Implementation of window shading models into dynamic whole-building simulation
NASA Astrophysics Data System (ADS)
Lomanowski, Bartosz Aleksander
resistances of sealed cavities between glazing/shading layers are calculated at each time-step for various fill gases and mixtures. In addition to modeling glazing/shading layer combinations, the CFC type also provides an alternate method of modeling unshaded windows without relying on third party software to supply the solar optics and cavity resistances. To build confidence in the CFC code implementation, two comparison studies were carried out to compare the CFC type against other models. The first study compared the CFC models for unshaded windows with the standard ESP-r transparent multi-layer construction (TMC) models. The second study compared the CFC slat-type blind models with EnergyPlus 2.0. Good agreement was seen in the simulation results in both studies. The successful implementation of the Complex Fenestration Construction within ESP-r has been demonstrated in the current research. In order for ESP-r users to fully exploit the capabilities of the CFC framework, it is recommended that the current models be extended to include a facility for dynamic shading control as well as the treatment of other types of shading layers. The coupling of daylighting models with the CFC type would provide a useful tool for modeling luminance control in combination with shading control strategies. With these enhancements, it is anticipated that the CFC implementation will be of significant value to practitioners.
Miller, J. P.; Zhivov, A.; Heron, D.; Deru, M.; Benne, K.
2010-08-01
Three technologies that have potential to save energy and improve sustainability of buildings are dedicated outdoor air systems, radiant heating and cooling systems and tighter building envelopes. To investigate the energy savings potential of these three technologies, whole building energy simulations were performed for a barracks facility and an administration facility in 15 U.S. climate zones and 16 international locations.
Haves, Philip; Salsbury, Tim; Claridge, David; Liu, Mingsheng
2001-06-15
The application of model-based performance assessment at the whole building level is explored. The information requirements for a simulation to predict the actual performance of a particular real building, as opposed to estimating the impact of design options, are addressed with particular attention to common sources of input error and important deficiencies in most simulation models. The role of calibrated simulations is discussed. The communication requirements for passive monitoring and active testing are identified and the possibilities for using control system communications protocols to link on-line simulation and energy management and control systems are discussed. The potential of simulation programs to act as ''plug-and-play'' components on building control networks is discussed.
Co-Simulation of Detailed Whole Building with the Power System to Study Smart Grid Applications
Makhmalbaf, Atefe; Fuller, Jason C.; Srivastava, Viraj; Ciraci, Selim; Daily, Jeffrey A.
2014-12-24
Modernization of the power system in a way that ensures a sustainable energy system is arguably one of the most pressing concerns of our time. Buildings are important components in the power system. First, they are the main consumers of electricity and secondly, they do not have constant energy demand. Conventionally, electricity has been difficult to store and should be consumed as it is generated. Therefore, maintaining the demand and supply is critical in the power system. However, to reduce the complexity of power models, buildings (i.e., end-use loads) are traditionally modeled and represented as aggregated “dumb” nodes in the power system. This means we lack effective detailed whole building energy models that can support requirements and emerging technologies of the smart power grid. To gain greater insight into the relationship between building energy demand and power system performance, it is important to constitute a co-simulation framework to support detailed building energy modeling and simulation within the power system to study capabilities promised by the modern power grid. This paper discusses ongoing work at Pacific Northwest National Laboratory and presents underlying tools and framework needed to enable co-simulation of building, building energy systems and their control in the power system to study applications such as demand response, grid-based HVAC control, and deployment of buildings for ancillary services. The optimal goal is to develop an integrated modeling and simulation platform that is flexible, reusable, and scalable. Results of this work will contribute to future building and power system studies, especially those related to the integrated ‘smart grid’. Results are also expected to advance power resiliency and local (micro) scale grid studies where several building and renewable energy systems transact energy directly. This paper also reviews some applications that can be supported and studied using the framework introduced
Whole Building Design Objectives for Campus Safety and Security: A System Dynamics Approach
ERIC Educational Resources Information Center
Oakes, Charles G.
2010-01-01
The May/June 2009 issue of "Facilities Manager" introduced APPA readers to the Whole Building Design Guide (WBDG)--today's most comprehensive Internet-based depository of resources contributing to a systems approach for everything of a building nature. The emphasis in that article was on Operations and Maintenance (O&M) issues and procedures. In…
Neymark, J,; Judkoff, R.; Knabe, G.; Le, H.-T.; Durig, M.; Glass, A.; Zweifel, G.
2001-07-03
Validation of Building Energy Simulation Programs consists of a combination of empirical validation, analytical verification, and comparative analysis techniques (Judkoff 1988). An analytical verification and comparative diagnostic procedure was developed to test the ability of whole-building simulation programs to model the performance of unitary space-cooling equipment that is typically modeled using manufacturer design data presented as empirically derived performance maps. Field trials of the method were conducted by researchers from nations participating in the International Energy Agency (IEA) Solar Heating and Cooling (SHC) Programme Task 22, using a number of detailed hourly simulation programs from Europe and the United States, including: CA-SIS, CLIM2000, PROMETHEUS, TRNSYS-TUD, and two versions of DOE-2.1E. Analytical solutions were also developed for the test cases.
Use of Energy and Other Monitored Data to Calibrate a Whole Building Energy Model
NASA Astrophysics Data System (ADS)
Reddy, David
This thesis documents an approach to utilize energy and other measured data to improve the calibration of a whole building energy model. Each chapter documents important steps of the process, and provides building energy analysts with insight on how to use this information to improve modeling assumptions, and hence energy model predictions. Important components of the study included creation of a custom, annual simulation weather file, designing and implementing an electrical sub-metering system, and disaggregating electrical energy use by model zone and energy end-use. Data and information were aggregated to create a DOE-2.2 whole building energy model, and the incremental improvement in model calibration was demonstrated as input assumptions were refined. The results of this study show accurate description of dynamic model inputs, particularly inputs that describe occupant's manipulation of building systems, was the most influential factor affecting energy model calibration.
A Framework for Daylighting Optimization in Whole Buildings with OpenStudio
2016-08-12
We present a toolkit and workflow for leveraging the OpenStudio (Guglielmetti et al. 2010) platform to perform daylighting analysis and optimization in a whole building energy modeling (BEM) context. We have re-implemented OpenStudio's integrated Radiance and EnergyPlus functionality as an OpenStudio Measure. The OpenStudio Radiance Measure works within the OpenStudio Application and Parametric Analysis Tool, as well as the OpenStudio Server large scale analysis framework, allowing a rigorous daylighting simulation to be performed on a single building model or potentially an entire population of programmatically generated models. The Radiance simulation results can automatically inform the broader building energy model, and provide dynamic daylight metrics as a basis for decision. Through introduction and example, this paper illustrates the utility of the OpenStudio building energy modeling platform to leverage existing simulation tools for integrated building energy performance simulation, daylighting analysis, and reportage.
Whole Building Energy Diagnostician, version 3.0
2005-02-03
The Whole Building Energy Diagnostician v. 3.x software detects anomalies in energy consumption of buildings and major building systems using metered energy-use data and measured values of driving variables (e.g., outdoor-air temperature, outdoor-air relative humidity, and building occupancy schedule). The software then provides alarms for anomalous consumption and information on energy and cost impacts. This version is intended to be implemented as a world wide web application and made accessible to end users by use of a Web browser and an Internet connection, but the web interface is not provided as part of the software - a web service provider must provide the web-based graphical user interface.
Molecular dynamics simulations.
Lindahl, Erik
2015-01-01
Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.
NASA Technical Reports Server (NTRS)
1987-01-01
The proceedings of the conference are presented. The objective was to provide a forum for the discussion of the structure and status of existing computer programs which are used to simulate the dynamics of a variety of tether applications in space. A major topic was different simulation models and the process of validating them. Guidance on future work in these areas was obtained from a panel discussion; the panel was composed of resource and technical managers and dynamic analysts in the tether field. The conclusions of this panel are also presented.
Dynamical Simulation of Probabilities
NASA Technical Reports Server (NTRS)
Zak, Michail
1996-01-01
It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-Lipschitz dynamics, without utilization of any man-made devices(such as random number generators). Self-orgainizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed. Special attention was focused upon coupled stochastic processes, defined in terms of conditional probabilities, for which joint probability does not exist. Simulations of quantum probabilities are also discussed.
Dynamical Simulation of Probabilities
NASA Technical Reports Server (NTRS)
Zak, Michail
1996-01-01
It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-Lipschitz dynamics, without utilization of any man-made devices(such as random number generators). Self-orgainizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed. Special attention was focused upon coupled stochastic processes, defined in terms of conditional probabilities, for which joint probability does not exist. Simulations of quantum probabilities are also discussed.
Molecular dynamics simulations.
Lindahl, Erik R
2008-01-01
Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.
NASA Technical Reports Server (NTRS)
Joncas, K. P.
1972-01-01
Concepts and techniques for identifying and simulating both the steady state and dynamic characteristics of electrical loads for use during integrated system test and evaluation are discussed. The investigations showed that it is feasible to design and develop interrogation and simulation equipment to perform the desired functions. During the evaluation, actual spacecraft loads were interrogated by stimulating the loads with their normal input voltage and measuring the resultant voltage and current time histories. Elements of the circuits were optimized by an iterative process of selecting element values and comparing the time-domain response of the model with those obtained from the real equipment during interrogation.
Using Whole Building Performance Measurement to Develop a Business Case
Fowler, Kimberly M.
2006-09-15
Since 1998 the U.S. Navy?s Naval Facilities Engineering Command (NAVFAC) has had a policy for incorporating sustainable design principles into new building construction. The policy also states it is the intent of NAVFAC to accomplish this within the given budget constraints and while meeting customer requirements. Programming a building using a first cost approach instead of a life cycle cost approach is one of the biggest challenges for integrating sustainable design into projects at the Navy. Due to this hurdle, an attempt to develop a Navy specific business case was undertaken. Through this process, it was discovered that consistent data were not being collected for all applicable Navy buildings. Therefore, the current business case information being used by the Navy is the conglomeration of existing business case analysis in the literature. Although this business case information is useful, there is still a need for collecting and analyzing the Navy business case. To develop the Navy specific business case, NAVFAC is developing program metrics to capture the status of buildings in the design and construction phase and they have started to collect whole building cost and performance data for 14 buildings (7 sustainably designed and 7 traditionally designed buildings) to capture data on their existing inventory of sustainably design buildings. Performance measurement data are being collected on water, energy, operations and maintenance, waste generation, purchasing, occupant satisfaction, and transportation. The building cost and performance data will be collected for a minimum of 12 months. Both of these data collection and analysis efforts have offered lessons learned that will be shared alongside the current Navy business case information.
Torcellini, P.; Judkoff, R.; Hayter, S.
2002-07-01
The National Park Service (NPS) applied a whole-building design process developed at the National Renewable Energy Laboratory (NREL) to create a building that performs more than 70% better than a comparable code-compliant building at no additional construction cost. This whole-building design process involves a committed design team, including the energy consultant, in the earliest conceptual design phase and continues through building commissioning. The design team for this project included the architect, engineer, energy consultant, landscape architect, owner, operator, and others who could influence the building design and operation. Extensive whole-building energy and lighting computer simulations were conducted throughout the process, which included the integration of energy efficient and renewable energy technologies into the building. The design team, inspired by natural cooling within the canyon, developed simple solutions to create an extremely energy efficient building. The se strategies included natural ventilation cooling, cooltowers for evaporative cooling without distribution fans, daylighting, massive building materials, Trombe walls and direct solar gains for heating, engineered window overhangs for solar load control, a building automation system to maintain comfort and control the energy-efficient lighting system, and a roof-mounted photovoltaic system to offset building electrical loads and ensure a power supply during the frequent utility grid outages.
Data Systems Dynamic Simulator
NASA Technical Reports Server (NTRS)
Rouff, Christopher; Clark, Melana; Davenport, Bill; Message, Philip
1993-01-01
The Data System Dynamic Simulator (DSDS) is a discrete event simulation tool. It was developed for NASA for the specific purpose of evaluating candidate architectures for data systems of the Space Station era. DSDS provides three methods for meeting this requirement. First, the user has access to a library of standard pre-programmed elements. These elements represent tailorable components of NASA data systems and can be connected in any logical manner. Secondly, DSDS supports the development of additional elements. This allows the more sophisticated DSDS user the option of extending the standard element set. Thirdly, DSDS supports the use of data streams simulation. Data streams is the name given to a technique that ignores packet boundaries, but is sensitive to rate changes. Because rate changes are rare compared to packet arrivals in a typical NASA data system, data stream simulations require a fraction of the CPU run time. Additionally, the data stream technique is considerably more accurate than another commonly-used optimization technique.
2015-10-20
Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.
Remote manipulator dynamic simulation
NASA Technical Reports Server (NTRS)
Wild, E. C.; Donges, P. K.; Garand, W. A.
1972-01-01
A simulator to generate the real time visual scenes required to perform man in the loop investigations of remote manipulator application and design concepts for the space shuttle is described. The simulated remote manipulator consists of a computed display system that uses a digital computer, the electronic scene generator, an operator's station, and associated interface hardware. A description of the capabilities of the implemented simulation is presented. The mathematical models and programs developed for the simulation are included.
Top, Philip; Woodward, Carol; Smith, Steve; Banks, Lawrence; Kelley, Brian
2015-09-14
GridDyn is a part of power grid simulation toolkit. The code is designed using modern object oriented C++ methods utilizing C++11 and recent Boost libraries to ensure compatibility with multiple operating systems and environments.
Floating orbital molecular dynamics simulations.
Perlt, Eva; Brüssel, Marc; Kirchner, Barbara
2014-04-21
We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated.
Modeling Molecular Dynamics from Simulations
Hinrichs, Nina Singhal
2009-01-28
Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.
Dynamical simulation of gravothermal catastrophe.
Klinko, Peter; Miller, Bruce N
2004-01-16
We investigate the dynamical evolution of gravothermal catastrophe in a model of a spherical cluster where, besides the energy and angular momentum, an additional integral of motion is also taken into account. Using dynamical simulation, we study a system of concentric, rotating, spherical shells employing a precise, event-driven, algorithm that permits the controlled exchange of internal angular momentum. Initially the system starts to relax to a locally stable state that is in good agreement with mean field predictions. This is followed by core collapse with the development of a core-halo structure and gravothermal oscillation.
Accelerated dynamics simulations of nanotubes.
Uberuaga, B. P.; Stuart, S. J.; Voter, A. F.
2002-01-01
We report on the application of accelerated dynamics techniques to the study of carbon nanotubes. We have used the parallel replica method and temperature accelerated dynamics simulations are currently in progress. In the parallel replica study, we have stretched tubes at a rate significantly lower than that used in previous studies. In these preliminary results, we find that there are qualitative differences in the rupture of the nanotubes at different temperatures. We plan on extending this investigation to include nanotubes of various chiralities. We also plan on exploring unique geometries of nanotubes.
Molecular dynamics simulation of pyridine
NASA Astrophysics Data System (ADS)
Trumpakaj, Zygmunt; Linde, Bogumił
2015-04-01
Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.
Dynamic simulations of tissue welding
Maitland, D.J.; Eder, D.C.; London, R.A.; Glinsky, M.E.
1996-02-01
The exposure of human skin to near-infrared radiation is numerically simulated using coupled laser, thermal transport and mass transport numerical models. The computer model LATIS is applied in both one-dimensional and two-dimensional geometries. Zones within the skin model are comprised of a topical solder, epidermis, dermis, and fatty tissue. Each skin zone is assigned initial optical, thermal and water density properties consistent with values listed in the literature. The optical properties of each zone (i.e. scattering, absorption and anisotropy coefficients) are modeled as a kinetic function of the temperature. Finally, the water content in each zone is computed from water diffusion where water losses are accounted for by evaporative losses at the air-solder interface. The simulation results show that the inclusion of water transport and evaporative losses in the model are necessary to match experimental observations. Dynamic temperature and damage distributions are presented for the skin simulations.
Molecular dynamics simulation of benzene
NASA Astrophysics Data System (ADS)
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Dynamic Multiscale Simulation of Polyelectrolyte Nanoassemblies
2008-08-21
REPORT Dynamic Multiscale Simulation of Polyelectrolyte Nanoassemblies 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The goal of this project is to...Std. Z39.18 - 31-May-2008 Dynamic Multiscale Simulation of Polyelectrolyte Nanoassemblies Report Title ABSTRACT The goal of this project is to...Total Number: Sub Contractors (DD882) Inventions (DD882) Final Progress Report Dynamic Multiscale Simulation of Polyelectrolyte Nanoassemblies
Whole Building Cost and Performance Measurement: Data Collection Protocol Revision 2
Fowler, Kimberly M.; Spees, Kathleen L.; Kora, Angela R.; Rauch, Emily M.; Hathaway, John E.; Solana, Amy E.
2009-03-27
This protocol was written for the Department of Energy’s Federal Energy Management Program (FEMP) to be used by the public as a tool for assessing building cost and performance measurement. The primary audiences are sustainable design professionals, asset owners, building managers, and research professionals within the Federal sector. The protocol was developed based on the need for measured performance and cost data on sustainable design projects. Historically there has not been a significant driver in the public or private sector to quantify whole building performance in comparable terms. The deployment of sustainable design into the building sector has initiated many questions on the performance and operational cost of these buildings.
Pratt, Robert G.; Bauman, Nathan N.; Katipamula, Srinivas
2003-01-17
This report describes results from an evaluation of the Whole Building Diagnostician's (WBD) ability to automatically and continually diagnose operational problems in building air handlers at the Federal Aviation Administration's Denver airport.
Jones, J.W. ); Deringer, J.J. ); Hall, J.D. )
1990-09-01
The Whole-Building Energy Design Targets project is being conducted for the US Department of Energy (DOE) by the Pacific Northwest Laboratory (PNL). The objective of the project is to develop a flexible methodology for setting energy performance guidelines with which architects, engineers, planners, and owners can assess energy efficiency in commercial building design. This volume, the third in the four-volume report on the Targets project concept stage, contains the minutes of the workshops as well as summaries of the expert's written comments prepared at the close of each workshop. In Section 2, the building energy simulation workshop is summarized. Section 3 provides a summary of the building cost workshop.
An Integrated Crustal Dynamics Simulator
NASA Astrophysics Data System (ADS)
Xing, H. L.; Mora, P.
2007-12-01
Numerical modelling offers an outstanding opportunity to gain an understanding of the crustal dynamics and complex crustal system behaviour. This presentation provides our long-term and ongoing effort on finite element based computational model and software development to simulate the interacting fault system for earthquake forecasting. A R-minimum strategy based finite-element computational model and software tool, PANDAS, for modelling 3-dimensional nonlinear frictional contact behaviour between multiple deformable bodies with the arbitrarily-shaped contact element strategy has been developed by the authors, which builds up a virtual laboratory to simulate interacting fault systems including crustal boundary conditions and various nonlinearities (e.g. from frictional contact, materials, geometry and thermal coupling). It has been successfully applied to large scale computing of the complex nonlinear phenomena in the non-continuum media involving the nonlinear frictional instability, multiple material properties and complex geometries on supercomputers, such as the South Australia (SA) interacting fault system, South California fault model and Sumatra subduction model. It has been also extended and to simulate the hot fractured rock (HFR) geothermal reservoir system in collaboration of Geodynamics Ltd which is constructing the first geothermal reservoir system in Australia and to model the tsunami generation induced by earthquakes. Both are supported by Australian Research Council.
