chang, D. T.; Willand, J. H.

    1972-01-01

    This study is a part of NASA's continued program to provide global statistics of cloud parameters for computer simulation. The primary emphasis was on the development of the data bank of the global statistical distributions of cloud types and cloud layers and their applications in the simulation of the vertical distributions of in-cloud parameters such as liquid water content. These statistics were compiled from actual surface observations as recorded in Standard WBAN forms. Data for a total of 19 stations were obtained and reduced. These stations were selected to be representative of the 19 primary cloud climatological regions defined in previous studies of cloud statistics. Using the data compiled in this study, a limited study was conducted of the hemogeneity of cloud regions, the latitudinal dependence of cloud-type distributions, the dependence of these statistics on sample size, and other factors in the statistics which are of significance to the problem of simulation. The application of the statistics in cloud simulation was investigated. In particular, the inclusion of the new statistics in an expanded multi-step Monte Carlo simulation scheme is suggested and briefly outlined.

  7. Three Dimensional Computer Graphics Federates for the 2012 Smackdown Simulation

    NASA Technical Reports Server (NTRS)

    Fordyce, Crystal; Govindaiah, Swetha; Muratet, Sean; O'Neil, Daniel A.; Schricker, Bradley C.

    2012-01-01

    The Simulation Interoperability Standards Organization (SISO) Smackdown is a two-year old annual event held at the 2012 Spring Simulation Interoperability Workshop (SIW). A primary objective of the Smackdown event is to provide college students with hands-on experience in developing distributed simulations using High Level Architecture (HLA). Participating for the second time, the University of Alabama in Huntsville (UAHuntsville) deployed four federates, two federates simulated a communications server and a lunar communications satellite with a radio. The other two federates generated 3D computer graphics displays for the communication satellite constellation and for the surface based lunar resupply mission. Using the Light-Weight Java Graphics Library, the satellite display federate presented a lunar-texture mapped sphere of the moon and four Telemetry Data Relay Satellites (TDRS), which received object attributes from the lunar communications satellite federate to drive their motion. The surface mission display federate was an enhanced version of the federate developed by ForwardSim, Inc. for the 2011 Smackdown simulation. Enhancements included a dead-reckoning algorithm and a visual indication of which communication satellite was in line of sight of Hadley Rille. This paper concentrates on these two federates by describing the functions, algorithms, HLA object attributes received from other federates, development experiences and recommendations for future, participating Smackdown teams.

  8. Computational simulation of materials notes for lectures given at UCSB, May 1996--June 1996

    SciTech Connect

    LeSar, R.

    1997-01-01

    This report presents information from a lecture given on the computational simulation of materials. The purpose is to introduce modern computerized simulation methods for materials properties and response.

  9. Scientific and computational challenges of the fusion simulation project (FSP)

    NASA Astrophysics Data System (ADS)

    Tang, W. M.

    2008-07-01

    This paper highlights the scientific and computational challenges facing the Fusion Simulation Project (FSP). The primary objective is to develop advanced software designed to use leadership-class computers for carrying out multiscale physics simulations to provide information vital to delivering a realistic integrated fusion simulation model with unprecedented physics fidelity. This multiphysics capability will be unprecedented in that in the current FES applications domain, the largest-scale codes are used to carry out first-principles simulations of mostly individual phenomena in realistic 3D geometry while the integrated models are much smaller-scale, lower-dimensionality codes with significant empirical elements used for modeling and designing experiments. The FSP is expected to be the most up-to-date embodiment of the theoretical and experimental understanding of magnetically confined thermonuclear plasmas and to provide a living framework for the simulation of such plasmas as the associated physics understanding continues to advance over the next several decades. Substantive progress on answering the outstanding scientific questions in the field will drive the FSP toward its ultimate goal of developing a reliable ability to predict the behavior of plasma discharges in toroidal magnetic fusion devices on all relevant time and space scales. From a computational perspective, the fusion energy science application goal to produce high-fidelity, whole-device modeling capabilities will demand computing resources in the petascale range and beyond, together with the associated multicore algorithmic formulation needed to address burning plasma issues relevant to ITER — a multibillion dollar collaborative device involving seven international partners representing over half the world's population. Even more powerful exascale platforms will be needed to meet the future challenges of designing a demonstration fusion reactor (DEMO). Analogous to other major applied

  10. A computationally efficient particle-simulation method suited to vector-computer architectures

    SciTech Connect

    McDonald, J.D.

