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Simulation Time (simulation + time)
Selected AbstractsA Multiresolution Model for Soft Objects Supporting Interactive Cuts and LacerationsCOMPUTER GRAPHICS FORUM, Issue 3 2000Fabio Ganovelli Performing a really interactive and physically-based simulation of complex soft objects is still an open problem in computer animation/simulation. Given the application domain of virtual surgery training, a complete model should be quite realistic, interactive and should enable the user to modify the topology of the objects. Recent papers propose the adoption of multiresolution techniques to optimize time performance by representing at high resolution only the object parts considered more important or critical. The speed up obtainable at simulation time are counterbalanced by the need of a preprocessing phase strongly dependent on the topology of the object, with the drawback that performing dynamic topology modification becomes a prohibitive issue. In this paper we present an approach that couples multiresolution and topological modifications, based on the adoption of a particle systems approach to the physical simulation. Our approach is based on a tetrahedral decomposition of the space, chosen both for its suitability to support a particle system and for the ready availability of many techniques recently proposed for the simplification and multiresolution management of 3D simplicial decompositions. The multiresolution simulation system is designed to ensure the required speedup and to support dynamic changes of the topology, e.g. due to cuts or lacerations of the represented tissue. [source] Performance of finite volume solutions to the shallow water equations with shock-capturing schemesINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 10 2002K. S. Erduran Abstract Numerical methods have become well established as tools for solving problems in hydraulic engineering. In recent years the finite volume method (FVM) with shock capturing capabilities has come to the fore because of its suitability for modelling a variety of types of flow; subcritical and supercritical; steady and unsteady; continuous and discontinuous and its ability to handle complex topography easily. This paper is an assessment and comparison of the performance of finite volume solutions to the shallow water equations with the Riemann solvers; the Osher, HLL, HLLC, flux difference splitting (Roe) and flux vector splitting. In this paper implementation of the FVM including the Riemann solvers, slope limiters and methods used for achieving second order accuracy are described explicitly step by step. The performance of the numerical methods has been investigated by applying them to a number of examples from the literature, providing both comparison of the schemes with each other and with published results. The assessment of each method is based on five criteria; ease of implementation, accuracy, applicability, numerical stability and simulation time. Finally, results, discussion, conclusions and recommendations for further work are presented. Copyright © 2002 John Wiley & Sons, Ltd. [source] Behaviour modelling of a PEMFC operating on diluted hydrogen feedINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 14 2008M. Minutillo Abstract The polymer electrolyte membrane fuel cell (PEMFC) using reformate gas as fuel is regarded as an attractive solution for the near-term introduction of fuel cells in stationary or mobile power generation market. With respect to hydrogen feeding, the reformate gas fuelling involves additional polarization losses because of the hydrogen dilution and the impurities contained in the gas. In this paper a one-dimensional model has been developed to investigate the behaviour of a PEMFC operating with reformate gas mixture. The model, based on a semi-empirical approach, considers the kinetic reactions in the anode side taking into account the effect of reverse water,gas shift (RWGS) due to the presence of CO2 in the fuel. As it is well known, the exhaust stream from fuel reformers can contain a high carbon dioxide concentration (>20%) that can have a detrimental effect on the fuel cell performance because of the combination of the dilution and the formation of CO by the RWGS reaction. The numerical simulation results have been compared with the experimental data, obtained in the test room of Industrial Engineering Department of Cassino University, and a good match has been observed. The model has been developed by using a simplified approach that, nevertheless, can allow to obtain a good numerical prediction of the fuel cell performance reducing the simulation time and computational efforts. Copyright © 2008 John Wiley & Sons, Ltd. [source] Sparse approximate inverse preconditioning of deflated block-GMRES algorithm for the fast monostatic RCS calculationINTERNATIONAL