Simulations of Dynamic Relativistic Magnetospheres
NASA Astrophysics Data System (ADS)
Parfrey, Kyle Patrick
Neutron stars and black holes are generally surrounded by magnetospheres of highly conducting plasma in which the magnetic flux density is so high that hydrodynamic forces are irrelevant. In this vanishing-inertia—or ultra-relativistic—limit, magnetohydrodynamics becomes force-free electrodynamics, a system of equations comprising only the magnetic and electric fields, and in which the plasma response is effected by a nonlinear current density term. In this dissertation I describe a new pseudospectral simulation code, designed for studying the dynamic magnetospheres of compact objects. A detailed description of the code and several numerical test problems are given. I first apply the code to the aligned rotator problem, in which a star with a dipole magnetic field is set rotating about its magnetic axis. The solution evolves to a steady state, which is nearly ideal and dissipationless everywhere except in a current sheet, or magnetic field discontinuity, at the equator, into which electromagnetic energy flows and is dissipated. Magnetars are believed to have twisted magnetospheres, due to internal magnetic evolution which deforms the crust, dragging the footpoints of external magnetic field lines. This twisting may be able to explain both magnetars' persistent hard X-ray emission and their energetic bursts and flares. Using the new code, I simulate the evolution of relativistic magnetospheres subjected to slow twisting through large angles. The field lines expand outward, forming a strong current layer; eventually the configuration loses equilibrium and a dynamic rearrangement occurs, involving large-scale rapid magnetic reconnection and dissipation of the free energy of the twisted magnetic field. When the star is rotating, the magnetospheric twisting leads to a large increase in the stellar spin-down rate, which may take place on the long twisting timescale or in brief explosive events, depending on where the twisting is applied and the history of the system
Dynamical simulations of sedimenting spheres
Ladd, A.J.C. )
1993-02-01
The sedimentation of monodisperse suspensions of rigid spheres has been studied by dynamical simulation; computational techniques are described and numerical results are reported. It has been found that there is a slow relaxation of the suspension microstructure during sedimentation, so that compared with the initial equilibrium distribution, there is an increased number of pairs of particles near contact; this leads to a 5%--10% increase in the average sedimentation velocity. Individual particle velocities fluctuate about the mean fall speed; these fluctuations are large and persist for long times. The resulting hydrodynamically induced dispersion of the particles can be characterized by strongly anisotropic diffusion coefficients; however, the dispersion process is non-Fickian at high solids concentrations.
Enabling Strain Hardening Simulations with Dislocation Dynamics
Arsenlis, A; Cai, W
2006-12-20
Numerical algorithms for discrete dislocation dynamics simulations are investigated for the purpose of enabling strain hardening simulations of single crystals on massively parallel computers. The algorithms investigated include the /(N) calculation of forces, the equations of motion, time integration, adaptive mesh refinement, the treatment of dislocation core reactions, and the dynamic distribution of work on parallel computers. A simulation integrating all of these algorithmic elements using the Parallel Dislocation Simulator (ParaDiS) code is performed to understand their behavior in concert, and evaluate the overall numerical performance of dislocation dynamics simulations and their ability to accumulate percents of plastic strain.
Asbestos release from whole-building demolition of buildings with asbestos-containing material.
Perkins, Robert A; Hargesheimer, John; Fourie, Walter
2007-12-01
The whole-building demolition method, which entails one-or two-story buildings pushed down by heavy equipment, loaded into trucks, and hauled away, is generally the most cost-effective means to remove small buildings. For taller buildings, a crane and wrecking ball may be used initially to reduce the height of the building. Demolitions might release asbestos fibers from friable asbestos-containing material (ACM). Fibers also might be released from nominally nonfriable ACM (Categories I and II nonfriable ACM) if it becomes friable after rough handling throughout the whole-building demolition process. This paper reports on asbestos air monitoring from two demolition projects involving ACM. In one building, Category II nonfriable ACM was present because it could not be removed safely prior to demolition. Both projects had large quantities of gypsum wallboard with ACM joint compound and ACM flooring. One building had large quantities of ACM spray-on ceiling material. During the demolitions personal air monitoring of the workers and area air monitoring downwind and around the sites were conducted. The monitoring found the concentrations of fibers detected by phase contrast microscopy were generally well below the permissible exposure limits (PEL) of workers. Electron microcopy analysis of samples at or near the PEL indicated most of the fibers were not asbestos, and the actual asbestos exposure was often below the detection limit of the procedure. The buildings were kept wet with fire hoses during the demolition and that required large quantities of water, 20,000-60,000 gal/day (75-225 m(3)/day). Earlier studies found little asbestos release from buildings containing only nonfriable ACM demolished by this method. This project found a negligible release of asbestos fibers, despite the presence of nonfriable materials that might become friable, such as ACM joint compound and spray-on ACM ceiling coating.
Molecular dynamics simulations of nanostructures
NASA Astrophysics Data System (ADS)
Yuan, Zaoshi
This dissertation is focused on multimillion-atom molecular dynamics (MD) simulations of nanoscale materials. In the past decade, nanoscale materials have made significant commercial impacts, which will potentially lead to the next industrial revolution. The interest lies in the novel and promising features nanoscale materials exhibit due to their confined sizes. However, not all novel behaviors are understood or controllable. Many uncontrollable parameters, e.g. defects and dangling bonds, are known to hinder the performance of nanodevices. Solutions to these problems rely on our understanding of fundamental elements in nanoscience: isolated individual nanostructures and their assemblies. In this dissertation, we will address atomistic foundations of several problems of technological importance in nanoscience. Specifically, three basic problems are discussed: (1) embrittlement of nanocrystalline metal; (2) novel thermo-mechanical behaviors of nanowires (NWs); and (3) planar defect generation in NWs. With a scalable algorithm implemented on massively parallel computing platforms and various data mining methods, MD simulations can provide valuable insights into these problems. An essential role of sulfur segregation-induced amorphization of crystalline nickel was recently discovered experimentally, but the atomistic mechanism of the amorphization remains unexplained. Our MD simulations reveal that the large steric size of sulfur impurity causes strong sulfur-sulfur interaction mediated by lattice distortion, which leads to amorphization near the percolation threshold at the sulfur-sulfur network in nickel crystal. The generality of the mechanism due to the percolation of an impurity network is further confirmed by a model binary system. In our study of novel behaviors of semiconductor NWs, MD simulations construct a rich size-temperature `phase diagram' for the mechanical response of a zinc-oxide NW under tension. For smaller diameters and higher temperatures, novel
Modeling Nanocomposites for Molecular Dynamics (MD) Simulations
2015-01-01
Maximum 200 Words) The minimum energy configuration for Molecular Dynamics (MD) simulations is found for a carbon nanotube (CNT)/polymer... Carbon Nanotubes (CNTs), Molecular Dynamics Simulations 15. NUMBER OF PAGES 18 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT... Carbon Nanotubes ,” Macromolecules, Volume 39, Number 16, pp. 5194-5205, July 2006. 6. “VMD-Visual Molecular Dynamics ,” March 2014, http
Molecular Dynamics Simulation of Supercritical Spray Phenomena
2008-09-26
Dynamics of the Rheological and Structural Properties of Linear and Branched Molecules. Simple Shear and Poiseuille Flows ; Instabilities and Slip...Michael Barrucco Publications: "Comparison of Wall Models for the Molecular Dynamics Simulation of Micro flows ," R. D. Branam and M. M...Performance 3. DATES COVERED (From - To) 1 Dec. 2003 - 31 May 2008 4. TITLE AND SUBTITLE Molecular Dynamics Simulation of Supercritical
Novel methods for molecular dynamics simulations.
Elber, R
1996-04-01
In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced.
Metrics for comparing dynamic earthquake rupture simulations
Barall, Michael; Harris, Ruth A.
2014-01-01
Earthquakes are complex events that involve a myriad of interactions among multiple geologic features and processes. One of the tools that is available to assist with their study is computer simulation, particularly dynamic rupture simulation. A dynamic rupture simulation is a numerical model of the physical processes that occur during an earthquake. Starting with the fault geometry, friction constitutive law, initial stress conditions, and assumptions about the condition and response of the near‐fault rocks, a dynamic earthquake rupture simulation calculates the evolution of fault slip and stress over time as part of the elastodynamic numerical solution (Ⓔ see the simulation description in the electronic supplement to this article). The complexity of the computations in a dynamic rupture simulation make it challenging to verify that the computer code is operating as intended, because there are no exact analytic solutions against which these codes’ results can be directly compared. One approach for checking if dynamic rupture computer codes are working satisfactorily is to compare each code’s results with the results of other dynamic rupture codes running the same earthquake simulation benchmark. To perform such a comparison consistently, it is necessary to have quantitative metrics. In this paper, we present a new method for quantitatively comparing the results of dynamic earthquake rupture computer simulation codes.
Mapping conformational dynamics of proteins using torsional dynamics simulations.
Gangupomu, Vamshi K; Wagner, Jeffrey R; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan
2013-05-07
All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein's experimentally established conformational substates. Conformational transition of calmodulin from the Ca(2+)-bound to the Ca(2+)-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in
Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations
Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan
2013-01-01
All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in
Leach, M.; Bonnema, E.; Pless, S.; Torcellini, P.
2012-08-01
This paper helps owners' efficiency representatives to inform executive management, contract development, and project management staff as to how specifying and applying whole-building absolute energy use targets for new construction or renovation projects can improve the operational energy performance of commercial buildings.
Simulation Exercises in Population Dynamics.
ERIC Educational Resources Information Center
Falk, Laurence L.; Falk, Carol J.
1986-01-01
Describes a computer simulation providing population change profiles at 5-year intervals for 100 years, projecting natural rate of increase and total population, per capita gross national product, energy consumption, age-specific fertility rates, and survival ratios. Data sources for the simulation, sample printed output, and learning activities…
Simulating protein dynamics: Novel methods and applications
NASA Astrophysics Data System (ADS)
Vishal, V.
This Ph.D dissertation describes several methodological advances in molecular dynamics (MD) simulations. Methods like Markov State Models can be used effectively in combination with distributed computing to obtain long time scale behavior from an ensemble of short simulations. Advanced computing architectures like Graphics Processors can be used to greatly extend the scope of MD. Applications of MD techniques to problems like Alzheimer's Disease and fundamental questions in protein dynamics are described.
Discrete Molecular Dynamics Simulation of Biomolecules
NASA Astrophysics Data System (ADS)
Ding, Feng
2011-10-01
Discrete molecular dynamics (DMD) simulation of hard spheres was the first implementation of molecular dynamics (MD) in history. DMD simulations are computationally more efficient than continuous MD simulations due to simplified interaction potentials. However, also due to these simplified potentials, DMD has often been associated with coarse-grained modeling, and hence continuous MD has become the dominant approach used to study the internal dynamics of biomolecules. With the recent advances in DMD methodology, including the development of high-resolution models for biomolecules and approaches to increase DMD efficiency, DMD simulations are emerging as an important tool in the field of molecular modeling, including the study of protein folding, protein misfolding and aggregation, and protein engineering. Recently, DMD methodology has been applied to modeling RNA folding and protein-ligand recognition. With these improvements to DMD methodology and the continuous increase in available computational power, we expect a growing role of DMD simulations in our understanding of biology.
The "Collisions Cube" Molecular Dynamics Simulator.
ERIC Educational Resources Information Center
Nash, John J.; Smith, Paul E.
1995-01-01
Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)
Visualizing Structure and Dynamics of Disaccharide Simulations
Matthews, J. F.; Beckham, G. T.; Himmel, M. E.; Crowley, M. F.
2012-01-01
We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.
Simulating Flexible-Spacecraft Dynamics and Control
NASA Technical Reports Server (NTRS)
Fedor, Joseph
1987-01-01
Versatile program applies to many types of spacecraft and dynamical problems. Flexible Spacecraft Dynamics and Control program (FSD) developed to aid in simulation of large class of flexible and rigid spacecraft. Extremely versatile and used in attitude dynamics and control analysis as well as in-orbit support of deployment and control of spacecraft. Applicable to inertially oriented spinning, Earth-oriented, or gravity-gradient-stabilized spacecraft. Written in FORTRAN 77.
Molecular Dynamics Simulations of Simple Liquids
ERIC Educational Resources Information Center
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Molecular Dynamics Simulations of Simple Liquids
ERIC Educational Resources Information Center
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Observing dynamical SUSY breaking with lattice simulation
Kanamori, Issaku
2008-11-23
On the basis of the recently developed lattice formulation of supersymmetric theories which keeps a part of the supersymmetry, we propose a method of observing dynamical SUSY breaking with lattice simulation. We use Hamiltonian as an order parameter and measure the ground state energy as a zero temperature limit of the finite temperature simulation. Our method provides a way of obtaining a physical result from the lattice simulation for supersymmetric theories.
Molecular dynamics simulations: advances and applications
Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L
2015-01-01
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800
Simulation of wetlands forest vegetation dynamics
Phipps, R.L.
1979-01-01
A computer program, SWAMP, was designed to simulate the effects of flood frequency and depth to water table on southern wetlands forest vegetation dynamics. By incorporating these hydrologic characteristics into the model, forest vegetation and vegetation dynamics can be simulated. The model, based on data from the White River National Wildlife Refuge near De Witt, Arkansas, "grows" individual trees on a 20 x 20-m plot taking into account effects on the tree growth of flooding, depth to water table, shade tolerance, overtopping and crowding, and probability of death and reproduction. A potential application of the model is illustrated with simulations of tree fruit production following flood-control implementation and lumbering. ?? 1979.
Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations
NASA Astrophysics Data System (ADS)
Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein
2015-12-01
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
Computational plasticity algorithm for particle dynamics simulations
NASA Astrophysics Data System (ADS)
Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.
2017-03-01
The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.
Peptide crystal simulations reveal hidden dynamics
Janowski, Pawel A.; Cerutti, David S.; Holton, James; Case, David A.
2013-01-01
Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in the X-ray diffraction data. We present here 9.6 microseconds of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom rmsd; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom rmsd. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(−) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data, as well as to validate computational chemistry methods. PMID:23631449
Spin dynamics simulations at AGS
Huang, H.; MacKay, W.W.; Meot, F.; Roser, T.
2010-05-23
To preserve proton polarization through acceleration, it is important to have a correct model of the process. It has been known that with the insertion of the two helical partial Siberian snakes in the Alternating Gradient Synchrotron (AGS), the MAD model of AGS can not deal with a field map with offset orbit. The stepwise ray-tracing code Zgoubi provides a tool to represent the real electromagnetic fields in the modeling of the optics and spin dynamics for the AGS. Numerical experiments of resonance crossing, including spin dynamics in presence of the snakes and Q-jump, have been performed in AGS lattice models, using Zgoubi. This contribution reports on various results so obtained.
Dynamic simulation of particle sedimentation
NASA Astrophysics Data System (ADS)
Zhang, Zhongzhen; Prosperetti, Andrea
2004-11-01
The sedimentation of 1024 spheres has been simulated via a recently developed method:Physalis Method. Particles are initially randomly distributed and periodic boundary conditions are assumed. The time evolution of the particle spatial distribution is studied by meassuering the structure factor. Properties of particles velocity distribution, e.g. variance, time autocorrelation, have been studied. The effects of particle rotation and collision are discussed.
The data system dynamic simulation /DSDS/
NASA Technical Reports Server (NTRS)
Hooper, J. W.; Piner, J. R.
1978-01-01
The paper describes the development by NASA of the data system dynamic simulation (DSDS) which provides a data system simulation capability for a broad range of programs, with the capability to model and simulate all or any portion of an end-to-end data system to multiple levels of fidelity. Versatility is achieved by specifying parameters which define the performance characteristics of data system components, and by specifying control and data paths in a data system. DSDS helps reduce overall simulation cost and the time required for obtaining a data systems analysis, and helps provide both early realistic representations of data systems and the flexibility to study design changes and operating strategies.
Multibody dynamic simulation of knee contact mechanics
Bei, Yanhong; Fregly, Benjamin J.
2006-01-01
Multibody dynamic musculoskeletal models capable of predicting muscle forces and joint contact pressures simultaneously would be valuable for studying clinical issues related to knee joint degeneration and restoration. Current three-dimensional multi-body knee models are either quasi-static with deformable contact or dynamic with rigid contact. This study proposes a computationally efficient methodology for combining multibody dynamic simulation methods with a deformable contact knee model. The methodology requires preparation of the articular surface geometry, development of efficient methods to calculate distances between contact surfaces, implementation of an efficient contact solver that accounts for the unique characteristics of human joints, and specification of an application programming interface for integration with any multibody dynamic simulation environment. The current implementation accommodates natural or artificial tibiofemoral joint models, small or large strain contact models, and linear or nonlinear material models. Applications are presented for static analysis (via dynamic simulation) of a natural knee model created from MRI and CT data and dynamic simulation of an artificial knee model produced from manufacturer’s CAD data. Small and large strain natural knee static analyses required 1 min of CPU time and predicted similar contact conditions except for peak pressure, which was higher for the large strain model. Linear and nonlinear artificial knee dynamic simulations required 10 min of CPU time and predicted similar contact force and torque but different contact pressures, which were lower for the nonlinear model due to increased contact area. This methodology provides an important step toward the realization of dynamic musculoskeletal models that can predict in vivo knee joint motion and loading simultaneously. PMID:15564115
Perspective: chemical dynamics simulations of non-statistical reaction dynamics.
Ma, Xinyou; Hase, William L
2017-04-28
Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Author(s).
Dynamic centrifugal compressor model for system simulation
NASA Astrophysics Data System (ADS)
Jiang, Wei; Khan, Jamil; Dougal, Roger A.
A dynamic model of a centrifugal compressor capable of system simulation in the virtual test bed (VTB) computational environment is presented. The model is based on first principles, i.e. the dynamic performance including the losses is determined from the compressor geometry and not from the experimentally determined characteristic performance curves. In this study, the compressor losses, such as incidence and friction losses, etc., are mathematically modeled for developing compressor characteristics. For easy implementation in the VTB platform, the non-linear governing equations are discretized in resistive companion (RC) form. The developed simulation model can be applied to virtually any centrifugal compressor. By interfacing with a composite system, such as a Brayton cycle gas turbine, or a fuel cell, the compressor dynamic performance can be evaluated. The surge line for the compressor can also be determined from the simulation results. Furthermore, the model presented here provides a valuable tool for evaluating the system performance as a function of various operating parameters.
Dynamic procedure for filtered gyrokinetic simulations
Morel, P.; Banon Navarro, A.; Albrecht-Marc, M.; Carati, D.; Merz, F.; Goerler, T.; Jenko, F.
2012-01-15
Large eddy simulations (LES) of gyrokinetic plasma turbulence are investigated as interesting candidates to decrease the computational cost. A dynamic procedure is implemented in the gene code, allowing for dynamic optimization of the free parameters of the LES models (setting the amplitudes of dissipative terms). Employing such LES methods, one recovers the free energy and heat flux spectra obtained from highly resolved direct numerical simulations. Systematic comparisons are performed for different values of the temperature gradient and magnetic shear, parameters which are of prime importance in ion temperature gradient driven turbulence. Moreover, the degree of anisotropy of the problem, which can vary with parameters, can be adapted dynamically by the method that shows gyrokinetic large eddy simulation to be a serious candidate to reduce numerical cost of gyrokinetic solvers.
Molecular dynamics simulations of substitutional diffusion
Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob
2016-12-18
In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less
Molecular dynamics simulations of substitutional diffusion
Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob
2016-12-18
In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example, we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.