    1990-01-01

    Recent interest in a National Aero-Space Plane (NASP) and various Aero-assisted Space Transfer Vehicles (ASTVs) presents the need for a greater understanding of high-speed rarefied flight conditions. Particle simulation techniques such as the Direct Simulation Monte Carlo (DSMC) method are well suited to such problems, but the high cost of computation limits the application of the methods to two-dimensional or very simple three-dimensional problems. This research re-examines the algorithmic structure of existing particle simulation methods and re-structures them to allow efficient implementation on vector-oriented supercomputers. A brief overview of the DSMC method and the Cray-2 vector computer architecture are provided, and the elements of the DSMC method that inhibit substantial vectorization are identified. One such element is the collision selection algorithm. A complete reformulation of underlying kinetic theory shows that this may be efficiently vectorized for general gas mixtures. The mechanics of collisions are vectorizable in the DSMC method, but several optimizations are suggested that greatly enhance performance. Also this thesis proposes a new mechanism for the exchange of energy between vibration and other energy modes. The developed scheme makes use of quantized vibrational states and is used in place of the Borgnakke-Larsen model. Finally, a simplified representation of physical space and boundary conditions is utilized to further reduce the computational cost of the developed method. Comparison to solutions obtained from the DSMC method for the relaxation of internal energy modes in a homogeneous gas, as well as single and multiple specie shock wave profiles, are presented. Additionally, a large scale simulation of the flow about the proposed Aeroassisted Flight Experiment (AFE) vehicle is included as an example of the new computational capability of the developed particle simulation method.

  11. Computer simulations of realistic three-dimensional microstructures

    NASA Astrophysics Data System (ADS)

    Mao, Yuxiong

    A novel and efficient methodology is developed for computer simulations of realistic two-dimensional (2D) and three-dimensional (3D) microstructures. The simulations incorporate realistic 2D and 3D complex morphologies/shapes, spatial patterns, anisotropy, volume fractions, and size distributions of the microstructural features statistically similar to those in the corresponding real microstructures. The methodology permits simulations of sufficiently large 2D as well as 3D microstructural windows that incorporate short-range (on the order of particle/feature size) as well as long-range (hundred times the particle/feature size) microstructural heterogeneities and spatial patterns at high resolution. The utility of the technique has been successfully demonstrated through its application to the 2D microstructures of the constituent particles in wrought Al-alloys, the 3D microstructure of discontinuously reinforced Al-alloy (DRA) composites containing SiC particles that have complex 3D shapes/morphologies and spatial clustering, and 3D microstructure of boron modified Ti-6Al-4V composites containing fine TiB whiskers and coarse primary TiB particles. The simulation parameters are correlated with the materials processing parameters (such as composition, particle size ratio, extrusion ratio, extrusion temperature, etc.), which enables the simulations of rational virtual 3D microstructures for the parametric studies on microstructure-properties relationships. The simulated microstructures have been implemented in the 3D finite-elements (FE)-based framework for simulations of micro-mechanical response and stress-strain curves. Finally, a new unbiased and assumption free dual-scale virtual cycloids probe for estimating surface area of 3D objects constructed by 2D serial section images is also presented.

  12. Quantum game simulator, using the circuit model of quantum computation

    NASA Astrophysics Data System (ADS)

    Vlachos, Panagiotis; Karafyllidis, Ioannis G.

    2009-10-01

    We present a general two-player quantum game simulator that can simulate any two-player quantum game described by a 2×2 payoff matrix (two strategy games).The user can determine the payoff matrices for both players, their strategies and the amount of entanglement between their initial strategies. The outputs of the simulator are the expected payoffs of each player as a function of the other player's strategy parameters and the amount of entanglement. The simulator also produces contour plots that divide the strategy spaces of the game in regions in which players can get larger payoffs if they choose to use a quantum strategy against any classical one. We also apply the simulator to two well-known quantum games, the Battle of Sexes and the Chicken game. Program summaryProgram title: Quantum Game Simulator (QGS) Catalogue identifier: AEED_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEED_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3416 No. of bytes in distributed program, including test data, etc.: 583 553 Distribution format: tar.gz Programming language: Matlab R2008a (C) Computer: Any computer that can sufficiently run Matlab R2008a Operating system: Any system that can sufficiently run Matlab R2008a Classification: 4.15 Nature of problem: Simulation of two player quantum games described by a payoff matrix. Solution method: The program calculates the matrices that comprise the Eisert setup for quantum games based on the quantum circuit model. There are 5 parameters that can be altered. We define 3 of them as constant. We play the quantum game for all possible values for the other 2 parameters and store the results in a matrix. Unusual features: The software provides an easy way of simulating any two-player quantum games. Running time: Approximately

  13. Use of a Computer Simulation To Develop Mental Simulations for Understanding Relative Motion Concepts.

    ERIC Educational Resources Information Center

    Monaghan, James M.; Clement, John

    1999-01-01

    Presents evidence for students' qualitative and quantitative difficulties with apparently simple one-dimensional relative-motion problems, students' spontaneous visualization of relative-motion problems, the visualizations facilitating solution of these problems, and students' memories of the online computer simulation used as a framework for…