JOURNAL OF NUMERICAL MODELLING: ELECTRONIC NETWORKS, DEVICES AND FIELDS, Issue 5 2008P. L. Rui Abstract A sparse approximate inverse (SAI) preconditioning of deflated block-generalized minimal residual (GMRES) algorithm is proposed to solve large dense linear systems with multiple right-hand sides arising from monostatic radar cross section (RCS) calculations. The multilevel fast multipole method (MLFMM) is used to accelerate the matrix,vector product operations, and the SAI preconditioning technique is employed to speed up the convergence rate of block-GMRES (BGMRES) iterations. The main purpose of this study is to show that the convergence rate of the SAI preconditioned BGMRES method can be significantly improved by deflating a few smallest eigenvalues. Numerical experiments indicate that the combined effect of the SAI preconditioning technique that clusters most of eigenvalues to one, coupled with the deflation technique that shifts the rest of the smallest eigenvalues in the spectrum, can be very beneficial in the MLFMM, thus reducing the overall simulation time substantially. Copyright © 2008 John Wiley & Sons, Ltd. [source] How to obtain statistically converged MM/GBSA resultsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2010Samuel Genheden Abstract The molecular mechanics/generalized Born surface area (MM/GBSA) method has been investigated with the aim of achieving a statistical precision of 1 kJ/mol for the results. We studied the binding of seven biotin analogues to avidin, taking advantage of the fact that the protein is a tetramer with four independent binding sites, which should give the same estimated binding affinities. We show that it is not enough to use a single long simulation (10 ns), because the standard error of such a calculation underestimates the difference between the four binding sites. Instead, it is better to run several independent simulations and average the results. With such an approach, we obtain the same results for the four binding sites, and any desired precision can be obtained by running a proper number of simulations. We discuss how the simulations should be performed to optimize the use of computer time. The correlation time between the MM/GBSA energies is ,5 ps and an equilibration time of 100 ps is needed. For MM/GBSA, we recommend a sampling time of 20,200 ps for each separate simulation, depending on the protein. With 200 ps production time, 5,50 separate simulations are required to reach a statistical precision of 1 kJ/mol (800,8000 energy calculations or 1.5,15 ns total simulation time per ligand) for the seven avidin ligands. This is an order of magnitude more than what is normally used, but such a number of simulations is needed to obtain statistically valid results for the MM/GBSA method. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010 [source] Converging free energy estimates: MM-PB(GB)SA studies on the protein,protein complex Ras,RafJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004Holger Gohlke Abstract Estimating protein,protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA), and entropic contributions calculated by normal mode analysis for snapshots obtained from 10 ns explicit-solvent molecular dynamics in general results in an overestimation of the binding affinity when a solvent-accessible surface area-dependent model is used to estimate the nonpolar solvation contribution. Applying the sum of a cavity solvation free energy and explicitly modeled solute,solvent van der Waals interaction energies instead provides less negative estimates for the nonpolar solvation contribution. When the polar contribution to the solvation free energy is determined by solving the Poisson,Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen. For three GB models investigated, different absolute deviations from PB energies were found for the unbound proteins and the complex. As an alternative to normal-mode calculations, quasiharmonic analyses have been performed to estimate entropic contributions due to changes of solute flexibility upon binding. However, such entropy estimates do not converge after 10 ns of simulation time, indicating that sampling issues may limit the applicability of this approach. Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity. This points to the need to exercise caution in applying the computationally cheaper "one-trajectory-alternative" to systems where there may be significant changes in flexibility and structure due to binding. The best estimate for the binding free energy of Ras,Raf obtained in this study of ,8.3 kcal mol,1 is in good agreement with the experimental result of ,9.6 kcal mol,1, however, further probing the transferability of the applied protocol that led to this result is necessary. © 2003 Wiley Periodicals, Inc. J Comput Chem 2: 238,250, 2003 [source] The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between ,-helical and ,-hairpin conformations mediated by collapsed conformational statesJOURNAL OF PEPTIDE SCIENCE, Issue 5 2007Sunita Patel Abstract The peptide TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase adopts a helical conformation in the crystal structure and is a site for two hydrated helical segments, which are thought to be helical folding intermediates. Overlapping sequences of four to five residues from the peptide, sample both helical and strand conformations in known protein structures, which are dissimilar to glyceraldehyde-3-phosphate dehydrogenase suggesting that the peptide may have a structural ambivalence. Molecular dynamics simulations of the peptide sequence performed for a total simulation time of 1.2 µs, starting from the various initial conformations using GROMOS96 force field under NVT conditions, show that the peptide samples a large number of conformational forms with transitions from ,-helix to ,-hairpin and vice versa. The peptide, therefore, displays a structural ambivalence. The mechanism from ,-helix to ,-hairpin transition and vice versa reveals that the compact bends and turns conformational forms mediate such conformational transitions. These compact structures including helices and hairpins have similar hydrophobic radius of gyration (Rgh) values suggesting that similar hydrophobic interactions govern these conformational forms. The distribution of conformational energies is Gaussian with helix sampling lowest energy followed by the hairpins and coil. The lowest potential energy of the full helix may enable the peptide to take up helical conformation in the crystal structure of the glyceraldehyde-3-phosphate dehydrogenase, even though the peptide has a preference for hairpin too. The relevance of folding and unfolding events observed in our simulations to hydrophobic collapse model of protein folding are discussed. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Numerical simulation of particle trajectory and atmospheric dispersion of airborne releasesMETEOROLOGICAL APPLICATIONS, Issue 3 2009S. Shoaib Raza Abstract Numerical simulation of particle trajectory and atmospheric dispersion has been performed for an airborne accidental release from a nuclear power plant site. A Long-range Particle transport and Dispersion Model (LPDM) based on a Lagrangian approach is developed and tested in this work. The Lagrangian transport/dispersion model is directly coupled with an atmospheric prediction model, RAMS (Regional Atmospheric Modeling System), to provide necessary meteorological fields in a three-dimensional domain. An advantage of this direct coupling is that the meteorological data generated by RAMS can be used directly for trajectory calculations without storage, thus reducing the CPU time consumed in the data storage and retrieval. This effort was done to be able to use this directly coupled modelling system for real-time predictions in case of an accidental release from a potential site. The simulated Lagrangian trajectories were compared with those obtained using observed hourly weather data obtained from an on-site meteorological tower. The results indicated that this one-way coupling between LPDM-RAMS provided almost identical trajectories when compared with those obtained using LPDM alone driven by hourly observed wind data. The comparison demonstrated the reliability of the RAMS meteorological predictions for the site under consideration. The comparison also indicated that LPDM (run in a stand alone mode), with hourly-observed wind data, could also be used for trajectory calculations over flat terrain. The model was developed on a parallel processing computer (SGI workstation, ORIGIN 2000 computer with eight processors) for use in real-time forecast mode. The computational time was about one-third of the simulation time, while using four processors. The model options need to be explored to reduce the computational time further and test its performance for real-time atmospheric dispersion applications. Copyright © 2009 Royal Meteorological Society [source] Neural network approach for comodeling design of multichip moduleMICROWAVE AND OPTICAL TECHNOLOGY LETTERS, Issue 7 2008M. El Zoghbi Abstract An original comodeling approach based on neural network is proposed in order to optimize multichip modules (MCM). This approach permits to characterize and to optimize millimeter-wave module behavior by taking into account electromagnetic phenomena. All the design procedure is implemented in a circuit software to reduce the simulation time. Encouraging results are obtained. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 50: 1770,1774, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.23530 [source] Dynameomics: Large-scale assessment of native protein flexibilityPROTEIN SCIENCE, Issue 12 2008Noah C. Benson Abstract Structure is only the first step in understanding the interactions and functions of proteins. In this paper, we explore the flexibility of proteins across a broad database of over 250 solvated protein molecular dynamics simulations in water for an aggregate simulation time of ,6 ,s. These simulations are from our Dynameomics project, and these proteins represent approximately 75% of all known protein structures. We employ principal component analysis of the atomic coordinates over time to determine the primary axis and magnitude of the flexibility of each atom in a simulation. This technique gives us both a database of flexibility for many protein fold families and a compact visual representation of a particular protein's native-state conformational space, neither of which are available using experimental methods alone. These tools allow us to better understand the nature of protein motion and to describe its relationship to other structural and dynamical characteristics. In addition to reporting general properties of protein flexibility and detailing many dynamic motifs, we characterize the relationship between protein native-state flexibility and early events in thermal unfolding and show that flexibility predicts how a protein will begin to unfold. We provide evidence that fold families have conserved flexibility patterns, and family members who deviate from the conserved patterns have very low sequence identity. Finally, we examine novel aspects of highly inflexible loops that are as important to structural integrity as conventional secondary structure. These loops, which are difficult if not impossible to locate without dynamic data, may constitute new structural motifs. [source] Gekoppelter Wärme- und Stofftransport einschließlich der Korrosionsprozesse in porösen Baustoffen mit dem Simulationsprogramm AStraBAUPHYSIK, Issue 3 2007Rosa Maria Espinosa Dr.-Ing. Zur Beschreibung von Wärme- und Feuchtetransportvorgängen gekoppelt mit Stofftransportprozessen in porösen Baustoffen ist ein Differentialgleichungssystem bestehend aus der Energieerhaltungsgleichung und den Massenerhaltungsgleichungen aller beteiligten Stoffe einschließlich des Wassers aufzulösen. Hierzu ist die Modellierung der stattfindenden Phasenumwandlungen der vorliegenden Stoffe und der chemischen Reaktionen der Porenlösung mit der Baustoffmatrix erforderlich. Zu unterscheiden sind dazu inerte, nicht reaktive Baustoffe und reaktionsfähige, zementgebundene Baustoffe. Für die numerische Simulation dieser Vorgänge bzw. die praktische Handhabbarkeit der Problemlösung wurde eine benutzerfreundliche Programmoberfläche AStra geschaffen, die neben dem eigentlichen Berechnungsmodul die benötigten Pre- und Postprocessing Möglichkeiten beinhaltet. Für die Berechnung des zeitlichen Verlaufs eines lösenden oder treibenden Angriffs auf zementgebundene Baustoffe wird durch eine in Abhängigkeit der beteiligten Spezies geeignete Vorauswahl von ablaufenden Reaktionen der Rechenaufwand für die Vorhersage von Nichtgleichgewichtszuständen optimiert und damit die Möglichkeit geschaffen zeitliche Abhängigkeiten mit vertretbarem Berechnungsaufwand zu beschreiben. Zusätzlich können mechanische Beanspruchungen als Folge von Kristallisationsvorgängen zumindest qualitativ vorhergesagt werden. Im Folgenden werden eine Übersicht der implementierten Berechnungsmodelle sowie drei Anwendungsbeispiele von AStra vorgestellt. Coupled heat and mass transfer simulation including corrosion in porous building materials with the program AStra. For the description of corrosion processes of porous building materials, it is necessary to solve a system of coupled (non-linear) differential equations, which consists of a conservation equation for the energy and one for the mass of each substance (including water and air), whose content may change within the simulated time period. Indeed, it must be distinguished between degradation of reactive and of inert materials. The computation program AStra simulates a coupled transport of heat, moisture, air and chemical substances in porous materials. AStra consists of a user interface for pre- and post-processing and a computation module (solver), which contains the necessary algorithms to solve the system of coupled differential equations. Mathematical models for phase changes of salts and for chemical reactions between substances, including the components of the material matrix in case of cementitious materials, were developed. Furthermore, the computational cost for the prediction of the corrosion of cementitious materials was optimized by means of an adequate pre-selection of chemical reactions. Thus, it is possible to simulate corrosion processes within justifiable simulation time. On the other hand, a simulation of the mechanical stress resulting from crystallization processes is possible. This paper presents some applications of the programs and a brief introduction into their theoretical basis. [source] Dynamisch-thermisches CFD-Verfahren mit angepaßter RegelungsmethodeBAUPHYSIK, Issue 1 2007Tobias Zitzmann Dipl.