Using Whole-Building Electric Load Data in Continuous or Retro-Commissioning
Price, Phillip N.; Mathieu, Johanna L.; Kiliccote, Sila; Piette, Mary Ann
2011-07-01
Whole-building electric load data can often reveal problems with building equipment or operations. In this paper, we present methods for analyzing 15-minute-interval electric load data. These methods allow building operators, energy managers, and commissioning agents to better understand a building's electricity consumption over time and to compare it to other buildings, helping them to 'ask the right questions' to discover opportunities for electricity waste elimination, energy efficiency, peak load management, and demand response. For example: Does the building use too much energy at night, or on hot days, or in the early evening? Knowing the answer to questions like these can help with retro-commissioning or continuous commissioning. The methods discussed here can also be used to assess how building energy performance varies with time. Comparing electric load before and after fixing equipment or changing operations can help verify that the fixes have the intended effect on energy consumption. Analysis methods discussed in this paper include: ways to graphically represent electric load data; the definition of various parameters that characterize facility electricity loads; and a regression-based electricity load model that accounts for both time of week and outdoor air temperature. The methods are illustrated by applying them to data from commercial buildings. We demonstrate the ability to recognize changes in building operation, and to quantify changes in energy performance. Some key findings are: 1) Plotting time series electric load data is useful for understanding electricity consumption patterns and changes to those patterns, but results may be misleading if data from different time intervals are not weather-normalized. 2) Parameter plots can highlight key features of electric load data and may be easier to interpret than plots of time series data themselves. 3) A time-of-week indicator variable (as compared to time-of-day and day-of-week indicator variables
Dynamic modeling and simulation of planetary rovers
NASA Technical Reports Server (NTRS)
Lindemann, Randel A.
1992-01-01
This paper documents a preliminary study into the dynamic modeling and computer simulation of wheeled surface vehicles. The research centered on the feasibility of using commercially available multibody dynamics codes running on engineering workstations to perform the analysis. The results indicated that physically representative vehicle mechanics can be modeled and simulated in state-of-the-art Computer Aided Engineering environments, but at excessive cost in modeling and computation time. The results lead to the recommendation for the development of an efficient rover mobility-specific software system. This system would be used for vehicle design and simulation in planetary environments; controls prototyping, design, and testing; as well as local navigation simulation and expectation planning.
Choice of timestep in molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Fincham, David
1986-06-01
In molecular dynamics computer simulation of liquids it is important to use as large a timestep as possible in order to sample phase space rapidly and save on computer expense. The effect of the resulting algorithm errors in the trajectories of the molecules is not well understood. An empirical investigation into this question is reported. Several simulations differing only in the timestep used are compared. It is found that much larger timesteps than usual can be employed without producing significant errors in observed thermodynamic, structural or dynamic properties.
Massively-Parallel Dislocation Dynamics Simulations
Cai, W; Bulatov, V V; Pierce, T G; Hiratani, M; Rhee, M; Bartelt, M; Tang, M
2003-06-18
Prediction of the plastic strength of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of the existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, in order to be statistically representative and to reproduce experimentally observed microstructures. A new massively-parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We discuss the general aspects of this code that make such large scale simulations possible, as well as a few initial simulation results.
Dynamic Fracture Simulations of Explosively Loaded Cylinders
Arthur, Carly W.; Goto, D. M.
2015-11-30
This report documents the modeling results of high explosive experiments investigating dynamic fracture of steel (AerMet® 100 alloy) cylinders. The experiments were conducted at Lawrence Livermore National Laboratory (LLNL) during 2007 to 2008 [10]. A principal objective of this study was to gain an understanding of dynamic material failure through the analysis of hydrodynamic computer code simulations. Two-dimensional and three-dimensional computational cylinder models were analyzed using the ALE3D multi-physics computer code.
Dynamics modeling and simulation of flexible airships
NASA Astrophysics Data System (ADS)
Li, Yuwen
The resurgence of airships has created a need for dynamics models and simulation capabilities of these lighter-than-air vehicles. The focus of this thesis is a theoretical framework that integrates the flight dynamics, structural dynamics, aerostatics and aerodynamics of flexible airships. The study begins with a dynamics model based on a rigid-body assumption. A comprehensive computation of aerodynamic effects is presented, where the aerodynamic forces and moments are categorized into various terms based on different physical effects. A series of prediction approaches for different aerodynamic effects are unified and applied to airships. The numerical results of aerodynamic derivatives and the simulated responses to control surface deflection inputs are verified by comparing to existing wind-tunnel and flight test data. With the validated aerodynamics and rigid-body modeling, the equations of motion of an elastic airship are derived by the Lagrangian formulation. The airship is modeled as a free-free Euler-Bernoulli beam and the bending deformations are represented by shape functions chosen as the free-free normal modes. In order to capture the coupling between the aerodynamic forces and the structural elasticity, local velocity on the deformed vehicle is used in the computation of aerodynamic forces. Finally, with the inertial, gravity, aerostatic and control forces incorporated, the dynamics model of a flexible airship is represented by a single set of nonlinear ordinary differential equations. The proposed model is implemented as a dynamics simulation program to analyze the dynamics characteristics of the Skyship-500 airship. Simulation results are presented to demonstrate the influence of structural deformation on the aerodynamic forces and the dynamics behavior of the airship. The nonlinear equations of motion are linearized numerically for the purpose of frequency domain analysis and for aeroelastic stability analysis. The results from the latter for the
Dynamic simulation recalls condensate piping event
Farrell, R.J.; Reneberg, K.O. ); Moy, H.C. )
1994-05-01
This article describes how experience gained from simulating and reconstructing a condensate piping event will be used by Consolidated Edison to analyze control system problems. A cooperative effort by Con Edison and the Chemical Engineering Department at Polytechnic University used modular modeling system to investigate the probable cause of a Con Edison condensate piping event. Con Edison commissioned the work to serve as a case study for the more general problem of control systems analysis using dynamic simulation and MMS.
Numerical simulation of interplanetary dynamics
NASA Astrophysics Data System (ADS)
Wu, Chin-Chun
This dissertation discusses investigations into the physics of the propagation of solar generated disturbances in the interplanetary medium. The motivation to initiate this study was two-fold: (1) understanding the fundamental physics of the nonlinear interactions of solar generated MHD shocks and non-homogeneous interplanetary medium, and (2) understanding the physics of solar generated disturbance effects on the Earth's environment, (i.e. the solar connection to the geomagnetic storm). In order to achieve these goals, the authors employed two numerical models to encompass these studies. In the first part, a one-dimensional MHD code with adaptive grids is used to study the evolution of interplanetary slow shocks (ISS), the interaction of a forward slow shock with a reverse slow shock, and the interaction of a fast shock with a slow shock. Results show that the slow shocks can be generated by a decreasing density, velocity or temperature perturbation or by a pressure pulse by following a forward fast shock and that slow shocks can propagate over 1 AU; results also show that the ISS never evolves into fast shocks. Interestingly, it is also found that an ISS could be 'eaten up' by an interplanetary fast shock (IFS) catching up from behind. This could be a reason that the slow shock has been difficult to observe near 1 AU. In addition, a forward slow shock could be dissipated by following a strong forward fast shock (Mach number greater than 1.7). In the second part, a fully three-dimensional (3D), time-dependent, MHD interplanetary global model (3D IGM) is used to study the relationship between different forms of solar activity and transient variations of the north-south component, Bx, of the interplanetary magnetic field, IMF, at 1 AU. One form of solar activity, the flare, is simulated by using a pressure pulse at different locations near the solar surface and observing the simulated IMF evolution of Btheta (= -Bx) at 1 AU. Results show that, for a given pressure
Molecular dynamic simulations of ocular tablet dissolution.
Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire
2013-11-25
Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies.
Quantum Simulation for Open-System Dynamics
NASA Astrophysics Data System (ADS)
Wang, Dong-Sheng; de Oliveira, Marcos Cesar; Berry, Dominic; Sanders, Barry
2013-03-01
Simulations are essential for predicting and explaining properties of physical and mathematical systems yet so far have been restricted to classical and closed quantum systems. Although forays have been made into open-system quantum simulation, the strict algorithmic aspect has not been explored yet is necessary to account fully for resource consumption to deliver bounded-error answers to computational questions. An open-system quantum simulator would encompass classical and closed-system simulation and also solve outstanding problems concerning, e.g. dynamical phase transitions in non-equilibrium systems, establishing long-range order via dissipation, verifying the simulatability of open-system dynamics on a quantum Turing machine. We construct an efficient autonomous algorithm for designing an efficient quantum circuit to simulate many-body open-system dynamics described by a local Hamiltonian plus decoherence due to separate baths for each particle. The execution time and number of gates for the quantum simulator both scale polynomially with the system size. DSW funded by USARO. MCO funded by AITF and Brazilian agencies CNPq and FAPESP through Instituto Nacional de Ciencia e Tecnologia-Informacao Quantica (INCT-IQ). DWB funded by ARC Future Fellowship (FT100100761). BCS funded by AITF, CIFAR, NSERC and USARO.
Airborne Simulation of Launch Vehicle Dynamics
NASA Technical Reports Server (NTRS)
Miller, Christopher J.; Orr, Jeb S.; Hanson, Curtis E.; Gilligan, Eric T.
2015-01-01
In this paper we present a technique for approximating the short-period dynamics of an exploration-class launch vehicle during flight test with a high-performance surrogate aircraft in relatively benign endoatmospheric flight conditions. The surrogate vehicle relies upon a nonlinear dynamic inversion scheme with proportional-integral feedback to drive a subset of the aircraft states into coincidence with the states of a time-varying reference model that simulates the unstable rigid body dynamics, servodynamics, and parasitic elastic and sloshing dynamics of the launch vehicle. The surrogate aircraft flies a constant pitch rate trajectory to approximate the boost phase gravity turn ascent, and the aircraft's closed-loop bandwidth is sufficient to simulate the launch vehicle's fundamental lateral bending and sloshing modes by exciting the rigid body dynamics of the aircraft. A novel control allocation scheme is employed to utilize the aircraft's relatively fast control effectors in inducing various failure modes for the purposes of evaluating control system performance. Sufficient dynamic similarity is achieved such that the control system under evaluation is configured for the full-scale vehicle with no changes to its parameters, and pilot-control system interaction studies can be performed to characterize the effects of guidance takeover during boost. High-fidelity simulation and flight-test results are presented that demonstrate the efficacy of the design in simulating the Space Launch System (SLS) launch vehicle dynamics using the National Aeronautics and Space Administration (NASA) Armstrong Flight Research Center Fullscale Advanced Systems Testbed (FAST), a modified F/A-18 airplane (McDonnell Douglas, now The Boeing Company, Chicago, Illinois), over a range of scenarios designed to stress the SLS's Adaptive Augmenting Control (AAC) algorithm.
Airborne Simulation of Launch Vehicle Dynamics
NASA Technical Reports Server (NTRS)
Gilligan, Eric T.; Miller, Christopher J.; Hanson, Curtis E.; Orr, Jeb S.
2014-01-01
In this paper we present a technique for approximating the short-period dynamics of an exploration-class launch vehicle during flight test with a high-performance surrogate aircraft in relatively benign endoatmospheric flight conditions. The surrogate vehicle relies upon a nonlinear dynamic inversion scheme with proportional-integral feedback to drive a subset of the aircraft states into coincidence with the states of a time-varying reference model that simulates the unstable rigid body dynamics, servodynamics, and parasitic elastic and sloshing dynamics of the launch vehicle. The surrogate aircraft flies a constant pitch rate trajectory to approximate the boost phase gravity-turn ascent, and the aircraft's closed-loop bandwidth is sufficient to simulate the launch vehicle's fundamental lateral bending and sloshing modes by exciting the rigid body dynamics of the aircraft. A novel control allocation scheme is employed to utilize the aircraft's relatively fast control effectors in inducing various failure modes for the purposes of evaluating control system performance. Sufficient dynamic similarity is achieved such that the control system under evaluation is optimized for the full-scale vehicle with no changes to its parameters, and pilot-control system interaction studies can be performed to characterize the effects of guidance takeover during boost. High-fidelity simulation and flight test results are presented that demonstrate the efficacy of the design in simulating the Space Launch System (SLS) launch vehicle dynamics using NASA Dryden Flight Research Center's Full-scale Advanced Systems Testbed (FAST), a modified F/A-18 airplane, over a range of scenarios designed to stress the SLS's adaptive augmenting control (AAC) algorithm.
Multiscale model approach for magnetization dynamics simulations
NASA Astrophysics Data System (ADS)
De Lucia, Andrea; Krüger, Benjamin; Tretiakov, Oleg A.; Kläui, Mathias
2016-11-01
Simulations of magnetization dynamics in a multiscale environment enable the rapid evaluation of the Landau-Lifshitz-Gilbert equation in a mesoscopic sample with nanoscopic accuracy in areas where such accuracy is required. We have developed a multiscale magnetization dynamics simulation approach that can be applied to large systems with spin structures that vary locally on small length scales. To implement this, the conventional micromagnetic simulation framework has been expanded to include a multiscale solving routine. The software selectively simulates different regions of a ferromagnetic sample according to the spin structures located within in order to employ a suitable discretization and use either a micromagnetic or an atomistic model. To demonstrate the validity of the multiscale approach, we simulate the spin wave transmission across the regions simulated with the two different models and different discretizations. We find that the interface between the regions is fully transparent for spin waves with frequency lower than a certain threshold set by the coarse scale micromagnetic model with no noticeable attenuation due to the interface between the models. As a comparison to exact analytical theory, we show that in a system with a Dzyaloshinskii-Moriya interaction leading to spin spirals, the simulated multiscale result is in good quantitative agreement with the analytical calculation.
Simulating Dynamic Equilibria: A Class Experiment
NASA Astrophysics Data System (ADS)
Harrison, John A.; Buckley, Paul D.
2000-08-01
A first-order reversible reaction is simulated on an overhead projector using small coins or discs. A simulation is carried out in which initially there are 24 discs representing reactant A and none representing reactant B. At the end of each minute half of the reactant A discs get converted to reactant B, and one quarter of the reactant B discs get converted to reactant A discs. Equilibrium is established with 8 A discs and 16 B discs, and no further net change is observed as the simulation continues. Another simulation beginning with 48 A discs and 0 B discs leads at equilibrium to 16 A discs and 32 B discs. These results illustrate how dynamic equilibria are established and allow the introduction of the concept of an equilibrium constant. Le Châtelier's principle is illustrated by further simulations.
Dynamic simulation of a reverse Brayton refrigerator
Peng, N.; Xiong, L. Y.; Dong, B.; Liu, L. Q.; Lei, L. L.; Tang, J. C.
2014-01-29
A test refrigerator based on the modified Reverse Brayton cycle has been developed in the Chinese Academy of Sciences recently. To study the behaviors of this test refrigerator, a dynamic simulation has been carried out. The numerical model comprises the typical components of the test refrigerator: compressor, valves, heat exchangers, expander and heater. This simulator is based on the oriented-object approach and each component is represented by a set of differential and algebraic equations. The control system of the test refrigerator is also simulated, which can be used to optimize the control strategies. This paper describes all the models and shows the simulation results. Comparisons between simulation results and experimental data are also presented. Experimental validation on the test refrigerator gives satisfactory results.
Digital simulation of stiff linear dynamic systems.
NASA Technical Reports Server (NTRS)
Holland, L. D.; Walsh, J. R., Jr.; Kerr, J. H.
1972-01-01
A method is derived for digital computer simulation of linear time-invariant systems when the insignificant eigenvalues involved in such systems are eliminated by an ALSAP root removal technique. The method is applied to a thirteenth-order dynamic system representing a passive RLC network.
Dynamics Simulation of Langmuir-Blodgett Films
1990-04-01
of water. During the dynamics simulation, theposition of the water molecules are frozen. A 1515 edge effect as shown in Fig. 4: the tilts for...temperature, I.e. 300K, by gradually assigning random understand. The strong edge effect makes it necessary to iintroduce periodic boundaries In future
Molecular dynamics simulations of magnetized dusty plasmas
NASA Astrophysics Data System (ADS)
Piel, Alexander; Reichstein, Torben; Wilms, Jochen
2012-10-01
The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)
Test of a flexible spacecraft dynamics simulator
NASA Technical Reports Server (NTRS)
Dichmann, Donald; Sedlak, Joseph
1998-01-01
There are a number of approaches one can take to modeling the dynamics of a flexible body. While one can attempt to capture the full dynamical behavior subject to disturbances from actuators and environmental torques, such a detailed description often is unnecessary. Simplification is possible either by limiting the amplitude of motion to permit linearization of the dynamics equations or by restricting the types of allowed motion. In this work, we study the nonlinear dynamics of bending deformations of wire booms on spinning spacecraft. The theory allows for large amplitude excursions from equilibrium while enforcing constraints on the dynamics to prohibit those modes that are physically less relevant or are expected to damp out fast. These constraints explicitly remove the acoustic modes (i.e., longitudinal sound waves and shear waves) while allowing for arbitrary bending and twisting, motions which typically are of lower frequency. As a test case, a spin axis reorientation maneuver by the Polar Plasma Laboratory (POLAR) spacecraft has been simulated. POLAR was chosen as a representative spacecraft because it has flexible wire antennas that extend to a length of 65 meters. Bending deformations in these antennas could be quite large and have a significant effect on the attitude dynamics of the spacecraft body. Summary results from the simulation are presented along, with a comparison with POLAR flight data.
GROSS- GAMMA RAY OBSERVATORY ATTITUDE DYNAMICS SIMULATOR
NASA Technical Reports Server (NTRS)
Garrick, J.
1994-01-01
The Gamma Ray Observatory (GRO) spacecraft will constitute a major advance in gamma ray astronomy by offering the first opportunity for comprehensive observations in the range of 0.1 to 30,000 megaelectronvolts (MeV). The Gamma Ray Observatory Attitude Dynamics Simulator, GROSS, is designed to simulate this mission. The GRO Dynamics Simulator consists of three separate programs: the Standalone Profile Program; the Simulator Program, which contains the Simulation Control Input/Output (SCIO) Subsystem, the Truth Model (TM) Subsystem, and the Onboard Computer (OBC) Subsystem; and the Postprocessor Program. The Standalone Profile Program models the environment of the spacecraft and generates a profile data set for use by the simulator. This data set contains items such as individual external torques; GRO spacecraft, Tracking and Data Relay Satellite (TDRS), and solar and lunar ephemerides; and star data. The Standalone Profile Program is run before a simulation. The SCIO subsystem is the executive driver for the simulator. It accepts user input, initializes parameters, controls simulation, and generates output data files and simulation status display. The TM subsystem models the spacecraft dynamics, sensors, and actuators. It accepts ephemerides, star data, and environmental torques from the Standalone Profile Program. With these and actuator commands from the OBC subsystem, the TM subsystem propagates the current state of the spacecraft and generates sensor data for use by the OBC and SCIO subsystems. The OBC subsystem uses sensor data from the TM subsystem, a Kalman filter (for attitude determination), and control laws to compute actuator commands to the TM subsystem. The OBC subsystem also provides output data to the SCIO subsystem for output to the analysts. The Postprocessor Program is run after simulation is completed. It generates printer and CRT plots and tabular reports of the simulated data at the direction of the user. GROSS is written in FORTRAN 77 and
GROSS- GAMMA RAY OBSERVATORY ATTITUDE DYNAMICS SIMULATOR
NASA Technical Reports Server (NTRS)
Garrick, J.
1994-01-01
The Gamma Ray Observatory (GRO) spacecraft will constitute a major advance in gamma ray astronomy by offering the first opportunity for comprehensive observations in the range of 0.1 to 30,000 megaelectronvolts (MeV). The Gamma Ray Observatory Attitude Dynamics Simulator, GROSS, is designed to simulate this mission. The GRO Dynamics Simulator consists of three separate programs: the Standalone Profile Program; the Simulator Program, which contains the Simulation Control Input/Output (SCIO) Subsystem, the Truth Model (TM) Subsystem, and the Onboard Computer (OBC) Subsystem; and the Postprocessor Program. The Standalone Profile Program models the environment of the spacecraft and generates a profile data set for use by the simulator. This data set contains items such as individual external torques; GRO spacecraft, Tracking and Data Relay Satellite (TDRS), and solar and lunar ephemerides; and star data. The Standalone Profile Program is run before a simulation. The SCIO subsystem is the executive driver for the simulator. It accepts user input, initializes parameters, controls simulation, and generates output data files and simulation status display. The TM subsystem models the spacecraft dynamics, sensors, and actuators. It accepts ephemerides, star data, and environmental torques from the Standalone Profile Program. With these and actuator commands from the OBC subsystem, the TM subsystem propagates the current state of the spacecraft and generates sensor data for use by the OBC and SCIO subsystems. The OBC subsystem uses sensor data from the TM subsystem, a Kalman filter (for attitude determination), and control laws to compute actuator commands to the TM subsystem. The OBC subsystem also provides output data to the SCIO subsystem for output to the analysts. The Postprocessor Program is run after simulation is completed. It generates printer and CRT plots and tabular reports of the simulated data at the direction of the user. GROSS is written in FORTRAN 77 and
Accelerated molecular dynamics simulations of protein folding.
Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew
2015-07-30
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.
Mesoscopic Simulation Methods for Polymer Dynamics
NASA Astrophysics Data System (ADS)
Larson, Ronald
2015-03-01
We assess the accuracy and efficiency of mesoscopic simulation methods, namely Brownian Dynamics (BD), Stochastic Rotation Dynamics (SRD) and Dissipative Particle Dynamics (DPD), for polymers in solution at equilibrium and in flows in microfluidic geometries. Both SRD and DPD use solvent ``particles'' to carry momentum, and so account automatically for hydrodynamic interactions both within isolated polymer coils, and with other polymer molecules and with nearby solid boundaries. We assess quantitatively the effects of artificial particle inertia and fluid compressibility and show that they can be made small with appropriate choice of simulation parameters. We then use these methods to study flow-induced migration of polymer chains produced by: 1) hydrodynamic interactions, 2) streamline curvature or stress-gradients, and 3) convection of wall depletion zones. We show that huge concentration gradients can be produced by these mechanisms in microfluidic geometries that can be exploited for separation of polymers by size in periodic contraction-expansion geometries. We also assess the range of conditions for which BD, SRD or DPD is preferable for mesoscopic simulations. Finally, we show how such methods can be used to simulate quantitatively the swimming of micro-organisms such as E. coli. In collaboration with Lei Jiang and Tongyang Zhao, University of Michigan, Ann Arbor, MI.
Microsecond Molecular Dynamics Simulations of Lipid Mixing
2015-01-01
Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na+ ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes. PMID:25237736
Dynamic Multicore Processing for Pandemic Influenza Simulation
Eriksson, Henrik; Timpka, Toomas; Spreco, Armin; Dahlström, Örjan; Strömgren, Magnus; Holm, Einar
2016-01-01
Pandemic simulation is a useful tool for analyzing outbreaks and exploring the impact of variations in disease, population, and intervention models. Unfortunately, this type of simulation can be quite time-consuming especially for large models and significant outbreaks, which makes it difficult to run the simulations interactively and to use simulation for decision support during ongoing outbreaks. Improved run-time performance enables new applications of pandemic simulations, and can potentially allow decision makers to explore different scenarios and intervention effects. Parallelization of infection-probability calculations and multicore architectures can take advantage of modern processors to achieve significant run-time performance improvements. However, because of the varying computational load during each simulation run, which originates from the changing number of infectious persons during the outbreak, it is not useful to us the same multicore setup during the simulation run. The best performance can be achieved by dynamically changing the use of the available processor cores to balance the overhead of multithreading with the performance gains of parallelization. PMID:28269849
Kinetic dynamics simulation of the detached plasma
NASA Astrophysics Data System (ADS)
Pianpanit, Theerasarn; Ishiguro, Seiji; Hasegawa, Hiroki
2015-11-01
The detached plasma has been proposed to reduce the heat flux to the divertor. Fluid code has been widely used to investigate the detached plasma but the cooling of plasma, trapped particle effects, and other kinetic dynamics in the detached plasma has not been well understood. Particle-in-Cell (PIC) simulation with the Monte Carlo collisions and the cumulative scattering angle coulomb collision are carried out to study dynamical kinetic behavior of the plasma. The constant pressure and temperature of neutral gas box in front of the divertor target model has been used in the simulation. The results show the decrease in electron temperature in front of the divertor plate strongly relate to the Coulomb collision frequency.
Brownian dynamics simulations of amelogenin microribbons formation
NASA Astrophysics Data System (ADS)
Li, Wei; Perez Lopez, Anthony; Liu, Ya; Chakrabarti, Amit; Gunton, James
2011-03-01
Recent advances in chemical particle synthesis have emphasized the fundamental role of surface colloidal heterogeneities and their detailed chemical composition, which is particularly significant for an important subclass of colloidal systems, namely, proteins. Recently, the process of self-assembly of amelogenin monomers with a hydrophobic/hydrophilic bipolar nature into ordered ribbon structures has been studied experimentally. In this work, we study this dynamical process by means of a Brownian dynamic simulation of a simple model which represents the bipolar character of the globular amelogenin molecule and the hydrophilic C-terminal tail. We monitor the kinetics of self-assembly through a study of the structure factor. We also calculate the phase diagram of the model using Gibbs ensemble Monte Carlo simulation and thermodynamic perturbation theory. This work is supported by grants from the NSF and Mathers Foundation.
Hydration dynamics in water clusters via quantum molecular dynamics simulations
Turi, László
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of
Simulation of counterflow pedestrian dynamics using spheropolygons.
Alonso-Marroquín, Fernando; Busch, Jonathan; Chiew, Coraline; Lozano, Celia; Ramírez-Gómez, Álvaro
2014-12-01
Pedestrian dynamic models are typically designed for comfortable walking or slightly congested conditions and typically use a single disk or combination of three disks for the shape of a pedestrian. Under crowd conditions, a more accurate pedestrian shape has advantages over the traditional single or three-disks model. We developed a method for simulating pedestrian dynamics in a large dense crowd of spheropolygons adapted to the cross section of the chest and arms of a pedestrian. Our numerical model calculates pedestrian motion from Newton's second law, taking into account viscoelastic contact forces, contact friction, and ground-reaction forces. Ground-reaction torque was taken to arise solely from the pedestrians' orientation toward their preferred destination. Simulations of counterflow pedestrians dynamics in corridors were used to gain insight into a tragic incident at the Madrid Arena pavilion in Spain, where five girls were crushed to death. The incident took place at a Halloween Celebration in 2012, in a long, densely crowded hallway used as entrance and exit at the same time. Our simulations reconstruct the mechanism of clogging in the hallway. The hypothetical case of a total evacuation order was also investigated. The results highlights the importance of the pedestrians' density and the effect of counterflow in the onset of avalanches and clogging and provides an estimation of the number of injuries based on a calculation of the contact-force network between the pedestrians.
Simulation of counterflow pedestrian dynamics using spheropolygons
NASA Astrophysics Data System (ADS)
Alonso-Marroquín, Fernando; Busch, Jonathan; Chiew, Coraline; Lozano, Celia; Ramírez-Gómez, Álvaro
2014-12-01
Pedestrian dynamic models are typically designed for comfortable walking or slightly congested conditions and typically use a single disk or combination of three disks for the shape of a pedestrian. Under crowd conditions, a more accurate pedestrian shape has advantages over the traditional single or three-disks model. We developed a method for simulating pedestrian dynamics in a large dense crowd of spheropolygons adapted to the cross section of the chest and arms of a pedestrian. Our numerical model calculates pedestrian motion from Newton's second law, taking into account viscoelastic contact forces, contact friction, and ground-reaction forces. Ground-reaction torque was taken to arise solely from the pedestrians' orientation toward their preferred destination. Simulations of counterflow pedestrians dynamics in corridors were used to gain insight into a tragic incident at the Madrid Arena pavilion in Spain, where five girls were crushed to death. The incident took place at a Halloween Celebration in 2012, in a long, densely crowded hallway used as entrance and exit at the same time. Our simulations reconstruct the mechanism of clogging in the hallway. The hypothetical case of a total evacuation order was also investigated. The results highlights the importance of the pedestrians' density and the effect of counterflow in the onset of avalanches and clogging and provides an estimation of the number of injuries based on a calculation of the contact-force network between the pedestrians.
IGCC Dynamic Simulator and Training Center
Zitney, S.E.; Erbes, M.R.
2006-10-01
Integrated Gasification Combined Cycle (IGCC) is emerging as the technology of choice for providing clean, low-cost electricity for the next generation of coal-fired power plants and will play a central role in the development of high-efficiency, zero-emissions power plants such as FutureGen. Several major utilities and developers recently announced plans to build IGCC plants and other major utilities are evaluating IGCC’s suitability for base-load capacity additions. This recent surge of attention to IGCC power generation is creating a growing demand for experience with the analysis, operation, and control of commercial-scale IGCC plants. To meet this need, the National Energy Technology Laboratory (NETL) has launched a project to develop a generic, full-scope, IGCC dynamic plant simulator for use in establishing a state-of-the-art simulator training center at West Virginia University’s (WVU) National Research Center for Coal and Energy (NRCCE). The IGCC Dynamic Simulator & Training (DS&T) Center will be established under the auspices of the Collaboratory for Process & Dynamic Systems Modeling (“Collaboratory”) organized between NETL, WVU, the University of Pittsburgh, and Carnegie Mellon University.
Integrated computer simulation on FIR FEL dynamics
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.
Adaptive wavelet simulation of global ocean dynamics
NASA Astrophysics Data System (ADS)
Kevlahan, N. K.-R.; Dubos, T.; Aechtner, M.
2015-07-01
In order to easily enforce solid-wall boundary conditions in the presence of complex coastlines, we propose a new mass and energy conserving Brinkman penalization for the rotating shallow water equations. This penalization does not lead to higher wave speeds in the solid region. The error estimates for the penalization are derived analytically and verified numerically for linearized one dimensional equations. The penalization is implemented in a conservative dynamically adaptive wavelet method for the rotating shallow water equations on the sphere with bathymetry and coastline data from NOAA's ETOPO1 database. This code could form the dynamical core for a future global ocean model. The potential of the dynamically adaptive ocean model is illustrated by using it to simulate the 2004 Indonesian tsunami and wind-driven gyres.
Brownian dynamics simulation of electrostatically interacting proteins
NASA Astrophysics Data System (ADS)
Ermakova, E.; Krushelnitsky, A. G.; Fedotov, V. D.
Brownian dynamics simulation software has been developed to study the dynamics of proteins as a whole in solution. The proteins were modelled as spheres with point dipoles embedded in the centre of sphere. A set of Brownian dynamics simulations at different values of the dipole moments, protein concentration and translational diffusion coefficient was performed to investigate the influence of interprotein electrostatic interactions on dynamic protein behaviour in solution. It was shown that these interactions led to the slowing down of protein rotation and a complex non-exponential shape of the rotational correlation function. Analysis of the correlation functions was performed within the frame of the model of electrostatic interprotein interactions advanced earlier on the basis of NMR and dielectric spectroscopy data. This model assumes that, due to electrostatic interactions, protein Brownian rotation becomes anisotropic. The lifetime of this anisotropy is controlled mainly by translational diffusion of proteins. Thus, the correlation function can be decomposed into two components corresponding to anisotropic Brownian rotation and an isotropic motion of an external electric field vector produced by the surrounding proteins.
Simulating stochastic dynamics using large time steps.
Corradini, O; Faccioli, P; Orland, H
2009-12-01
We present an approach to investigate the long-time stochastic dynamics of multidimensional classical systems, in contact with a heat bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short- and long-time scales and both molecular dynamics or Monte Carlo (MC) simulations are generally inefficient. Using a field theoretic approach, we perform analytically the average over the short-time stochastic fluctuations. This way, we obtain an effective theory, which generates the same long-time dynamics of the original theory, but has a lower time-resolution power. Such an approach is used to develop an improved version of the MC algorithm, which is particularly suitable to investigate the dynamics of rare conformational transitions. In the specific case of molecular systems at room temperature, we show that elementary integration time steps used to simulate the effective theory can be chosen a factor approximately 100 larger than those used in the original theory. Our results are illustrated and tested on a simple system, characterized by a rugged energy landscape.
Molecular Dynamics Simulations of Network Glasses
NASA Astrophysics Data System (ADS)
Drabold, David A.
The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References
Dynamic adaptive chemistry for turbulent flame simulations
NASA Astrophysics Data System (ADS)
Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.
2013-02-01
The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.
MDLab: a molecular dynamics simulation prototyping environment.
Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R; Izaguirre, Jesús A
2010-05-01
Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net. Copyright 2009 Wiley Periodicals, Inc.
Molecular dynamics simulation in virus research
Ode, Hirotaka; Nakashima, Masaaki; Kitamura, Shingo; Sugiura, Wataru; Sato, Hironori
2012-01-01
Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique. PMID:22833741
Nanodrop contact angles from molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim
2016-11-01
The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.
Dynamic simulator for PEFC propulsion plant
Hiraide, Masataka; Kaneda, Eiichi; Sato, Takao
1996-12-31
This report covers part of a joint study on a PEFC propulsion system for surface ships, summarized in a presentation to this Seminar, entitled {open_quote}Study on a Polymer Electrolyte Fuel Cell (PEFC) Propulsion System for Surface Ships{close_quotes}, and which envisages application to a 1,500 DWT cargo vessel. The work presented here focuses on a simulation study on PEFC propulsion plant performance, and particularly on the system response to changes in load. Using a dynamic simulator composed of system components including fuel cell, various simulations were executed, to examine the performance of the system as a whole and of the individual system components under quick and large load changes such as occasioned by maneuvering operations and by racing when the propeller emerges above water in heavy sea.
Classical Molecular Dynamics Simulation of Nuclear Fuel
Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie
2015-10-10
Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.
Molecular-dynamics simulations of lead clusters
NASA Astrophysics Data System (ADS)
Hendy, S. C.; Hall, B. D.
2001-08-01
Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.
Dynamic simulation of regulatory networks using SQUAD
Di Cara, Alessandro; Garg, Abhishek; De Micheli, Giovanni; Xenarios, Ioannis; Mendoza, Luis
2007-01-01
Background The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. Results We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. Conclusion The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or
INCORPORATING DYNAMIC 3D SIMULATION INTO PRA
Steven R Prescott; Curtis Smith
2011-07-01
provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.
Molecular dynamics simulation of fractal aggregate diffusion
NASA Astrophysics Data System (ADS)
Pranami, Gaurav; Lamm, Monica H.; Vigil, R. Dennis
2010-11-01
The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)10.1088/0305-4470/27/9/012] comprised of Np spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D) , but these can be corrected by carrying out simulations using different simulation box sizes. Specifically, the diffusion coefficient is inversely proportional to the length of a cubic simulation box, and the constant of proportionality appears to be independent of the aggregate mass and fractal dimension. Using this result, it is possible to compute infinite dilution diffusion coefficients (Do) for aggregates of arbitrary size and fractal dimension, and it was found that Do∝Np-1/df , as is often assumed by investigators simulating Brownian aggregation of fractal aggregates. The ratio of hydrodynamic radius to radius of gyration is computed and shown to be independent of mass for aggregates of fixed fractal dimension, thus enabling an estimate of the diffusion coefficient for a fractal aggregate based on its radius of gyration.
Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.
Luk, Hoi Ling; Feist, Johannes; Toppari, J Jussi; Groenhof, Gerrit
2017-09-12
When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model with which the effect of the light-matter coupling on the molecular dynamics can be predicted accurately. Here we present a multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons. Using this model we have performed simulations with up to 1600 Rhodamine molecules in a cavity. The results of these simulations reveal that the contributions of the molecules to the polariton are time-dependent due to thermal fluctuations that break symmetry. Furthermore, the simulations suggest that in addition to the cavity quality factor, also the Stokes shift and number of molecules control the lifetime of the polariton. Because large numbers of molecules interacting with confined light can now be simulated in atomic detail, we anticipate that our method will lead to a better understanding of the effects of strong coupling on chemical reactivity. Ultimately the method may even be used to systematically design cavities to control photochemistry.
Detecting Allosteric Networks Using Molecular Dynamics Simulation.
Bowerman, S; Wereszczynski, J
2016-01-01
Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. © 2016 Elsevier Inc. All rights reserved.
Monoamine transporters: insights from molecular dynamics simulations
Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit
2015-01-01
The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185
Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties
Mereghetti, Paolo; Gabdoulline, Razif R.; Wade, Rebecca C.
2010-01-01
The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments. PMID:21112303
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.
2016-10-01
SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
Dynamic transitions in molecular dynamics simulations of supercooled silicon
NASA Astrophysics Data System (ADS)
Mei, Xiaojun; Eapen, Jacob
2013-04-01
Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.
Dynamical simulation of dipolar Janus colloids: Dynamical properties
NASA Astrophysics Data System (ADS)
Hagy, Matthew C.; Hernandez, Rigoberto
2013-05-01
The dynamical properties of dipolar Janus particles are studied through simulation using our previously-developed detailed pointwise (PW) model and an isotropically coarse-grained (CG) model [M. C. Hagy and R. Hernandez, J. Chem. Phys. 137, 044505 (2012), 10.1063/1.4737432]. The CG model is found to have accelerated dynamics relative to the PW model over a range of conditions for which both models have near identical static equilibrium properties. Physically, this suggests dipolar Janus particles have slower transport properties (such as diffusion) in comparison to isotropically attractive particles. Time rescaling and damping with Langevin friction are explored to map the dynamics of the CG model to that of the PW model. Both methods map the diffusion constant successfully and improve the velocity autocorrelation function and the mean squared displacement of the CG model. Neither method improves the distribution of reversible bond durations f(tb) observed in the CG model, which is found to lack the longer duration reversible bonds observed in the PW model. We attribute these differences in f(tb) to changes in the energetics of multiple rearrangement mechanisms. This suggests a need for new methods that map the coarse-grained dynamics of such systems to the true time scale.
Mobility Laws in Dislocation Dynamics Simulations
Cai, W; Bulatov, V V
2003-10-21
Prediction of the plastic deformation behavior of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, to establish a statistically representative model of crystal plasticity. A new massively-parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We discuss an important ingredient of this code--the mobility laws dictating the behavior of individual dislocations. They are materials input for DD simulations and are constructed based on the understanding of dislocation motion at the atomistic level.
Molecular dynamics simulation of aluminium melting
NASA Astrophysics Data System (ADS)
Novak, Jakob
2016-06-01
Solid-liquid phase transition has been simulated by the molecular dynamics method, using isobaric-isoenthalpic ensemble. For interatomic potential, glue potential has been selected. The original algorithm for bookkeeping of the information on neighbouring relationships of the atoms has been developed and used in this research. Time consumption for calculation of interatomic forces has been reduced from o(N2) to o(N) by the use of this algorithm. Calculations show that phase transition from solid to liquid occurs between 1,000 K and 1,300 K. The simulated temperature of phase transition is higher than the experimental value due to the absence of crystal defects. If constant heat flux is supplied, temperature decreases during melting because the superheated state becomes unstable. During the cooling process, no significant changes of the observed variables were detected due to the high cooling rate, which prevents crystallisation.
Molecular Dynamics Simulations of Hypervelocity Impacts
NASA Astrophysics Data System (ADS)
Owens, Eli T.; Bachlechner, Martina E.
2007-03-01
Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.
Isotropic MD simulations of dynamic brittle fracture
Espanol, P.; Rubio, M.A.; Zuniga, I.
1996-12-01
The authors present results obtained by molecular dynamics simulations on the propagation of fast cracks in triangular 2D lattices. Their aim is to simulate Mode 1 fracture of brittle isotropic materials. They propose a force law that respects the isotropy of the material. The code yields the correct imposed sound c{sub {parallel}}, shear c{sub {perpendicular}} and surface V{sub R} wave speeds. Different notch lengths are systematically studied. They observed that initially the cracks are linear and always branch at a particular critical velocity c* {approx} 0.8V{sub R} and that this occurs when the crack tip reaches the position of a front emitted from the initial crack tip and propagating at a speed c = 0.68V{sub R}.