  14. A COMPUTATIONAL WORKBENCH ENVIRONMENT FOR VIRTUAL POWER PLANT SIMULATION

    SciTech Connect

    Mike Bockelie; Dave Swensen; Martin Denison; Zumao Chen; Temi Linjewile; Mike Maguire; Adel Sarofim; Connie Senior; Changguan Yang; Hong-Shig Shim

    2004-04-28

    This is the fourteenth Quarterly Technical Report for DOE Cooperative Agreement No: DE-FC26-00NT41047. The goal of the project is to develop and demonstrate a Virtual Engineering-based framework for simulating the performance of Advanced Power Systems. Within the last quarter, good progress has been made on all aspects of the project. Software development efforts have focused primarily on completing a prototype detachable user interface for the framework and on integrating Carnegie Mellon Universities IECM model core with the computational engine. In addition to this work, progress has been made on several other development and modeling tasks for the program. These include: (1) improvements to the infrastructure code of the computational engine, (2) enhancements to the model interfacing specifications, (3) additional development to increase the robustness of all framework components, (4) enhanced coupling of the computational and visualization engine components, (5) a series of detailed simulations studying the effects of gasifier inlet conditions on the heat flux to the gasifier injector, and (6) detailed plans for implementing models for mercury capture for both warm and cold gas cleanup have been created.

  15. Benchmarking computational fluid dynamics models for lava flow simulation

    NASA Astrophysics Data System (ADS)

    Dietterich, Hannah; Lev, Einat; Chen, Jiangzhi

    2016-04-01

    Numerical simulations of lava flow emplacement are valuable for assessing lava flow hazards, forecasting active flows, interpreting past eruptions, and understanding the controls on lava flow behavior. Existing lava flow models vary in simplifying assumptions, physics, dimensionality, and the degree to which they have been validated against analytical solutions, experiments, and natural observations. In order to assess existing models and guide the development of new codes, we conduct a benchmarking study of computational fluid dynamics models for lava flow emplacement, including VolcFlow, OpenFOAM, FLOW-3D, and COMSOL. Using the new benchmark scenarios defined in Cordonnier et al. (Geol Soc SP, 2015) as a guide, we model viscous, cooling, and solidifying flows over horizontal and sloping surfaces, topographic obstacles, and digital elevation models of natural topography. We compare model results to analytical theory, analogue and molten basalt experiments, and measurements from natural lava flows. Overall, the models accurately simulate viscous flow with some variability in flow thickness where flows intersect obstacles. OpenFOAM, COMSOL, and FLOW-3D can each reproduce experimental measurements of cooling viscous flows, and FLOW-3D simulations with temperature-dependent rheology match results from molten basalt experiments. We can apply these models to reconstruct past lava flows in Hawai'i and Saudi Arabia using parameters assembled from morphology, textural analysis, and eruption observations as natural test cases. Our study highlights the strengths and weaknesses of each code, including accuracy and computational costs, and provides insights regarding code selection.

  16. Trace contaminant control simulation computer program, version 8.1

    NASA Technical Reports Server (NTRS)

    Perry, J. L.

    1994-01-01

    The Trace Contaminant Control Simulation computer program is a tool for assessing the performance of various process technologies for removing trace chemical contamination from a spacecraft cabin atmosphere. Included in the simulation are chemical and physical adsorption by activated charcoal, chemical adsorption by lithium hydroxide, absorption by humidity condensate, and low- and high-temperature catalytic oxidation. Means are provided for simulating regenerable as well as nonregenerable systems. The program provides an overall mass balance of chemical contaminants in a spacecraft cabin given specified generation rates. Removal rates are based on device flow rates specified by the user and calculated removal efficiencies based on cabin concentration and removal technology experimental data. Versions 1.0 through 8.0 are documented in NASA TM-108409. TM-108409 also contains a source file listing for version 8.0. Changes to version 8.0 are documented in this technical memorandum and a source file listing for the modified version, version 8.1, is provided. Detailed descriptions for the computer program subprograms are extracted from TM-108409 and modified as necessary to reflect version 8.1. Version 8.1 supersedes version 8.0. Information on a separate user's guide is available from the author.