-Ing. (FH) Zur Reduktion des Zeitaufwands von dynamisch-thermischen Langzeitsimulationen mit CFD-Programmen wurde in kürzlich veröffentlichten Studien eine neuartige Freeze-Flow Methode vorgestellt. Diese basiert auf der periodischen Umschaltung zwischen der volldynamischen Lösung aller Gleichungen und der ausschließlichen Lösung der Enthalpie-Gleichungen (eingefrorene Luftströmung). Dieser Artikel beschreibt eine neue, angepaßte Regelung für diese Umschaltung, wodurch eine zusätzliche Reduzierung der Simulationszeit erzielt wird. In Tests an Modellen für die mechanische und freie Lüftung sowie der freien Konvektion im geschlossenen Raum für feste und zeitveränderliche thermische Randbedingungen wurde im Vergleich zur ununterbrochenen volldynamischen Simulation eine Simulationszeiteinsparung von bis zu 93% erreicht. Dynamic thermal CFD approach using an adaptive control method. Previously published studies have presented a novel freeze-flow method for reducing CPU requirements of long-term dynamic thermal simulations using CFD programs. This works by intermittently switching between solution of the full dynamic equations and solution of the enthalpy equation only (frozen flow). This paper describes a new automated control method for this switching strategy and shows an additional decrease in simulation time. In tests with models for mechanical and natural ventilation and for free convection in a sealed room with constant and time varying thermal boundary conditions, a simulation time reduction of up to 93% was achieved when compared to a continuous fully dynamic simulation. [source] Stability and Dynamics of Domain-Swapped Bovine-Seminal RibonucleaseCHEMISTRY & BIODIVERSITY, Issue 5 2004Kalyan The proteins of the ribonuclease-A (RNase-A) family are monomeric, with the exception of bovine-seminal ribonuclease (BS-RNase). BS-RNase is formed by swapping the N-terminal helices across the two monomeric units. A molecular-dynamics (MD) study has been performed on the protein for a simulation time of 5.5,ns to understand the factors responsible for the stability of the dimer. Essential dynamics analysis and motional correlation of the protein atoms yielded the picture of a stabilising, yet flexible, interface. We have investigated the role of intermolecular H-bonding, protein/water interaction, and protein/water networks in stabilising the dimer. The networks of interchain H-bonds involving side-chain/side-chain or side-chain/main-chain (ScHB) interactions between the two chains have also been studied. The ability of protein atoms in retaining particular H2O molecules was investigated as a function of the accessible surface area (ASA), depth, and hydration parameters, as well as their participation in protein/water networks. [source] A catchment scale evaluation of the SIBERIA and CAESAR landscape evolution modelsEARTH SURFACE PROCESSES AND LANDFORMS, Issue 8 2010GR Hancock Abstract Landscape evolution models provide a way to determine erosion rates and landscape stability over times scales from tens to thousands of years. The SIBERIA and CAESAR landscape evolution models both have the capability to simulate catchment,wide erosion and deposition over these time scales. They are both cellular, operate over a digital elevation model of the landscape, and represent fluvial and slope processes. However, they were initially developed to solve research questions at different time and space scales and subsequently the perspective, detail and process representation vary considerably between the models. Notably, CAESAR simulates individual events with a greater emphasis on fluvial processes whereas SIBERIA averages erosion rates across annual time scales. This paper describes how both models are applied to Tin Camp Creek, Northern Territory, Australia, where soil erosion rates have been closely monitored over the last 10 years. Results simulating 10,000 years of erosion are similar, yet also pick up subtle differences that indicate the relative strengths and weaknesses of the two models. The results from both the SIBERIA and CAESAR models compare well with independent field data determined for the site over different time scales. Representative hillslope cross-sections are very similar between the models. Geomorphologically there was little difference between the modelled catchments after 1000 years but significant differences were revealed at longer simulation times. Importantly, both models show that they are sensitive to input parameters and that hydrology and erosion parameter derivation has long-term implications for sediment transport prediction. Therefore selection of input parameters is critical. This study also