Molecular Dynamics Simulations of Interface Failure
NASA Astrophysics Data System (ADS)
Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.
2007-03-01
The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.
Parallel beam dynamics simulation of linear accelerators
Qiang, Ji; Ryne, Robert D.
2002-01-31
In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity beams and to the study of beam transport in a proposed accelerator for the development of accelerator-driven waste transmutation technologies.
Dynamic Deployment Simulations of Inflatable Space Structures
NASA Technical Reports Server (NTRS)
Wang, John T.
2005-01-01
The feasibility of using Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method in LSDYNA to simulate the dynamic deployment of inflatable space structures is investigated. The CV and ALE methods were used to predict the inflation deployments of three folded tube configurations. The CV method was found to be a simple and computationally efficient method that may be adequate for modeling slow inflation deployment sine the inertia of the inflation gas can be neglected. The ALE method was found to be very computationally intensive since it involves the solving of three conservative equations of fluid as well as dealing with complex fluid structure interactions.
Molecular dynamics simulations of dense plasmas
Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.
1993-12-31
We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.
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..
Dynamic Shade and Irradiance Simulation of Aquatic ...
Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulates across landscapes and is the main energy driver for increasing aquatic and landscape temperatures at both local and holistic scales. Landscape disturbances such as landuse change, clear cutting, and fire can cause significant variations in the resulting irradiance reaching particular locations. Penumbra can simulate solar angles and irradiance at definable temporal grains as low as one minute while simulating landscape shadowing up to an entire year. Landscapes can be represented at sub-meter resolutions with appropriate spatial data inputs, such as field data or elevation and surface object heights derived from light detection and ranging (LiDAR) data. This work describes Penumbra’s framework and methodology, external model integration capability, and appropriate model application for a variety of watershed restoration project types. First, an overview of Penumbra’s framework reveals what this model adds to the existing ecological modeling domain. Second, Penumbra’s stand-alone and integration modes are explained and demonstrated. Stand-alone modeling results are showcased within the 3-D visualization tool VISTAS (VISualizing Terrestrial-Aquatic Systems), which fluently summariz
Brownian dynamics simulation of restricted rotational diffusion.
Martínez, M C; García de la Torre, J
1987-01-01
The restricted rotational diffusion of an axially symmetric particle is simulated by the Brownian dynamics technique. In addition to the wobbling-in-a-cone model, several continuous potentials are considered. The particle studied is particularly simple: a sphere anchored to a point fixed in space. However, presenting the results in a convenient, reduced form, they are valid for any axially symmetric particle. From simulated rotational trajectories, we calculate (P2(cos alpha] as a function of t, where alpha is the angle between two orientations separated by time t and P2 is the second Legendre polynomial. This correlation function is closely related to time-resolved electro-optic and spectroscopic properties. Simulated results for the cone model are in excellent agreement with the quasiexact results of Lipari and Szabo (1981, J. Chem. Phys., 75:2971-2976). Thus we confirm the good performance of the simulation technique and the validity of our working conditions. Novel results are presented for continuous restricting potentials, V(theta). The (P2) results for V = 1/2K theta 2 and V = Q(1 - cos theta) are practically the same if K and Q are chosen so tht the long-time (P2) values coincide. Thus, the quadratic potential seems to be a good representation of any monotonically increasing potential. However, for an uniaxial potential such as V = Csin2 theta, the decay is appreciably faster. The (P2) decays simulated for the continuous potentials are analyzed by the monoexponential version of the cone model. We found that such an analysis produces an overestimation of the true rotational diffusion coefficient of approximately 15% only, although for uniaxial potentials the error may be larger. PMID:3663834
The Dynamics of Miscible Interfaces: Simulations
NASA Technical Reports Server (NTRS)
Meiburg, Eckart
2005-01-01
This research project focuses on the dynamics of interfacial regions between miscible fluids. While much attention has focused on immiscible interfaces in the past, miscible interfaces have been explored to a much lesser degree, so that there are many open questions regarding their dynamics at this time. Among the more pressing issues is the role that nonconventional stresses can play in such interfacial regions. Such stresses are typically not accounted for in efforts to model the dynamics of miscible flows. Our research aims to clarify under which circumstances these stresses do have to be taken into account, and what quantitative approaches are most suitable in this regard. In order to address these issues, we have focused on conducting linear stability analyses and nonlinear simulations for capillary tube and Hele-Shaw flows, and to compare the results with corresponding experiments performed in the labs of our co-investigators Prof. Maxworthy at USC, and Dr. Balasubramaniam at NASA. Over the duration of the project we have, among other things, focused on the effects of variable diffusion coefficients in such flows, and specifically on their influence in the growth of instabilities. Furthermore, our three-dimensional spectral element simulations have made good progress, so that we have come to a point where we can conduct more detailed comparisons with experimental observations. We are currently focusing our efforts on reproducing the tip-splitting instability observed by Maxworthy. Finally, we have discovered a new core-annular flow instability in the Stokes flow regime during the last year. This represents a significant finding, as this instability does not have an immiscible counterpart.
Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations.
Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong
2016-08-21
Herein we have used combined static electronic structure calculations and "on-the-fly" global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the (1)ππ(∗), (1)nπ(∗), and S0 states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated (1)ππ(∗) system. The first is the diabatic ESIPT process along the (1)ππ(∗) potential energy profile. The generated (1)ππ(∗) keto species then decays to the S0 state via the keto (1)ππ(∗)/gs conical intersection. The second is internal conversion to the dark (1)nπ(∗) state near the (1)ππ(∗) /(1)nπ(∗) crossing point in the course of the diabatic (1)ππ(∗) ESIPT process. Our following dynamics simulations have shown that the ESIPT and (1)ππ(∗) → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the (1)ππ(∗) → S0 internal conversion in the keto region, the (1)ππ(∗) → (1)nπ(∗) internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.
Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations
NASA Astrophysics Data System (ADS)
Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong
2016-08-01
Herein we have used combined static electronic structure calculations and "on-the-fly" global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the 1ππ∗, 1nπ∗, and S0 states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated 1ππ∗ system. The first is the diabatic ESIPT process along the 1ππ∗ potential energy profile. The generated 1ππ∗ keto species then decays to the S0 state via the keto 1ππ∗/gs conical intersection. The second is internal conversion to the dark 1nπ∗ state near the 1ππ∗ /1nπ∗ crossing point in the course of the diabatic 1ππ∗ ESIPT process. Our following dynamics simulations have shown that the ESIPT and 1ππ∗ → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the 1ππ∗ → S0 internal conversion in the keto region, the 1ππ∗ → 1nπ∗ internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.
Dynamical simulations of vesicle growth and division
NASA Astrophysics Data System (ADS)
Ruiz-Herrero, Teresa; Mahadevan, L.
2015-03-01
Prebiotic cells constitute a beautiful and intriguing example of self-replicating vesicles. How these cells managed to grow and divide without sophisticated machinery is still an open question. The properties of these primitive vesicles can shed light on the ways modern cells have evolved by exploiting those characteristics to develop their replication mechanisms. The equilibrium configurations of elastic shells are well understood, however the dynamical behavior during growth still lacks of a deep theoretical understanding. To study vesicle growth from a general perspective, we have developed a minimal generic model where vesicles are represented by a 2D spring network and characterized by a minimum set of magnitudes: growth rate, permeability, bending stiffness, viscosity and temperature. We have performed hybrid molecuar dynamic simulations as a function of a reduced set of dimensionless parameters. Three main outcomes were observed: vesicles that grow without division, vesicles that divide symmetrically, and vesicles that act as generators of daughter vesicles. The type of outcome depends on the system parameters and specifically on its dynamics via two timescales. Furthermore, we found sets of parameters where the system shows size homeostasis. TRH was supported by Ramon Areces Foundation.
Molecular dynamics simulations of xDNA.
Varghese, Mathew K; Thomas, Renjith; Unnikrishnan, N V; Sudarsanakumar, C
2009-05-01
xDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force-field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5' G xT A xC xG C xA xG T3').(xA5' C T xG C G xT A xC A3') was explored using a 22 ns molecular dynamics simulation in explicit solvent. During the simulation, the duplex retained its Watson-Crick base-pairing and double helical structure, with deviations from the starting B-form geometry towards A-form; the deviations are mainly in the backbone torsion angles and in the helical parameters. The sugar pucker of the residues were distributed among a variety of modes; C2' endo, C1' exo, O4' endo, C4' exo, C2' exo, and C3' endo. The enhanced stacking interactions on account of the modification in the bases could help to retain the duplex nature of the helix with minor deviations from the ideal geometry. In our simulation, the xDNA showed a reduced minor groove width and an enlarged major groove width in comparison with the NMR structure. Both the grooves are larger than that of standard B-DNA, but major groove width is larger than that of A-DNA with almost equal minor groove width. The enlarged groove widths and the possibility of additional hydration in the grooves makes xDNA a potential molecule for various applications. Copyright (c) 2009 Wiley Periodicals, Inc.
Quantum molecular dynamics simulations of dense matter
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
Molecular Dynamics Simulation of a RNA Aptasensor.
Ruan, Min; Seydou, Mahamadou; Noel, Vincent; Piro, Benoit; Maurel, François; Barbault, Florent
2017-04-14
Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.
Brownian dynamics simulation of DNA condensation.
Sottas, P E; Larquet, E; Stasiak, A; Dubochet, J
1999-01-01
DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA. PMID:10512808
Digital system for structural dynamics simulation
NASA Technical Reports Server (NTRS)
Krauter, A. I.; Lagace, L. J.; Wojnar, M. K.; Glor, C.
1982-01-01
State-of-the-art digital hardware and software for the simulation of complex structural dynamic interactions, such as those which occur in rotating structures (engine systems). System were incorporated in a designed to use an array of processors in which the computation for each physical subelement or functional subsystem would be assigned to a single specific processor in the simulator. These node processors are microprogrammed bit-slice microcomputers which function autonomously and can communicate with each other and a central control minicomputer over parallel digital lines. Inter-processor nearest neighbor communications busses pass the constants which represent physical constraints and boundary conditions. The node processors are connected to the six nearest neighbor node processors to simulate the actual physical interface of real substructures. Computer generated finite element mesh and force models can be developed with the aid of the central control minicomputer. The control computer also oversees the animation of a graphics display system, disk-based mass storage along with the individual processing elements.
Dynamics simulations for engineering macromolecular interactions.
Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A; Way, Jeffrey
2013-06-01
The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20,000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could
Dynamics simulations for engineering macromolecular interactions
NASA Astrophysics Data System (ADS)
Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey
2013-06-01
The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could
An expandable software model for collaborative decision making during the whole building life cycle
Papamichael, K.; Pal, V.; Bourassa, N.; Loffeld, J.; Capeluto, G.
2000-04-01
Decisions throughout the life cycle of a building, from design through construction and commissioning to operation and demolition, require the involvement of multiple interested parties (e.g., architects, engineers, owners, occupants and facility managers). The performance of alternative designs and courses of action must be assessed with respect to multiple performance criteria, such as comfort, aesthetics, energy, cost and environmental impact. Several stand-alone computer tools are currently available that address specific performance issues during various stages of a building's life cycle. Some of these tools support collaboration by providing means for synchronous and asynchronous communications, performance simulations, and monitoring of a variety of performance parameters involved in decisions about a building during building operation. However, these tools are not linked in any way, so significant work is required to maintain and distribute information to all parties. In this paper we describe a software model that provides the data management and process control required for collaborative decision making throughout a building's life cycle. The requirements for the model are delineated addressing data and process needs for decision making at different stages of a building's life cycle. The software model meets these requirements and allows addition of any number of processes and support databases over time. What makes the model infinitely expandable is that it is a very generic conceptualization (or abstraction) of processes as relations among data. The software model supports multiple concurrent users, and facilitates discussion and debate leading to decision making. The software allows users to define rules and functions for automating tasks and alerting all participants to issues that need attention. It supports management of simulated as well as real data and continuously generates information useful for improving performance prediction and
On sequential dynamical systems and simulation
Barrett, C.L.; Mortveit, H.S.; Reidys, C.M.
1999-06-01
The generic structure of computer simulations motivates a new class of discrete dynamical systems that captures this structure in a mathematically precise way. This class of systems consists of (1) a loopfree graph {Upsilon} with vertex set {l_brace}1,2,{hor_ellipsis},n{r_brace} where each vertex has a binary state, (2) a vertex labeled set of functions (F{sub i,{Upsilon}}:F{sub 2}{sup n} {r_arrow} F{sub 2}{sup n}){sub i} and (3) a permutation {pi} {element_of} S{sub n}. The function F{sub i,{Upsilon}} updates the state of vertex i as a function of the states of vertex i and its {Upsilon}-neighbors and leaves the states of all other vertices fixed. The permutation {pi} represents the update ordering, i.e., the order in which the functions F{sub i,{Upsilon}} are applied. By composing the functions F{sub i,{Upsilon}} in the order given by {pi} one obtains the dynamical system (equation given in paper) which the authors refer to as a sequential dynamical system, or SDS for short. The authors will present bounds for the number of functionally different systems and for the number of nonisomorphic digraphs {Gamma}[F{sub {Upsilon}},{pi}] that can be obtained by varying the update order and applications of these to specific graphs and graph classes. This will be done using both combinatorial/algebraic techniques and probabilistic techniques. Finally the authors give results on dynamical system properties for some special systems.
CADS:Cantera Aerosol Dynamics Simulator.
Moffat, Harry K.
2007-07-01
This manual describes a library for aerosol kinetics and transport, called CADS (Cantera Aerosol Dynamics Simulator), which employs a section-based approach for describing the particle size distributions. CADS is based upon Cantera, a set of C++ libraries and applications that handles gas phase species transport and reactions. The method uses a discontinuous Galerkin formulation to represent the particle distributions within each section and to solve for changes to the aerosol particle distributions due to condensation, coagulation, and nucleation processes. CADS conserves particles, elements, and total enthalpy up to numerical round-off error, in all of its formulations. Both 0-D time dependent and 1-D steady state applications (an opposing-flow flame application) have been developed with CADS, with the initial emphasis on developing fundamental mechanisms for soot formation within fires. This report also describes the 0-D application, TDcads, which models a time-dependent perfectly stirred reactor.
Protein Dynamics from NMR and Computer Simulation
NASA Astrophysics Data System (ADS)
Wu, Qiong; Kravchenko, Olga; Kemple, Marvin; Likic, Vladimir; Klimtchuk, Elena; Prendergast, Franklyn
2002-03-01
Proteins exhibit internal motions from the millisecond to sub-nanosecond time scale. The challenge is to relate these internal motions to biological function. A strategy to address this aim is to apply a combination of several techniques including high-resolution NMR, computer simulation of molecular dynamics (MD), molecular graphics, and finally molecular biology, the latter to generate appropriate samples. Two difficulties that arise are: (1) the time scale which is most directly biologically relevant (ms to μs) is not readily accessible by these techniques and (2) the techniques focus on local and not collective motions. We will outline methods using ^13C-NMR to help alleviate the second problem, as applied to intestinal fatty acid binding protein, a relatively small intracellular protein believed to be involved in fatty acid transport and metabolism. This work is supported in part by PHS Grant GM34847 (FGP) and by a fellowship from the American Heart Association (QW).
Mathematical simulation of Earth system dynamics
NASA Astrophysics Data System (ADS)
Dymnikov, V. P.; Lykosov, V. N.; Volodin, E. M.
2015-05-01
The mathematical simulation of the Earth system, the dynamics of which depends on physical, chemical, biological, and other processes and which requires interdisciplinary approaches to studying this problem, is considered. The term "the Earth system" extends the concept "the climatic system," since additional geospheres (lithosphere, heliosphere, etc.) are taken into account and a wider range of physical, chemical, biological, and social interactions is described. The present-day level of climate modeling is discussed, and some data obtained at the Institute of Numerical Mathematics, Russian Academy of Sciences (INM RAS), are presented for this purpose. The prospects for further development of climate models toward the creation of the Earth system models based on a seamless approach, according to which a unified model is used to make short-term (several days) and long-term (climatic) prediction, are considered.
Simulating the dynamics of complex plasmas.
Schwabe, M; Graves, D B
2013-08-01
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively coupled plasma with a fluid code written for the commercial package comsol. The output of this model is used to calculate forces on microparticles. The microparticles are modeled using the molecular dynamics package lammps, which we extended to include the forces from the plasma. Using this method, we are able to reproduce void formation, the separation of particles of different sizes into layers, lane formation, vortex formation, and other effects.
Euclidean lattice simulation for dynamical supersymmetry breaking
Kanamori, Issaku; Suzuki, Hiroshi; Sugino, Fumihiko
2008-05-01
The global supersymmetry is spontaneously broken if and only if the ground-state energy is strictly positive. We propose to use this fact to observe the spontaneous supersymmetry breaking in Euclidean lattice simulations. For lattice formulations that possess a manifest fermionic symmetry, there exists a natural choice of a Hamiltonian operator that is consistent with a topological property of the Witten index. We confirm validity of our idea in models of the supersymmetric quantum mechanics. We then examine a possibility of a dynamical supersymmetry breaking in the two-dimensional N=(2,2) super Yang-Mills theory with the gauge group SU(2), for which the Witten index is unknown. Differently from a recent conjectural claim, our numerical result tempts us to conclude that supersymmetry is not spontaneously broken in this system.
Simulating dynamical features of escape panic
NASA Astrophysics Data System (ADS)
Helbing, Dirk; Farkas, Illés; Vicsek, Tamás
2000-09-01
One of the most disastrous forms of collective human behaviour is the kind of crowd stampede induced by panic, often leading to fatalities as people are crushed or trampled. Sometimes this behaviour is triggered in life-threatening situations such as fires in crowded buildings; at other times, stampedes can arise during the rush for seats or seemingly without cause. Although engineers are finding ways to alleviate the scale of such disasters, their frequency seems to be increasing with the number and size of mass events. But systematic studies of panic behaviour and quantitative theories capable of predicting such crowd dynamics are rare. Here we use a model of pedestrian behaviour to investigate the mechanisms of (and preconditions for) panic and jamming by uncoordinated motion in crowds. Our simulations suggest practical ways to prevent dangerous crowd pressures. Moreover, we find an optimal strategy for escape from a smoke-filled room, involving a mixture of individualistic behaviour and collective `herding' instinct.
Magnetotail dynamics: MHD simulations of driven and spontaneous dynamic changes
Birn, J.; Schindler, K.; Hesse, M.
1994-05-01
The dynamic evolution of the magnetotail during growth phase and expansion phase of a substorm is studied through threedimensional time-dependent MHD simulations. To model growth phase effects, an external electric field with an equatorward inflow is applied at the boundaries over a finite time period. This leads to the formation of a thin current sheet with greatly enhanced current density in the near tail, embedded in the wider plasma/current sheet, which becomes diminished in strength. A faster, spontaneous current sheet formation occurs when entropy conservation is released in an isobaric model, while the ideal MHD constraint persists. This may be a suitable model for the late, explosive part of the growth phase. The transition to the substorm expansive phase is modeled by an increase in anomalous resistivity, using either uniform resistivity or a current density dependent resistivity which is turned on when the current density exceeds a certain threshold. In both cases the violation of ideal MHD leads to resistive instability and the formation of a near-Earth neutral line, fast flow, and plasmoid ejection, together with the dipolarization and current reduction in the region further earthward. The spontaneous increase in total region 1 type field-aligned currents associated with the disruptions of the thin current sheets is less significant than that found in earlier simulations of the disruption of a wider current sheet, whereas the driven increase in the region 1 type current is substantial. The results demonstrate that the same dynamic process which appears spontaneous in the behavior of some quantities might be interpreted as entirely driven from the observation of others.