  17. A COMPUTATIONAL WORKBENCH ENVIRONMENT FOR VIRTUAL POWER PLANT SIMULATION

    SciTech Connect

    Mike Bockelie; Dave Swensen; Martin Denison; Connie Senior; Zumao Chen; Temi Linjewile; Adel Sarofim; Bene Risio

    2003-04-25

    This is the tenth Quarterly Technical Report for DOE Cooperative Agreement No: DE-FC26-00NT41047. The goal of the project is to develop and demonstrate a computational workbench for simulating the performance of Vision 21 Power Plant Systems. Within the last quarter, good progress has been made on all aspects of the project. Calculations for a full Vision 21 plant configuration have been performed for two gasifier types. An improved process model for simulating entrained flow gasifiers has been implemented into the workbench. Model development has focused on: a pre-processor module to compute global gasification parameters from standard fuel properties and intrinsic rate information; a membrane based water gas shift; and reactors to oxidize fuel cell exhaust gas. The data visualization capabilities of the workbench have been extended by implementing the VTK visualization software that supports advanced visualization methods, including inexpensive Virtual Reality techniques. The ease-of-use, functionality and plug-and-play features of the workbench were highlighted through demonstrations of the workbench at a DOE sponsored coal utilization conference. A white paper has been completed that contains recommendations on the use of component architectures, model interface protocols and software frameworks for developing a Vision 21 plant simulator.

  18. Simulating Subsurface Reactive Flows on Ultrascale Computers with PFLOTRAN

    NASA Astrophysics Data System (ADS)

    Mills, R. T.; Hammond, G. E.; Lichtner, P. C.; Lu, C.; Smith, B. F.; Philip, B.

    2009-12-01

    To provide true predictive utility, subsurface simulations often must accurately resolve--in three dimensions--complicated, multi-phase flow fields in highly heterogeneous geology with numerous chemical species and complex chemistry. This task is especially daunting because of the wide range of spatial scales involved--from the pore scale to the field scale--ranging over six orders of magnitude, and the wide range of time scales ranging from seconds or less to millions of years. This represents a true "Grand Challenge" computational problem, requiring not only the largest-scale ("ultrascale") supercomputers, but accompanying advances in algorithms for the efficient numerical solution of systems of PDEs using these machines, and in mathematical modeling techniques that can adequately capture the truly multi-scale nature of these problems. We describe some of the specific challenges involved and present the software and algorithmic approaches that are being using in the computer code PFLOTRAN to provide scalable performance for such simulations on tens of thousands of processors. We focus particularly on scalable techniques for solving the large (up to billions of total degrees of freedom), sparse algebraic systems that arise. We also describe ongoing work to address disparate time and spatial scales by both the development of adaptive mesh refinement methods and the use of multiple continuum formulations. Finally, we present some examples from recent simulations conducted on Jaguar, the 150152 processor core Cray XT5 system at Oak Ridge National Laboratory that is currently one of the most powerful supercomputers in the world.

  19. Textbook Multigrid Efficiency for Computational Fluid Dynamics Simulations

    NASA Technical Reports Server (NTRS)

    Brandt, Achi; Thomas, James L.; Diskin, Boris

    2001-01-01

    Considerable progress over the past thirty years has been made in the development of large-scale computational fluid dynamics (CFD) solvers for the Euler and Navier-Stokes equations. Computations are used routinely to design the cruise shapes of transport aircraft through complex-geometry simulations involving the solution of 25-100 million equations; in this arena the number of wind-tunnel tests for a new design has been substantially reduced. However, simulations of the entire flight envelope of the vehicle, including maximum lift, buffet onset, flutter, and control effectiveness have not been as successful in eliminating the reliance on wind-tunnel testing. These simulations involve unsteady flows with more separation and stronger shock waves than at cruise. The main reasons limiting further inroads of CFD into the design process are: (1) the reliability of turbulence models; and (2) the time and expense of the numerical simulation. Because of the prohibitive resolution requirements of direct simulations at high Reynolds numbers, transition and turbulence modeling is expected to remain an issue for the near term. The focus of this paper addresses the latter problem by attempting to attain optimal efficiencies in solving the governing equations. Typically current CFD codes based on the use of multigrid acceleration techniques and multistage Runge-Kutta time-stepping schemes are able to converge lift and drag values for cruise configurations within approximately 1000 residual evaluations. An optimally convergent method is defined as having textbook multigrid efficiency (TME), meaning the solutions to the governing system of equations are attained in a computational work which is a small (less than 10) multiple of the operation count in the discretized system of equations (residual equations). In this paper, a distributed relaxation approach to achieving TME for Reynolds-averaged Navier-Stokes (RNAS) equations are discussed along with the foundations that form the

  20. An analysis of the 70-meter antenna hydrostatic bearing by means of computer simulation

    NASA Technical Reports Server (NTRS)

    Bartos, R. D.

    1993-01-01

    Recently, the computer program 'A Computer Solution for Hydrostatic Bearings with Variable Film Thickness,' used to design the hydrostatic bearing of the 70-meter antennas, was modified to improve the accuracy with which the program predicts the film height profile and oil pressure distribution between the hydrostatic bearing pad and the runner. This article presents a description of the modified computer program, the theory upon which the computer program computations are based, computer simulation results, and a discussion of the computer simulation results.