provides a good example of how different models may be better suited to different applications or research questions. Copyright © 2010 John Wiley & Sons, Ltd and Commonwealth of Australia [source] Evaluation of model complexity and space,time resolution on the prediction of long-term soil salinity dynamics, western San Joaquin Valley, CaliforniaHYDROLOGICAL PROCESSES, Issue 13 2006G. Schoups Abstract The numerical simulation of long-term large-scale (field to regional) variably saturated subsurface flow and transport remains a computational challenge, even with today's computing power. Therefore, it is appropriate to develop and use simplified models that focus on the main processes operating at the pertinent time and space scales, as long as the error introduced by the simpler model is small relative to the uncertainties associated with the spatial and temporal variation of boundary conditions and parameter values. This study investigates the effects of various model simplifications on the prediction of long-term soil salinity and salt transport in irrigated soils. Average root-zone salinity and cumulative annual drainage salt load were predicted for a 10-year period using a one-dimensional numerical flow and transport model (i.e. UNSATCHEM) that accounts for solute advection, dispersion and diffusion, and complex salt chemistry. The model uses daily values for rainfall, irrigation, and potential evapotranspiration rates. Model simulations consist of benchmark scenarios for different hypothetical cases that include shallow and deep water tables, different leaching fractions and soil gypsum content, and shallow groundwater salinity, with and without soil chemical reactions. These hypothetical benchmark simulations are compared with the results of various model simplifications that considered (i) annual average boundary conditions, (ii) coarser spatial discretization, and (iii) reducing the complexity of the salt-soil reaction system. Based on the 10-year simulation results, we conclude that salt transport modelling does not require daily boundary conditions, a fine spatial resolution, or complex salt chemistry. Instead, if the focus is on long-term salinity, then a simplified modelling approach can be used, using annually averaged boundary conditions, a coarse spatial discretization, and inclusion of soil chemistry that only accounts for cation exchange and gypsum dissolution,precipitation. We also demonstrate that prediction errors due to these model simplifications may be small, when compared with effects of parameter uncertainty on model predictions. The proposed model simplifications lead to larger time steps and reduced computer simulation times by a factor of 1000. Copyright © 2006 John Wiley & Sons, Ltd. [source] Optimal modal reduction of vibrating substructuresINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 3 2003Paul E. Barbone Abstract A structure which consists of a main part and a number of attached substructures is considered. A ,model reduction' scheme is developed and applied to each of the discrete substructures. Linear undamped transient vibrational motion of the structure is assumed, with general external forcing and initial conditions. The goal is to replace each discrete substructure by another substructure with a much smaller number of degrees of freedom, while minimizing the effect this reduction has on the dynamic behaviour of the main structure. The approach taken here involves Ritz reduction and the Dirichlet-to-Neumann map as analysis tools. The resulting scheme is based on a special form of modal reduction, and is shown to be optimal in a certain sense, for long simulation times. The performance of the scheme is demonstrated via numerical examples, and is compared to that of standard modal reduction. Copyright © 2003 John Wiley & Sons, Ltd. [source] From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Sergio A. Hassan Abstract Biological macromolecules and other polymers belong to the class of mesoscopic systems, with characteristic length scale of the order of a nanometer. Although microscopic models would be the preferred choice in theoretical calculations, their use in computer simulations becomes prohibitive for large systems or long simulation times. On the other hand, the use of purely macroscopic models in the mesoscopic domain may introduce artifacts, with effects that are difficult to assess and that may compromise the reliability of the calculations. Here is proposed an approach with the aim of minimizing the empirical nature of continuum approximations of solvent effects within the scope of molecular mechanics (MM) approximations in mesoscopic systems. Using quantum chemical methods, the potential generated by the molecular electron density is first decomposed in a multicenter-multipole expansion around predetermined centers. The monopole and