Fiber lubrication: A molecular dynamics simulation study
NASA Astrophysics Data System (ADS)
Liu, Hongyi
Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence
In silico FRET from simulated dye dynamics
NASA Astrophysics Data System (ADS)
Hoefling, Martin; Grubmüller, Helmut
2013-03-01
Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via the Förster formula, E=1/(1+(). The energy transfer however also depends on the mutual orientation of the two dyes used as distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on approximations, which reduce the accuracy of these distance measurements. A common approximation is an isotropic and uncorrelated dye orientation distribution. To assess the impact of such approximations, we present the algorithms and implementation of a computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated using a Monte Carlo algorithm. The application of the developed toolkit on a poly-proline system demonstrated good agreement between smFRET simulations and experimental results and therefore confirms our computational method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity. The presented computational toolkit is written in Python, available as open-source, applicable to arbitrary systems and can easily be extended and adapted to further problems. Catalogue identifier: AENV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3, the bundled SIMD friendly Mersenne twister implementation [1] is provided under the SFMT-License. No. of lines in distributed program, including test data, etc.: 317880 No. of bytes in distributed program, including test data, etc.: 54774217 Distribution format: tar.gz Programming language
Coarse-grained protein molecular dynamics simulations.
Derreumaux, Philippe; Mousseau, Normand
2007-01-14
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Coarse-grained protein molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Molecular Dynamics Simulations of Ferroelectric Phase Transitions
NASA Astrophysics Data System (ADS)
Yu, Rici; Krakauer, Henry
1997-03-01
Based on an analysis of the wavevector dependence of the lattice instabilities in KNbO_3, we proposed a real-space chain-like instability and a scenario of sequential freezing out or onset of coherence of these instabilities, which qualitatively explains the sequence of observed temperature-dependent ferroelectric phases.(R. Yu and H. Krakauer, Phys. Rev. Lett. 74), 4067 (1995). We suggested that this chain-like instability should also be found in BaTiO_3, and this has been subsequently confirmed by Ghosez et al.(P. Ghosez et al.), Proc. 4th Williamsburg Workshop on First-Principles Calculations for Ferroelectrics, to be published We will present molecular dynamics simulations on BaTiO_3, using effective Hamiltonians constructed from first-principles calculations,(W. Zhong, D. Vanderbilt, and K. M. Rabe, Phys. Rev. Lett. 73), 1861 (1994). that reproduce the essential features of diffuse x-ray scattering measurements in the cubic, tetragonal, orthorhombic, and rhombohedral phases. The good agreement supports the interpretation of real-space chain-formation. Simulations for KNbO3 may also be reported.
Molecular dynamics simulations of microscale fluid transport
Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.
1998-02-01
Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.
Numerical simulation of tulip flame dynamics
Cloutman, L.D.
1991-11-30
A finite difference reactive flow hydrodynamics program based on the full Navier-Stokes equations was used to simulate the combustion process in a homogeneous-charge, constant-volume combustion bomb in which an oddly shaped flame, known as a tulip flame'' in the literature, occurred. The tulip flame'' was readily reproduced in the numerical simulations, producing good agreement with the experimental flame shapes and positions at various times. The calculations provide sufficient detail about the dynamics of the experiment to provide some insight into the physical mechanisms responsible for the peculiar flame shape. Several factors seem to contribute to the tulip formation. The most important process is the baroclinic production of vorticity by the flame front, and this rate of production appears to be dramatically increased by the nonaxial flow generated when the initial semicircular flame front burns out along the sides of the chamber. The vorticity produces a pair of vortices behind the flame that advects the flame into the tulip shape. Boundary layer effects contribute to the details of the flame shape next to the walls of the chamber, but are otherwise not important. 24 refs.
Numerical simulation of tulip flame dynamics
Cloutman, L.D.
1991-11-30
A finite difference reactive flow hydrodynamics program based on the full Navier-Stokes equations was used to simulate the combustion process in a homogeneous-charge, constant-volume combustion bomb in which an oddly shaped flame, known as a ``tulip flame`` in the literature, occurred. The ``tulip flame`` was readily reproduced in the numerical simulations, producing good agreement with the experimental flame shapes and positions at various times. The calculations provide sufficient detail about the dynamics of the experiment to provide some insight into the physical mechanisms responsible for the peculiar flame shape. Several factors seem to contribute to the tulip formation. The most important process is the baroclinic production of vorticity by the flame front, and this rate of production appears to be dramatically increased by the nonaxial flow generated when the initial semicircular flame front burns out along the sides of the chamber. The vorticity produces a pair of vortices behind the flame that advects the flame into the tulip shape. Boundary layer effects contribute to the details of the flame shape next to the walls of the chamber, but are otherwise not important. 24 refs.
Dynamical simulation of tether in orbit deployment
NASA Astrophysics Data System (ADS)
Smirnov, N. N.; Demyanov, Yu. A.; Zvyaguin, A. V.; Malashin, A. A.; Luzhin, A. A.
2010-08-01
The paper is aimed at studying the peculiarities of dynamical behavior of tether in its deployment in low Earth orbit during YES2 experiment in Foton-M3 mission, and performing flight data analysis with account of these effects. The analysis in the first part of the paper uses as input a pre-provided tension profile for the mission (resulting from a simulation to be independently validated). With this input it then performs an open-loop simulation which explains the sensitivity to the initial parameters. For the actual flight design a feedback mechanism and algorithm was used in order to control the deployment speed along a nominal profile, minimizing sensitivity to conditions such as initial velocity and endmass value. The paper provides solutions accounting for final velocities of wave propagation in tether, which is especially important for such stages of the deployment as sharp changing of the velocity direction and intensive braking. Moreover the YES2 data is used to validate the theoretical derivations.
PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations.
Berti, Claudio; Furini, Simone; Gillespie, Dirk
2016-03-08
We present PACO, a computationally efficient method for concentration boundary conditions in nonequilibrium particle simulations. Because it requires only particle counting, its computational effort is significantly smaller than other methods. PACO enables Brownian dynamics simulations of micromolar electrolytes (3 orders of magnitude lower than previously simulated). PACO for Brownian dynamics is integrated in the BROWNIES package (www.phys.rush.edu/BROWNIES). We also introduce a molecular dynamics PACO implementation that allows for very accurate control of concentration gradients.
Frontiers in molecular dynamics simulations of DNA.
Pérez, Alberto; Luque, F Javier; Orozco, Modesto
2012-02-21
It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global
The Dynamics of Miscible Interfaces: Simulations
NASA Technical Reports Server (NTRS)
Meiburg, Eckart
2002-01-01
The goal of this experimental/computational investigation (joint with Prof Maxworthy at USC) has been to study the dynamics of miscible interfaces, both from a scientific and a practical point of view, and to prepare a related experiment to be flown on the International Space Station. In order to address these effects, we have focused experimental and computational investigations on miscible displacements in cylindrical capillary tubes, as well as in Hele-Shaw cells. Regarding the flow in a capillary tube, the question was addressed as to whether Korteweg stresses and/or divergence effects can potentially account for discrepancies observed between conventional Stokes flow simulations and experiments for miscible flows in capillary tubes. An estimate of the vorticity and streamfunction fields induced by the Kortewegs stresses was derived, which shows these stresses to result in the formation of a vortex ring structure near the tip of the concentration front. Through this mechanism the propagation velocity of the concentration front is reduced, in agreement with the experimental observations. Divergence effects, on the other hand, were seen to be very small, and they have a negligible influence on the tip velocity. As a result, it can be concluded that they are not responsible for the discrepancies between experiments and conventional Stokes simulations. A further part of our investigation focussed on the development of high-accuracy three-dimensional spectral element simulation techniques for miscible flows in capillary tubes, including the effects of variable density and viscosity. Towards this end, the conservation equations are treated in cylindrical coordinates.
Consequence modeling using the fire dynamics simulator.
Ryder, Noah L; Sutula, Jason A; Schemel, Christopher F; Hamer, Andrew J; Van Brunt, Vincent
2004-11-11
The use of Computational Fluid Dynamics (CFD) and in particular Large Eddy Simulation (LES) codes to model fires provides an efficient tool for the prediction of large-scale effects that include plume characteristics, combustion product dispersion, and heat effects to adjacent objects. This paper illustrates the strengths of the Fire Dynamics Simulator (FDS), an LES code developed by the National Institute of Standards and Technology (NIST), through several small and large-scale validation runs and process safety applications. The paper presents two fire experiments--a small room fire and a large (15 m diameter) pool fire. The model results are compared to experimental data and demonstrate good agreement between the models and data. The validation work is then extended to demonstrate applicability to process safety concerns by detailing a model of a tank farm fire and a model of the ignition of a gaseous fuel in a confined space. In this simulation, a room was filled with propane, given time to disperse, and was then ignited. The model yields accurate results of the dispersion of the gas throughout the space. This information can be used to determine flammability and explosive limits in a space and can be used in subsequent models to determine the pressure and temperature waves that would result from an explosion. The model dispersion results were compared to an experiment performed by Factory Mutual. Using the above examples, this paper will demonstrate that FDS is ideally suited to build realistic models of process geometries in which large scale explosion and fire failure risks can be evaluated with several distinct advantages over more traditional CFD codes. Namely transient solutions to fire and explosion growth can be produced with less sophisticated hardware (lower cost) than needed for traditional CFD codes (PC type computer verses UNIX workstation) and can be solved for longer time histories (on the order of hundreds of seconds of computed time) with
Dynamic Shade and Irradiance Simulation of Aquatic Landscapes and Watersheds
Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulate...
Dynamic Shade and Irradiance Simulation of Aquatic Landscapes and Watersheds
Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulate...
Batôt, G; Dahirel, V; Mériguet, G; Louis, A A; Jardat, M
2013-10-01
The dynamics of particles in solution or suspension is influenced by thermal fluctuations and hydrodynamic interactions. Several mesoscale methods exist to account for these solvent-induced effects such as Brownian dynamics with hydrodynamic interactions and hybrid molecular dynamics-stochastic rotation dynamics methods. Here we compare two ways of coupling solutes to the solvent with stochastic rotation dynamics (SRD) to Brownian dynamics with and without explicit hydrodynamic interactions. In the first SRD scheme [SRD with collisional coupling (CC)] the solutes participate in the collisional step with the solvent and in the second scheme [SRD with central force coupling (CFC)] the solutes interact through direct forces with the solvent, generating slip boundary conditions. We compare the transport coefficients of neutral and charged solutes in a model system obtained by these simulation schemes. Brownian dynamics without hydrodynamic interactions is used as a reference to quantify the influence of hydrodynamics on the transport coefficients as modeled by the different methods. We show that, in the dilute range, the SRD CFC method provides results similar to those of Brownian dynamics with hydrodynamic interactions for the diffusion coefficients and for the electrical conductivity. The SRD CC scheme predicts diffusion coefficients close to those obtained by Brownian dynamic simulations without hydrodynamic interactions, but accounts for part of the influence of hydrodynamics on the electrical conductivity.
Shen, Tongye; Wong, Chung F
2015-01-01
This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum relaxation time. On the other hand, it is faster than molecular dynamics by approximating the solvent by a continuum and by operating in the over-damped limit. This chapter introduces the use of the University of Houston Brownian Dynamics (UHBD) program [1, 2] to perform Brownian dynamics simulation on peptides.
Rotational Brownian Dynamics simulations of clathrin cage formation
Ilie, Ioana M.; Briels, Wim J.; Otter, Wouter K. den
2014-08-14
The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.
Rotational Brownian dynamics simulations of clathrin cage formation.
Ilie, Ioana M; den Otter, Wouter K; Briels, Wim J
2014-08-14
The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.
Simulation of chemical isomerization reaction dynamics on a NMR quantum simulator.
Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng
2011-07-08
Quantum simulation can beat current classical computers with minimally a few tens of qubits. Here we report an experimental demonstration that a small nuclear-magnetic-resonance quantum simulator is already able to simulate the dynamics of a prototype laser-driven isomerization reaction using engineered quantum control pulses. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.
High frequency dynamic engine simulation. [TF-30 engine
NASA Technical Reports Server (NTRS)
Schuerman, J. A.; Fischer, K. E.; Mclaughlin, P. W.
1977-01-01
A digital computer simulation of a mixed flow, twin spool turbofan engine was assembled to evaluate and improve the dynamic characteristics of the engine simulation to disturbance frequencies of at least 100 Hz. One dimensional forms of the dynamic mass, momentum and energy equations were used to model the engine. A TF30 engine was simulated so that dynamic characteristics could be evaluated against results obtained from testing of the TF30 engine at the NASA Lewis Research Center. Dynamic characteristics of the engine simulation were improved by modifying the compression system model. Modifications to the compression system model were established by investigating the influence of size and number of finite dynamic elements. Based on the results of this program, high frequency engine simulations using finite dynamic elements can be assembled so that the engine dynamic configuration is optimum with respect to dynamic characteristics and computer execution time. Resizing of the compression systems finite elements improved the dynamic characteristics of the engine simulation but showed that additional refinements are required to obtain close agreement simulation and actual engine dynamic characteristics.
Nanoscale deicing by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-07-01
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice
Nonlinear Resonance Artifacts in Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Schlick, Tamar; Mandziuk, Margaret; Skeel, Robert D.; Srinivas, K.
1998-02-01
The intriguing phenomenon of resonance, a pronounced integrator-induced corruption of a system's dynamics, is examined for simple molecular systems subject to the classical equations of motion. This source of timestep limitation is not well appreciated in general, and certainly analyses of resonance patterns have been few in connection to biomolecular dynamics. Yet resonances are present in the commonly used Verlet integrator, in symplectic implicit schemes, and also limit the scope of current multiple-timestep methods that are formulated as symplectic and reversible. The only general remedy to date has been to reduce the timestep. For this purpose, we derive method-dependent timestep thresholds (e.g., Tables 1 and 2) that serve as useful guidelines in practice for biomolecular simulations. We also devise closely related symplectic implicit schemes for which the limitation on the discretization stepsize is much less severe. Specifically, we design methods to remove third-order, or both the third- and fourth-order, resonances. These severe low-order resonances can lead to instability or very large energies. Our tests on two simple molecular problems (Morse and Lennard-Jones potentials), as well as a 22-atom molecule, N-acetylalanyl-N '-methylamide, confirm this prediction; our methods can delay resonances so that they occur only at larger timesteps (EW method) or are essentially removed (LIM2 method). Although stable for large timesteps by this approach, trajectories show large energy fluctuations, perhaps due to the coupling with other factors that induce instability in complex nonlinear systems. Thus, the methods developed here may be more useful for conformational sampling of biomolecular structures. The analysis presented here for the blocked alanine model emphasizes that one-dimensional analysis of resonances can be applied to a more complex, multimode system to analyze resonance behavior, but that resonance due to frequency coupling is more complex to pinpoint
Molecular dynamics simulations of glycoclusters and glycodendrimers.
von der Lieth, Claus W; Frank, Martin; Lindhorst, Thisbe K
2002-05-01
Protein-carbohydrate recognition plays a crucial role in a wide range of biological processes, required both for normal physiological functions and the onset of disease. Nature uses multivalency in carbohydrate-protein interactions as a strategy to overcome the low affinity found for singular binding of an individual saccharide epitope to a single carbohydrate recognition domain of a lectin. To mimic the complex multi-branched oligosaccharides found in glycoconjugates, which form the structural basis of multivalent carbohydrate-protein interactions, so-called glycoclusters and glycodendrimers have been designed to serve as high-affinity ligands of the respective receptor proteins. To allow a rational design of glycodendrimer-type molecules with regard to the receptor structures involved in carbohydrate recognition, a deeper knowledge of the dynamics of such molecules is desirable. Most glycodendrimers have to be considered highly flexible molecules with their conformational preferences most difficult to elucidate by experimental methods. Longtime molecular dynamics (MD) simulations with inclusion of explicit solvent molecules are suited to explore the conformational space accessible to glycodendrimers. Here, a detailed geometric and conformational analysis of 15 glycodendrimers and glycoclusters has been accomplished, which differ with regard to their core moieties, spacer characteristics and the type of terminal carbohydrate units. It is shown that the accessible conformational space depends strongly on the structural features of the core and spacer moieties and even on the type of terminating sugars. The obtained knowledge about possible spatial distributions of the sugar epitopes exposed on the investigated hyperbranched neoglycoconjugates is detailed for all examples and forms important information for the interpretation and prediction of affinity data, which can be deduced from biological testing of these multivalent neoglycoconjugates.
Molecular Dynamics Simulation of Disordered Zircon
Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin
2004-02-27
The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.
Crawley, D.B.; Briggs, R.S.; Jones, J.W.; Seaton, W.W.; Kaufman, J.E.; Deringer, J.J.; Kennett, E.W.
1987-08-01
This is the second volume of the Phase 1 report and discusses the 10 tasks performed in Phase 1. The objective of this research is to develop a methodology for setting energy design targets to provide voluntary guidelines for the buildings industry. The whole-building energy targets project is being conducted at the Pacific Northwest Laboratory (PNL) for the US Department of Energy (DOE) to encourage the construction of energy-efficient buildings by informing designers and owners about cost-effective goals for energy use in new commercial buildings. The outcome of this research will be a flexible methodology for setting such targets. The tasks are listed and discussed in this report as follows: Task 1 - Develop Detailed Project Goals and Objectives; Task 2 - Establish Buildings-Industry Liaison; Task 3 - Develop Approaches to the Energy Targets Model, Building Operations, and Climate; Task 4 - Develop an Approach for Treating Economic Considerations; Task 5 - Develop an Approach for Treating Energy Sources; Task 6 - Collect Energy-Use Data; Task 7 - Survey Energy Expert Opinion; Task 8 - Evaluation Procedure Specification and Integration; Task 9 - Phase 1 Report Development; and Task 10 - Phase 1 Review Planning.
Expansion techniques for collisionless stellar dynamical simulations
Meiron, Yohai; Li, Baile; Holley-Bockelmann, Kelly; Spurzem, Rainer
2014-09-10
We present graphics processing unit (GPU) implementations of two fast force calculation methods based on series expansions of the Poisson equation. One method is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other method is the multipole expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field methods and optimized for collisionless galactic dynamics, but while SCF is a 'pure' expansion, MEX is an expansion in just the angular part; thus, MEX is capable of capturing radial structure easily, while SCF needs a large number of radial terms. We show that despite the expansion bias, these methods are more accurate than direct techniques for the same number of particles. The performance of our GPU code, which we call ETICS, is profiled and compared to a CPU implementation. On the tested GPU hardware, a full force calculation for one million particles took ∼0.1 s (depending on expansion cutoff), making simulations with as many as 10{sup 8} particles fast for a comparatively small number of nodes.
Molecular Dynamics Simulations of Coulomb Explosion
Bringa, E M
2002-05-17
A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a ''Coulomb Explosion'', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) simulations of Coulomb explosion for a cylindrical track as a function of charge density and neutralization/quenching time, {tau}. Screening by the free electrons is accounted for using a screened Coulomb potential for the interaction among charges. The yield exhibits a prompt component from the track core and a component, which dominates at higher excitation density, from the heated region produced. For the cases studied, the number of atoms ejected per incident ion, i.e. the sputtering yield Y, is quadratic with charge density along the track as suggested by simple models. Y({tau} = 0.2 Debye periods) is nearly 20% of the yield when there is no neutralization ({tau} {yields} {infinity}). The connections between ''Coulomb explosions'', thermal spikes and measurements of electronic sputtering are discussed.
Annual Report 1999 Environmental Dynamics and Simulation
NS Foster-Mills
2000-06-28
This annual report describes selected 1999 research accomplishments for the Environmental Dynamics and Simulation (ED and S) directorate, one of six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). These accomplishments are representative of the different lines of research underway in the ED and S directorate. EMSL is one of US Department of Energy's (DOE) national scientific user facilities and is the centerpiece of DOE's commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems. Capabilities in the EMSL include over 100 major instrument systems for use by the resident research staff, their collaborators, and users of the EMSL. These capabilities are used to address the fundamental science that will be the basis for finding solutions to national environmental issues such as cleaning up contamianted areas at DOE sites across the country and developing green technologies that will reduce or eliminate future pollution production. The capabilities are also used to further the understanding of global climate change and environmental issues relevant to energy production and use and health effects resulting from exposure to contaminated environments.