dipole terms of the expansion at each site create electric fields that polarize the surrounding aqueous medium whose dielectric properties can be described by the classical theory of polar liquids. Debye's theory allows a derivation of the dielectric profiles created around isolated point charges and dipoles that can incorporate Onsager reaction field corrections. A superposition of screened Coulomb potentials obtained from this theory makes possible a simple derivation of a formal expression for the total electrostatic energy and the polar component of the solvation energy of the system. A discussion is presented on the physical meaning of the model parameters, their transferability, and their convergence to calculable quantities in the limit of simple systems. The performance of this continuum approximation in computer calculations of amino acids in the context of an atomistic force field is discussed. Applications of a continuum model based on screened Coulomb potentials in multinanosecond simulations of peptides and proteins are briefly reviewed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Molecular dynamic simulations of nanomechanic chaperone peptide and effects of in silico His mutations on nanostructured functionJOURNAL OF PEPTIDE SCIENCE, Issue 11 2008Abolfazl Barzegar Abstract The nanoscale peptide YSGVCHTDLHAWHGDWPLPVK exhibits molecular chaperone activity and prevents protein aggregation under chemical and/or thermal stress. Here, His mutations of this peptide and their impact on chaperone activity were evaluated using theoretical techniques. Molecular dynamic (MD) simulations with simulated annealing (SA) of different mutant nanopeptides were employed to determine the contribution of the scaffolding His residues (H45, H49, H52), when mutated to Pro, on chaperone action in vitro. The in silico mutations of His residues to Pro (H45P, H49P, H52P) revealed loss of secondary ordered strand structure. However, a small part of the strand conformation was formed in the middle region of the native chaperone peptide. The His-to-Pro mutations resulted in decreased gyration radius (Rg) values and surface accessibility of the mutant peptides under the simulation times. The invariant dihedral angle (,) values and the disrupting effects of the Pro residues indicated the coil conformation of mutant peptides. The failure of the chaperone-like action in the Pro mutant peptides was consistent with their decreased effective accessible surfaces. The high variation of , value for His residues in native chaperone peptide leads to high flexibility, such as a minichaperone acting as a nanomachine at the molecular level. Our findings demonstrate that the peptide strand conformation motif with high flexibility at nanoscale is critical for chaperone activity. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Temperature and Pressure Effects on Local Structure and Chain Packing in cis -1,4-Polybutadiene from Detailed Molecular Dynamics SimulationsMACROMOLECULAR THEORY AND SIMULATIONS, Issue 5 2006Georgia Tsolou Abstract Summary: We present results for the temperature and pressure dependence of local structure and chain packing in cis -1,4-polybutadiene (cis -1,4-PB) from detailed molecular dynamics (MD) simulations with a united-atom model. The simulations have been executed in the NPT statistical ensemble with a parallel, multiple time step MD algorithm, which allowed us to access simulation times up to 1 µs. Because of this, a 32 chain C128cis -1,4-PB system was successfully simulated over a wide range of temperature (from 430 to 195 K) and pressure (from 1 atm to 3 kbar) conditions. Simulation predictions are reported for the temperature and pressure dependence of the: (a) density; (b) chain characteristic ratio, Cn; (c) intermolecular pair distribution function, g(r), static structure factor, S(q), and first peak position, Qmax, in the S(q) pattern; (d) free volume around each monomer unit along a chain for the simulated polymer system. These were thoroughly compared against available experimental data. One of the most important findings of this work is that the component of the S(q) vs. q plot representing intramolecular contributions in a fully deuterated cis -1,4-PB sample exhibits a monotonic decrease with q which remains completely unaffected by the pressure. In contrast, the intermolecular contribution exhibits a distinct peak (at around 1.4 Å,1) whose position shifts towards higher q values as the pressure is raised, accompanied by a decrease in its intensity. 3D view of the simulation box containing 32 chains of C128cis -1,4-polybutadiene at density ,,=,0.849 g,·,cm,3 and the conformation of a single C128cis -1,4-PB chain fully unwrapped in space. [source] Large Scale Simulation with Scaled Boundary Finite Element MethodPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2009Marco Schauer Nowadays scientific and engineering applications often require wave propagation in infinite or unbounded domains. In order to model such applications we separate our model into near-field and far-field. The near-field is represented by the well-known finite element method (FEM), whereas the far-field is mapped by a scaled boundary finite element (SBFE) approach. This latter approach allows wave propagation in infinite domains and suppresses the reflection of waves at the boundary, thus being a suitable method to model wave propagation to infinity. It is non-local in time and space. From a computational point of view, those characteristics are a drawback because they lead to storage consuming calculations with high computational time-effort. The non-locality in space causes fully populated unit-impulse acceleration influence matrices for each time step, leading to immense storage consumption for problems with a large number of degrees of freedom. Additionally, a different influence matrix has to be assembled for each time step which yields unacceptable storage requirements for long simulation times. For long slender domains, where many nodes are rather far from each other and where the influence of the degrees of freedom of those distant nodes is neglectable, substructuring represents an efficient method to reduce storage requirements and computational effort. The presented simulation with substructuring still yields satisfactory results. (© 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Impact of the Endoscopic Sinus Surgical Simulator on Operating Room PerformanceTHE LARYNGOSCOPE, Issue 7 2002Charles V. Edmond Jr. MD Abstract Objectives/Hypothesis The aim of this study is to evaluate an endoscopic sinus surgical simulator (ESS) as a training device and to introduce a methodology to assess its impact on actual operating room performance. Study Design Prospective evaluation of the endoscopic sinus surgical simulator as a trainer. Methods Ten junior and senior ear, nose and throat residents served as subjects, some of whom had prior training with the simulator. The evaluation team collected several measures, which were analyzed for a statistical correlation, including simulator scores, operating room performance rating, ratings of videotaped operating room procedures, and surgical competency rating. Results These findings suggest the ESS simulator positively affects initial operating room performance across all measures as judged by senior surgeons rating anonymous videotapes of those procedures. The two simulation-trained residents were rated consistently better than the other two residents across all measures. These differences approached statistical significance for two items: anterior ethmoidectomy (P = .06;P <.05) and surgical confidence (P = .09;P <.05). In addition, the 3 subjects with the highest overall scores on the competency evaluation also had 3 of the 4 highest cumulative simulation times. Conclusions The endoscopic sinus surgical simulator is a valid training device and appears to positively impact operating room performance among junior otolaryngology residents. [source] An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis,BIOTECHNOLOGY & BIOENGINEERING, Issue 3 2008Jamey D. Young Abstract Nonstationary metabolic flux analysis (NMFA) is at present a very computationally intensive exercise, especially for large reaction networks. We applied elementary metabolite unit (EMU) theory to NMFA, dramatically reducing computational difficulty. We also introduced block decoupling, a new method that systematically and comprehensively divides EMU systems of equations into smaller subproblems to further reduce computational difficulty. These improvements led to a 5000-fold reduction in simulation times, enabling an entirely new and more complicated set of problems to be analyzed with NMFA. We simulated a series of nonstationary and stationary GC/MS measurements for a large E. coli network that was then used to estimate parameters and their associated confidence intervals. We found that fluxes could be successfully estimated using only nonstationary labeling data and external flux measurements. Addition of near-stationary and stationary time points increased the precision of most parameters. Contrary to prior reports, the precision of nonstationary estimates proved to be comparable to the precision of estimates based solely on stationary data. Finally, we applied EMU-based NMFA to experimental nonstationary measurements taken from brown adipocytes and successfully estimated fluxes and some metabolite concentrations. By using NFMA instead of traditional MFA, the experiment required only 6 h instead of 50 (the time necessary for most metabolite labeling to reach 99% of isotopic steady state). Biotechnol. Bioeng. 2008;99: 686,699. © 2007 Wiley Periodicals, Inc. [source] | |||||||||||||||||||