Dynamical simulation of an abrasive wear process
NASA Astrophysics Data System (ADS)
Elalem, Khaled; Li, D. Y.
1999-05-01
A dynamic computer model was developed to simulate wear behavior of materials on micro-scales. In this model, a material system is discretized and mapped onto a lattice or grid. Each lattice site represents a small volume of the material. During a wear process, a lattice site may move under the influence of external force and the interaction between the site and its adjacent sites. The site-site interaction is a function of mechanical properties of the material such as the elastic modulus, yield strength, work hardening and the fracture strain. Newton's law of motion is used to determine the movement of lattice sites during a wear process. The strain between a pair of sites is recoverable if it is within the elastic deformation range; otherwise plastic deformation takes place. A bond between two adjacent sites is broken when its strain exceeds a critical value. A site or a cluster of sites is worn away if all bonds connecting the site or the cluster to its nearest neighbors are broken. The model well describes the strain distribution in a contact region, in consistence with a finite element analysis. This model was applied to several metallic materials abraded under the ASTM G65 abrasion condition, and the results were compared to experimental observations. Good agreement between the modeling and the experiment was found.
Application of control theory to dynamic systems simulation
NASA Technical Reports Server (NTRS)
Auslander, D. M.; Spear, R. C.; Young, G. E.
1982-01-01
The application of control theory is applied to dynamic systems simulation. Theory and methodology applicable to controlled ecological life support systems are considered. Spatial effects on system stability, design of control systems with uncertain parameters, and an interactive computing language (PARASOL-II) designed for dynamic system simulation, report quality graphics, data acquisition, and simple real time control are discussed.
Dynamic Simulation over Long Time Periods with 100% Solar Generation.
Concepcion, Ricky James; Elliott, Ryan Thomas
2015-12-01
This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.
Controlled multibody dynamics simulation for large space structures
NASA Technical Reports Server (NTRS)
Housner, J. M.; Wu, S. C.; Chang, C. W.
1989-01-01
Multibody dynamics discipline, and dynamic simulation in control structure interaction (CSI) design are discussed. The use, capabilities, and architecture of the Large Angle Transient Dynamics (LATDYN) code as a simulation tool are explained. A generic joint body with various types of hinge connections; finite element and element coordinate systems; results of a flexible beam spin-up on a plane; mini-mast deployment; space crane and robotic slewing manipulations; a potential CSI test article; and multibody benchmark experiments are also described.
A Simulation Program for Dynamic Infrared (IR) Spectra
ERIC Educational Resources Information Center
Zoerb, Matthew C.; Harris, Charles B.
2013-01-01
A free program for the simulation of dynamic infrared (IR) spectra is presented. The program simulates the spectrum of two exchanging IR peaks based on simple input parameters. Larger systems can be simulated with minor modifications. The program is available as an executable program for PCs or can be run in MATLAB on any operating system. Source…
A Simulation Program for Dynamic Infrared (IR) Spectra
ERIC Educational Resources Information Center
Zoerb, Matthew C.; Harris, Charles B.
2013-01-01
A free program for the simulation of dynamic infrared (IR) spectra is presented. The program simulates the spectrum of two exchanging IR peaks based on simple input parameters. Larger systems can be simulated with minor modifications. The program is available as an executable program for PCs or can be run in MATLAB on any operating system. Source…
Multimillion atom molecular dynamics simulations of glasses and ceramic materials
NASA Astrophysics Data System (ADS)
Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro
1999-11-01
Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed.
Protein dynamics and enzyme catalysis: insights from simulations.
McGeagh, John D; Ranaghan, Kara E; Mulholland, Adrian J
2011-08-01
The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Dynamics modeling and simulation of autonomous underwater vehicles with appendages
NASA Astrophysics Data System (ADS)
Su, Yumin; Zhao, Jinxin; Cao, Jian; Zhang, Guocheng
2013-03-01
To provide a simulation system platform for designing and debugging a small autonomous underwater vehicle's (AUV) motion controller, a six-degree of freedom (6-DOF) dynamic model for AUV controlled by thruster and fins with appendages is examined. Based on the dynamic model, a simulation system for the AUV's motion is established. The different kinds of typical motions are simulated to analyze the motion performance and the maneuverability of the AUV. In order to evaluate the influences of appendages on the motion performance of the AUV, simulations of the AUV with and without appendages are performed and compared. The results demonstrate the AUV has good maneuverability with and without appendages.
Comparisons of Kinematics and Dynamics Simulation Software Tools
NASA Technical Reports Server (NTRS)
Shiue, Yeu-Sheng Paul
2002-01-01
Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.
Comparisons of Kinematics and Dynamics Simulation Software Tools
NASA Technical Reports Server (NTRS)
Shiue, Yeu-Sheng Paul
2002-01-01
Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.
Mosquito population dynamics from cellular automata-based simulation
NASA Astrophysics Data System (ADS)
Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning
2016-02-01
In this paper we present an innovative model for simulating mosquito-vector population dynamics. The simulation consist of two stages: demography and dispersal dynamics. For demography simulation, we follow the existing model for modeling a mosquito life cycles. Moreover, we use cellular automata-based model for simulating dispersal of the vector. In simulation, each individual vector is able to move to other grid based on a random walk. Our model is also capable to represent immunity factor for each grid. We simulate the model to evaluate its correctness. Based on the simulations, we can conclude that our model is correct. However, our model need to be improved to find a realistic parameters to match real data.
Simulating Hamiltonian Dynamics with a Truncated Taylor Series
NASA Astrophysics Data System (ADS)
Somma, Rolando
2015-03-01
One of the main motivations for quantum computers is their ability to efficiently simulate the dynamics of quantum systems. Since the mid-1990s, many algorithms have been developed to simulate Hamiltonian dynamics on a quantum computer, with applications to problems such as simulating spin models and quantum chemistry. While it is now well known that quantum computers can efficiently simulate Hamiltonian dynamics, ongoing work has improved the performance and expanded the scope of such simulations. In this talk, I will describe a very simple and efficient algorithm for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. This algorithm can simulate the time evolution of a wide variety of physical systems. The cost of this algorithm depends only logarithmically on the inverse of the desired precision, and can be shown to be optimal. Such a cost also represents an exponential improvement over known methods for Hamiltonian simulation based on, e.g., Trotter-Suzuki approximations. Roughly speaking, doubling the number of digits of accuracy of the simulation only doubles the complexity. The new algorithm and its analysis are highly simplified due to a technique for implementing linear combinations of unitary operations to directly apply the truncated Taylor series. This is joint work with Dominic Berry, Andrew Childs, Richard Cleve, and Robin Kothari.
NASA Astrophysics Data System (ADS)
Mantha, Sriteja; Yethiraj, Arun
2016-02-01
The properties of water under confinement are of practical and fundamental interest. In this work, we study the properties of water in the self-assembled lyotropic phases of Gemini surfactants with a focus on testing the standard analysis of quasi-elastic neutron scattering (QENS) experiments. In QENS experiments, the dynamic structure factor is measured and fit to models to extract the translational diffusion constant, DT, and rotational relaxation time, τR. We test this procedure by using simulation results for the dynamic structure factor, extracting the dynamic parameters from the fit as is typically done in experiments, and comparing the values to those directly measured in the simulations. We find that the de-coupling approximation, where the intermediate scattering function is assumed to be a product of translational and rotational contributions, is quite accurate. The jump-diffusion and isotropic rotation models, however, are not accurate when the degree of confinement is high. In particular, the exponential approximations for the intermediate scattering function fail for highly confined water and the values of DT and τR can differ from the measured value by as much as a factor of two. Other models have more fit parameters, however, and with the range of energies and wave-vectors accessible to QENS, the typical analysis appears to be the best choice. In the most confined lamellar phase, the dynamics are sufficiently slow that QENS does not access a large enough time scale.
Mantha, Sriteja; Yethiraj, Arun
2016-02-28
The properties of water under confinement are of practical and fundamental interest. In this work, we study the properties of water in the self-assembled lyotropic phases of Gemini surfactants with a focus on testing the standard analysis of quasi-elastic neutron scattering (QENS) experiments. In QENS experiments, the dynamic structure factor is measured and fit to models to extract the translational diffusion constant, D(T), and rotational relaxation time, τ(R). We test this procedure by using simulation results for the dynamic structure factor, extracting the dynamic parameters from the fit as is typically done in experiments, and comparing the values to those directly measured in the simulations. We find that the de-coupling approximation, where the intermediate scattering function is assumed to be a product of translational and rotational contributions, is quite accurate. The jump-diffusion and isotropic rotation models, however, are not accurate when the degree of confinement is high. In particular, the exponential approximations for the intermediate scattering function fail for highly confined water and the values of D(T) and τ(R) can differ from the measured value by as much as a factor of two. Other models have more fit parameters, however, and with the range of energies and wave-vectors accessible to QENS, the typical analysis appears to be the best choice. In the most confined lamellar phase, the dynamics are sufficiently slow that QENS does not access a large enough time scale.
Bauman, Nathan N.; Hail, John C.
2003-12-30
In an effort to expand the energy savings programs within the State, the Wisconsin Division of Energy obtained funding through the Federal Energy Management Program (FEMP), with additional funding assistance through the Rebuild America Program (RBA) to install the Whole Building Diagnostician (WBD) software program as a test bed project in two of the State’s facilities in Wisconsin. This report discusses the results of this effort.
McKay, H.N. ); Deringer, J.J. ); Jones, J.W. ); Hall, J.D. )
1990-09-01
This report documents eight tasks performed as part of the Whole-Building Energy Design Targets project, in which detailed conceptual approaches were produced for each element of the proposed Targets model. The eight task reports together describe the important modules proposed for inclusion in the Targets model: input module, energy module, characteristic development moduel, building cost module, analysis control module, energy cost module, search routines module, and economic analysis module. 16 refs., 16 figs., 5 tabs.
A fast recursive algorithm for molecular dynamics simulation
NASA Technical Reports Server (NTRS)
Jain, A.; Vaidehi, N.; Rodriguez, G.
1993-01-01
The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.
Large-Scale Hybrid Dynamic Simulation Employing Field Measurements
Huang, Zhenyu; Guttromson, Ross T.; Hauer, John F.
2004-06-30
Simulation and measurements are two primary ways for power engineers to gain understanding of system behaviors and thus accomplish tasks in system planning and operation. Many well-developed simulation tools are available in today's market. On the other hand, large amount of measured data can be obtained from traditional SCADA systems and currently fast growing phasor networks. However, simulation and measurement are still two separate worlds. There is a need to combine the advantages of simulation and measurements. In view of this, this paper proposes the concept of hybrid dynamic simulation which opens up traditional simulation by providing entries for measurements. A method is presented to implement hybrid simulation with PSLF/PSDS. Test studies show the validity of the proposed hybrid simulation method. Applications of such hybrid simulation include system event playback, model validation, and software validation.
Dynamics of adaptive structures: Design through simulations
NASA Technical Reports Server (NTRS)
Park, K. C.; Alexander, S.
1993-01-01
The use of a helical bi-morph actuator/sensor concept by mimicking the change of helical waveform in bacterial flagella is perhaps the first application of bacterial motions (living species) to longitudinal deployment of space structures. However, no dynamical considerations were analyzed to explain the waveform change mechanisms. The objective is to review various deployment concepts from the dynamics point of view and introduce the dynamical considerations from the outset as part of design considerations. Specifically, the impact of the incorporation of the combined static mechanisms and dynamic design considerations on the deployment performance during the reconfiguration stage is studied in terms of improved controllability, maneuvering duration, and joint singularity index. It is shown that intermediate configurations during articulations play an important role for improved joint mechanisms design and overall structural deployability.
Perspective: Computer simulations of long time dynamics
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
Perspective: Computer simulations of long time dynamics
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.
Climate dynamics experiments using a GCM simulations
NASA Technical Reports Server (NTRS)
Fitzjarrald, Dan; Robertson, Franklin R.; Christy, John R.; Lu, H.-I.; Sohn, B.; Srikishen, J.
1991-01-01
The study of surface-atmosphere interactions has begun with studies of the effect of altering the ocean and land boundaries. A ten year simulation of global climate using observed sea surface temperature anomalies has begun using the NCAR Community Climate Model (CCM1). The results for low resolution (R15) were computed for the first 8 years of the simulation and compared with the observed surface temperatures and the MSU (Microwave Sounding Unit) observations of tropospheric temperature. A simulation at higher resolution (T42) was done to ascertain the effect of interactive soil hydrology on the system response to an El Nino sea surface temperature perturbation. Initial analysis of this simulations was completed.
Colloidal suspension simulates linear dynamic pressure profile
NASA Technical Reports Server (NTRS)
Mc Cann, R. J.
1966-01-01
Missile nose fairings immersed in colloidal suspension prepared with various specific gravities simulate pressure profiles very similar to those encountered during reentry. Stress and deflection conditions similar to those expected during atmospheric reentry are thus attained in the laboratory.
Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence
Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M.
2012-01-01
Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics
Simulating food web dynamics along a gradient: quantifying human influence.
Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M
2012-01-01
Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
Lau, E Y; Krishnan, V V
2007-07-18
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
A Molecular Dynamics Simulation of C60-C60 Collision
NASA Astrophysics Data System (ADS)
Liu, Lei; Chen, Kaitai; Li, Yufen
1993-12-01
The formation process of C120-complex in C60-C60 collision has been clearly demonstrated by a molecular dynamics simulation. The complex, with a peanut-shell-like structure, is in a quite stable dynamical state. The results are consistent with recent observations.
A Process for Comparing Dynamics of Distributed Space Systems Simulations
NASA Technical Reports Server (NTRS)
Cures, Edwin Z.; Jackson, Albert A.; Morris, Jeffery C.
2009-01-01
The paper describes a process that was developed for comparing the primary orbital dynamics behavior between space systems distributed simulations. This process is used to characterize and understand the fundamental fidelities and compatibilities of the modeling of orbital dynamics between spacecraft simulations. This is required for high-latency distributed simulations such as NASA s Integrated Mission Simulation and must be understood when reporting results from simulation executions. This paper presents 10 principal comparison tests along with their rationale and examples of the results. The Integrated Mission Simulation (IMSim) (formerly know as the Distributed Space Exploration Simulation (DSES)) is a NASA research and development project focusing on the technologies and processes that are related to the collaborative simulation of complex space systems involved in the exploration of our solar system. Currently, the NASA centers that are actively participating in the IMSim project are the Ames Research Center, the Jet Propulsion Laboratory (JPL), the Johnson Space Center (JSC), the Kennedy Space Center, the Langley Research Center and the Marshall Space Flight Center. In concept, each center participating in IMSim has its own set of simulation models and environment(s). These simulation tools are used to build the various simulation products that are used for scientific investigation, engineering analysis, system design, training, planning, operations and more. Working individually, these production simulations provide important data to various NASA projects.
Student Diagnostic Strategies in a Dynamic Simulation Environment.
ERIC Educational Resources Information Center
Recker, Mimi M.; Govindaraj, T.; Vasandani, Vijay
1998-01-01
Demonstrates the use of simulation systems for studying diagnostic problem solving and presents results from two empirical studies in which undergraduates diagnosed faults that occurred in a computer-based, dynamic simulation. Discusses dual problem space search that includes generating and testing hypotheses; suggests implications for designing…
Simulation, modeling and dynamical analysis of multibody flows
NASA Astrophysics Data System (ADS)
Blackmore, Denis; Rosato, Anthony; Sen, Surajit; Wu, Hao
2017-04-01
Recent particulate flow research using a discrete element simulation-dynamical systems approach is described. The simulation code used is very efficient and the mathematical model is an integro-partial differential equation. Examples are presented to show the effectiveness of the approach.
Yi, Zheng; Lindner, Benjamin; Prinz, Jan -Hendrik; Noe, Frank; Smith, Jeremy C.
2013-11-01
Here, neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.
ROCKET THRUST STAND SIMULATION OF SPACE VEHICLE FLIGHT DYNAMICS
The concept of rocket thrust stand simulation of space vehicle flight dynamics is developed. An electro-mechanical system is described wherein the... space vehicle rocket motor attach point motion may be simulated. The physical dimensions of the system are small such that it may be used in conjunction...with current environmental test cells. The degree of space vehicle simulation is a consequence of the limitations on the excursions of the active
Dynamics Simulation Model for Space Tethers
NASA Technical Reports Server (NTRS)
Levin, E. M.; Pearson, J.; Oldson, J. C.
2006-01-01
This document describes the development of an accurate model for the dynamics of the Momentum Exchange Electrodynamic Reboost (MXER) system. The MXER is a rotating tether about 100-km long in elliptical Earth orbit designed to catch payloads in low Earth orbit and throw them to geosynchronous orbit or to Earth escape. To ensure successful rendezvous between the MXER tip catcher and a payload, a high-fidelity model of the system dynamics is required. The model developed here quantifies the major environmental perturbations, and can predict the MXER tip position to within meters over one orbit.
Gamma ray observatory dynamics simulator in Ada (GRODY)
NASA Technical Reports Server (NTRS)
1990-01-01
This experiment involved the parallel development of dynamics simulators for the Gamma Ray Observatory in both FORTRAN and Ada for the purpose of evaluating the applicability of Ada to the NASA/Goddard Space Flight Center's flight dynamics environment. The experiment successfully demonstrated that Ada is a viable, valuable technology for use in this environment. In addition to building a simulator, the Ada team evaluated training approaches, developed an Ada methodology appropriate to the flight dynamics environment, and established a baseline for evaluating future Ada projects.
Gamma ray observatory dynamics simulator in Ada (GRODY)
Not Available
1990-09-01
This experiment involved the parallel development of dynamics simulators for the Gamma Ray Observatory in both FORTRAN and Ada for the purpose of evaluating the applicability of Ada to the NASA/Goddard Space Flight Center's flight dynamics environment. The experiment successfully demonstrated that Ada is a viable, valuable technology for use in this environment. In addition to building a simulator, the Ada team evaluated training approaches, developed an Ada methodology appropriate to the flight dynamics environment, and established a baseline for evaluating future Ada projects.
Movement Characteristics Analysis and Dynamic Simulation of Collaborative Measuring Robot
NASA Astrophysics Data System (ADS)
guoqing, MA; li, LIU; zhenglin, YU; guohua, CAO; yanbin, ZHENG
2017-03-01
Human-machine collaboration is becoming increasingly more necessary, and so collaborative robot applications are also in high demand. We selected a UR10 robot as our research subject for this study. First, we applied D-H coordinate transformation of the robot to establish a link system, and we then used inverse transformation to solve the robot’s inverse kinematics and find all the joints. Use Lagrange method to analysis UR robot dynamics; use ADAMS multibody dynamics simulation software to dynamic simulation; verifying the correctness of the derived kinetic models.
Semiconductor nanostructure properties. Molecular Dynamic Simulations
NASA Astrophysics Data System (ADS)
Podolska, N. I.; Zhmakin, A. I.
2013-08-01
The need for research is based on the fact that development of non-planar semiconductor nanosystems and nanomaterials with controlled properties is an important scientific and industrial problem. So, final scientific and technological problem is the creation of adequate modern methods and software for growth and properties simulation and optimization of various III-V (GaAs, InAs, InP, InGaAs etc.) nanostructures (e.g. nanowires) with controlled surface morphology, crystal structure, optical, transport properties etc. Accordingly, now we are developing a specialized computer code for atomistic simulation of structural (distribution of atoms and impurities, elastic and force constants, strain distribution etc.) and thermodynamic (mixing energy, interaction energy, surface energy etc.) properties of the nanostructures. Some simulation results are shown too.
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.
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.
Molecular Dynamics Simulations of Crystal Copper: Bulk Modulus and Shocks
NASA Astrophysics Data System (ADS)
Warrier, M.; Rawat, S.; Chaturvedi, S.
2011-07-01
Molecular dynamics is used to study the response of single crystal copper target to impacts by single crystal copper at velocities in the range 1 km/s to 3 km/s. The Embedded Atom Method (EAM) potential by Foiles et al. for Cu [1] was used in the simulation. The potential and its implementation in the open source, Large-scale Atomic Molecular Massively Parallel Simulator (LAMMPS) [2] was verified by reproducing the experimental values of bulk modulus of Cu. The shock velocity (us) as a function of particle velocity (up) matches published experimental and molecular dynamic simulations results.
Robust state preparation in quantum simulations of Dirac dynamics
NASA Astrophysics Data System (ADS)
Song, Xue-Ke; Deng, Fu-Guo; Lamata, Lucas; Muga, J. G.
2017-02-01
A nonrelativistic system such as an ultracold trapped ion may perform a quantum simulation of a Dirac equation dynamics under specific conditions. The resulting Hamiltonian and dynamics are highly controllable, but the coupling between momentum and internal levels poses some difficulties to manipulate the internal states accurately in wave packets. We use invariants of motion to inverse engineer robust population inversion processes with a homogeneous, time-dependent simulated electric field. This exemplifies the usefulness of inverse-engineering techniques to improve the performance of quantum simulation protocols.
AceCloud: Molecular Dynamics Simulations in the Cloud.
Harvey, M J; De Fabritiis, G
2015-05-26
We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.
Destination state screening of active spaces in spin dynamics simulations
NASA Astrophysics Data System (ADS)
Krzystyniak, M.; Edwards, Luke J.; Kuprov, Ilya
2011-06-01
We propose a novel avenue for state space reduction in time domain Liouville space spin dynamics simulations, using detectability as a selection criterion - only those states that evolve into or affect other detectable states are kept in the simulation. This basis reduction procedure (referred to as destination state screening) is formally exact and can be applied on top of the existing state space restriction techniques. As demonstrated below, in many cases this results in further reduction of matrix dimension, leading to considerable acceleration of many spin dynamics simulation types. Destination state screening is implemented in the latest version of the Spinach library (http://spindynamics.org).
Test and validation for robot arm control dynamics simulation
NASA Technical Reports Server (NTRS)
Yae, K. Harold; Kim, Sung-Soo; Haug, Edward J.; Seering, Warren; Sundaram, Kamala; Thompson, Bruce; Turner, James; Chun, Hon; Frisch, Harold P.; Schnurr, Richard
1989-01-01
The Flight Telerobotic Servicer (FTS) program will require an ability to develop, in a cost effective manner, many simulation models for design, analysis, performance evaluation, and crew training. Computational speed and the degree of modeling fidelity associated with each simulation must be commensurate with problem objectives. To demonstrate evolving state-of-the-art general purpose multibody modeling capabilities, to validate these by laboratory testing, and to expose their modeling shortcomings, two focus problems at the opposite ends of the simulation spectrum are defined: (1) Coarse Acquisition Control Dynamics. Create a real time man-in-the-control-loop simulator. Provide animated graphical display of robot arm dynamics and tactile feedback sufficient for cueing the operator. Interface simulator software with human operated tactile feedback controller; i.e., the Kraft mini-master. (2) Fine, Precision Mode Control Dynamics. Create a high speed, high fidelity simulation model for the design, analysis, and performance evaluation of autonomous 7 degree-of-freedom (DOF) trajectory control algorithms. This model must contain detail dynamic models for all significant dynamics elements within the robot arm, such as joint drive mechanisms.
Simulation analysis of dynamic working performance for star trackers.
Shen, Juan; Zhang, Guangjun; Wei, Xinguo
2010-12-01
The elongated imaging track pertaining to a star spot recorded in the image sensor of a star tracker will diffuse over several pixels at a high angular velocity, leading to an inaccurate, even false, attitude value. A computer simulation of the attitude determination from a dynamic star tracker is developed first, based on a dynamic mathematical model of the star-spot imaging and an efficiency validation of the star centroiding algorithm in the dynamic condition. Then major error sources affecting the attitude accuracy in the dynamic condition are analyzed and discussed systematically based on the simulation results. A mathematical model calculating the average star number detected in the field of view is also deduced, using simulation results and signal processing theory, with image trailing ranging from 0 to 20 pixels during exposure. The summarized regularity is helpful in the system design and accuracy evaluation of a star tracker.
SIMULATIONS OF ENERGETIC PARTICLES INTERACTING WITH DYNAMICAL MAGNETIC TURBULENCE
Hussein, M.; Shalchi, A. E-mail: husseinm@myumanitoba.ca
2016-02-01
We explore the transport of energetic particles in interplanetary space by using test-particle simulations. In previous work such simulations have been performed by using either magnetostatic turbulence or undamped propagating plasma waves. In the current paper we simulate for the first time particle transport in dynamical turbulence. To do so we employ two models, namely the damping model of dynamical turbulence and the random sweeping model. We compute parallel and perpendicular diffusion coefficients and compare our numerical findings with solar wind observations. We show that good agreement can be found between simulations and the Palmer consensus range for both dynamical turbulence models if the ratio of turbulent magnetic field and mean field is δB/B{sub 0} = 0.5.
Simulations of Energetic Particles Interacting with Dynamical Magnetic Turbulence
NASA Astrophysics Data System (ADS)
Hussein, M.; Shalchi, A.
2016-02-01
We explore the transport of energetic particles in interplanetary space by using test-particle simulations. In previous work such simulations have been performed by using either magnetostatic turbulence or undamped propagating plasma waves. In the current paper we simulate for the first time particle transport in dynamical turbulence. To do so we employ two models, namely the damping model of dynamical turbulence and the random sweeping model. We compute parallel and perpendicular diffusion coefficients and compare our numerical findings with solar wind observations. We show that good agreement can be found between simulations and the Palmer consensus range for both dynamical turbulence models if the ratio of turbulent magnetic field and mean field is δB/B0 = 0.5.
Computational models of protein kinematics and dynamics: beyond simulation.
Gipson, Bryant; Hsu, David; Kavraki, Lydia E; Latombe, Jean-Claude
2012-01-01
Physics-based simulation represents a powerful method for investigating the time-varying behavior of dynamic protein systems at high spatial and temporal resolution. Such simulations, however, can be prohibitively difficult or lengthy for large proteins or when probing the lower-resolution, long-timescale behaviors of proteins generally. Importantly, not all questions about a protein system require full space and time resolution to produce an informative answer. For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger, domain-level picture of protein dynamics can be revealed. The purpose of this review is to highlight the growing body of complementary work that goes beyond simulation. In particular, this review focuses on methods that address kinematics and dynamics, as well as those that address larger organizational questions and can quickly yield useful information about the long-timescale behavior of a protein.
Computational Models of Protein Kinematics and Dynamics: Beyond Simulation
Gipson, Bryant; Hsu, David; Kavraki, Lydia E.; Latombe, Jean-Claude
2016-01-01
Physics-based simulation represents a powerful method for investigating the time-varying behavior of dynamic protein systems at high spatial and temporal resolution. Such simulations, however, can be prohibitively difficult or lengthy for large proteins or when probing the lower-resolution, long-timescale behaviors of proteins generally. Importantly, not all questions about a protein system require full space and time resolution to produce an informative answer. For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger, domain-level picture of protein dynamics can be revealed. The purpose of this review is to highlight the growing body of complementary work that goes beyond simulation. In particular, this review focuses on methods that address kinematics and dynamics, as well as those that address larger organizational questions and can quickly yield useful information about the long-timescale behavior of a protein. PMID:22524225
Generalized dynamic engine simulation techniques for the digital computer
NASA Technical Reports Server (NTRS)
Sellers, J.; Teren, F.
1974-01-01
Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design-point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar all-digital programs on future engine simulation philosophy is also discussed.
Generalized dynamic engine simulation techniques for the digital computer
NASA Technical Reports Server (NTRS)
Sellers, J.; Teren, F.
1974-01-01
Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program, DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design-point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar all-digital programs on future engine simulation philosophy is also discussed.
Generalized dynamic engine simulation techniques for the digital computers
NASA Technical Reports Server (NTRS)
Sellers, J.; Teren, F.
1975-01-01
Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program, DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar digital programs on future engine simulation philosophy is also discussed.
Dynamic Process Simulation for Analysis and Design.
ERIC Educational Resources Information Center
Nuttall, Herbert E., Jr.; Himmelblau, David M.
A computer program for the simulation of complex continuous process in real-time in an interactive mode is described. The program is user oriented, flexible, and provides both numerical and graphic output. The program has been used in classroom teaching and computer aided design. Typical input and output are illustrated for a sample problem to…
SSME-HAS dynamic load simulators
NASA Technical Reports Server (NTRS)
1975-01-01
The space shuttle main engine propellant valve actuators (SSME) were designed to simulate the loads reflected into the SSME by the chamber coolant valve, the fuel preburner, and the oxidizer. The design, and functional description are included along with a list of the drawings. The load fixture control transform, friction torque, and flow calculations are reported.
SIMULATING FISH ASSEMBLAGE DYNAMICS IN RIVER NETWORKS
My recently retired colleague, Joan Baker, and I have developed a prototype computer simulation model for studying the effects of human and non-human alterations of habitats and species availability on fish assemblage populations. The fish assemblage model, written in R, is a sp...
SIMULATING FISH ASSEMBLAGE DYNAMICS IN RIVER NETWORKS
My recently retired colleague, Joan Baker, and I have developed a prototype computer simulation model for studying the effects of human and non-human alterations of habitats and species availability on fish assemblage populations. The fish assemblage model, written in R, is a sp...
Classical trajectory simulations of post-transition state dynamics
NASA Astrophysics Data System (ADS)
Lourderaj, Upakarasamy; Park, Kyoyeon; Hase, William L.
Classical chemical dynamics simulations of post-transition state dynamics are reviewed. Most of the simulations involve direct dynamics for which the potential energy and gradient are obtained directly from an electronic structure theory. The chemical reaction attributes and chemical systems presented are product energy partitioning for Cl- ··· CH3Br → ClCH3 + Br- and C2H5F → C2H4 + HF dissociation, non-RRKM dynamics for cyclopropane stereomutation and the Cl- ··· CH3Cl complexes mediating the Cl- + CH3Cl SN2 nucleophilic substitution reaction, and non-IRC dynamics for the OH- + CH3F and F- + CH3OOH chemical reactions. These studies illustrate the important role of chemical dynamics simulations in understanding atomic-level reaction dynamics and interpreting experiments. They also show that widely used paradigms and model theories for interpreting reaction kinetics and dynamics are often inaccurate and are not applicable.
šponer, Jiří; Cang, Xiaohui; Cheatham, Thomas E.
2013-01-01
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids. PMID:22525788
Simulating the dynamic response of magnesium alloys
NASA Astrophysics Data System (ADS)
Lloyd, Jeffrey; Becker, Richard
Unlike several conventional metals, the mechanical response of magnesium is severely anisotropic for quasistatic and dynamic loading conditions. In this work we present a crystal-based strength model that is the same order of magnitude in computational cost as rate-dependent isotropic strength models, yet is able to capture essential features exhibited by textured magnesium polycrystals. The model demarcates plastic deformation into contributions from basal slip, extension twinning, and non-basal slip mechanisms. Comparisons are made between model predictions and experiments for two magnesium alloys with differing processing histories. The model is then used to explore and quantify the dependence of metallurgical and processing variations for several dynamic experiments that probe propensity for localization and failure under complex loading conditions.
Hybrid Dynamics Simulation Engine for Metalloproteins
Sparta, Manuel; Shirvanyants, David; Ding, Feng; Dokholyan, Nikolay V.; Alexandrova, Anastassia N.
2012-01-01
Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins’ structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca2+ form of the enzyme catechol O-methyl transferase, which, unlike the native Mg2+ form, is catalytically inactive. The Mg2+ site is ochtahedral, but the Ca2+ is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight. PMID:22947938
Improvement of surgical simulation using dynamic volume rendering.
Radetzky, A; Schröcker, F; Auer, L M
2000-01-01
In the last years high efforts have been taken to develop surgical simulators for computer assisted training. However, most of these simulators use simple models of the human's anatomy, which are manually created using modeling software. Nevertheless, medical experts need to perform the training directly with the patient's complex anatomy, which can be received, for example, from digital imaging datasets (CT, MR). A common technique to display these datasets is volume rendering. However, even with high-end hardware only static models can be handled interactively. In surgical simulators a dynamic component is also needed because tissues must be deformed and partially removed. With the combination of springmass models, which are improved by neuro-fuzzy systems, and the recently developed OpenGL Volumizer, surgical simulation using real-time deformable (or dynamic) volume rendering became possible. As an application example the simulator ROBOSIM for minimally invasive neurosurgery is presented.
Strong Analog Classical Simulation of Coherent Quantum Dynamics
NASA Astrophysics Data System (ADS)
Wang, Dong-Sheng
2017-02-01
A strong analog classical simulation of general quantum evolution is proposed, which serves as a novel scheme in quantum computation and simulation. The scheme employs the approach of geometric quantum mechanics and quantum informational technique of quantum tomography, which applies broadly to cases of mixed states, nonunitary evolution, and infinite dimensional systems. The simulation provides an intriguing classical picture to probe quantum phenomena, namely, a coherent quantum dynamics can be viewed as a globally constrained classical Hamiltonian dynamics of a collection of coupled particles or strings. Efficiency analysis reveals a fundamental difference between the locality in real space and locality in Hilbert space, the latter enables efficient strong analog classical simulations. Examples are also studied to highlight the differences and gaps among various simulation methods. Funding support from NSERC of Canada and a research fellowship at Department of Physics and Astronomy, University of British Columbia are acknowledged
Simulation in a dynamic prototyping environment: Petri nets or rules?
NASA Technical Reports Server (NTRS)
Moore, Loretta A.; Price, Shannon W.; Hale, Joseph P.
1994-01-01
An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are normally delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.
Simulation in a dynamic prototyping environment: Petri nets or rules?
NASA Technical Reports Server (NTRS)
Moore, Loretta A.; Price, Shannon; Hale, Joseph P.
1994-01-01
An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.
Fast simulation of Brownian dynamics in a crowded environment.
Smith, Stephen; Grima, Ramon
2017-01-14
Brownian dynamics simulations are an increasingly popular tool for understanding spatially extended biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics (BD) simulations; however these methods are extremely slow owing to the sheer number of possible collisions between particles. Here we propose a rigorous "crowder-free" method to dramatically increase the simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the cases where the reactive particles are point particles, and where they themselves occupy a volume. Using simulations of simple chemical reaction networks, we show that the "crowder-free" method is up to three orders of magnitude faster than conventional BD and yet leads to nearly indistinguishable results from the latter.
Mantha, Sriteja; Yethiraj, Arun
2016-02-24
The properties of water under confinement are of practical and fundamental interest. Here in this work we study the properties of water in the self-assembled lyotropic phases of gemini surfactants with a focus on testing the standard analysis of quasi-elastic neutron scattering (QENS) experiments. In QENS experiments the dynamic structure factor is measured and fit to models to extract the translational diffusion constant, D_{T} , and rotational relaxation time, τ_{R}. We test this procedure by using simulation results for the dynamic structure factor, extracting the dynamic parameters from the fit as is typically done in experiments, and comparing the values to those directly measured in the simulations. We find that the decoupling approximation, where the intermediate scattering function is assumed to be a product of translational and rotational contributions, is quite accurate. The jump-diffusion and isotropic rotation models, however, are not accurate when the degree of confinement is high. In particular, the exponential approximations for the intermediate scattering function fail for highly confined water and the values of D_{T} and τ_{R} can differ from the measured value by as much as a factor of two. Other models have more fit parameters, however, and with the range of energies and wave-vectors accessible to QENS, the typical analysis appears to be the best choice. In the most confined lamellar phase, the dynamics are sufficiently slow that QENS does not access a large enough time scale and neutron spin echo measurements would be a valuable technique in addition to QENS.
Mantha, Sriteja; Yethiraj, Arun
2016-02-24
The properties of water under confinement are of practical and fundamental interest. Here in this work we study the properties of water in the self-assembled lyotropic phases of gemini surfactants with a focus on testing the standard analysis of quasi-elastic neutron scattering (QENS) experiments. In QENS experiments the dynamic structure factor is measured and fit to models to extract the translational diffusion constant, DT , and rotational relaxation time, τR. We test this procedure by using simulation results for the dynamic structure factor, extracting the dynamic parameters from the fit as is typically done in experiments, and comparing the valuesmore » to those directly measured in the simulations. We find that the decoupling approximation, where the intermediate scattering function is assumed to be a product of translational and rotational contributions, is quite accurate. The jump-diffusion and isotropic rotation models, however, are not accurate when the degree of confinement is high. In particular, the exponential approximations for the intermediate scattering function fail for highly confined water and the values of DT and τR can differ from the measured value by as much as a factor of two. Other models have more fit parameters, however, and with the range of energies and wave-vectors accessible to QENS, the typical analysis appears to be the best choice. In the most confined lamellar phase, the dynamics are sufficiently slow that QENS does not access a large enough time scale and neutron spin echo measurements would be a valuable technique in addition to QENS.« less
Gas dynamics for accretion disk simulations
NASA Technical Reports Server (NTRS)
Whitehurst, R.
1994-01-01
The behavior of accretion disks can largely be understood in terms of the basic physical processes of mass, energy, and momentum conservation. Despite this, detailed modeling of these systems using modern computational techniques is challenging and controversial. Disturbing differences exist between methods used widely in astrophysics, namely Eulerian finite-difference techniques and particle codes such as SPH. Therefore neither technique is fully satisfactory for accretion disk simulations. This paper describes a new fully Lagrangian method designed to resolve these difficulties.
Molecular dynamics simulation of propagating cracks
NASA Technical Reports Server (NTRS)
Mullins, M.
1982-01-01
Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.
Molecular dynamics simulation of propagating cracks
NASA Technical Reports Server (NTRS)
Mullins, M.
1982-01-01
Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.
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.
GRODY - GAMMA RAY OBSERVATORY DYNAMICS SIMULATOR IN ADA
NASA Technical Reports Server (NTRS)
Stark, M.
1994-01-01
Analysts use a dynamics simulator to test the attitude control system algorithms used by a satellite. The simulator must simulate the hardware, dynamics, and environment of the particular spacecraft and provide user services which enable the analyst to conduct experiments. Researchers at Goddard's Flight Dynamics Division developed GRODY alongside GROSS (GSC-13147), a FORTRAN simulator which performs the same functions, in a case study to assess the feasibility and effectiveness of the Ada programming language for flight dynamics software development. They used popular object-oriented design techniques to link the simulator's design with its function. GRODY is designed for analysts familiar with spacecraft attitude analysis. The program supports maneuver planning as well as analytical testing and evaluation of the attitude determination and control system used on board the Gamma Ray Observatory (GRO) satellite. GRODY simulates the GRO on-board computer and Control Processor Electronics. The analyst/user sets up and controls the simulation. GRODY allows the analyst to check and update parameter values and ground commands, obtain simulation status displays, interrupt the simulation, analyze previous runs, and obtain printed output of simulation runs. The video terminal screen display allows visibility of command sequences, full-screen display and modification of parameters using input fields, and verification of all input data. Data input available for modification includes alignment and performance parameters for all attitude hardware, simulation control parameters which determine simulation scheduling and simulator output, initial conditions, and on-board computer commands. GRODY generates eight types of output: simulation results data set, analysis report, parameter report, simulation report, status display, plots, diagnostic output (which helps the user trace any problems that have occurred during a simulation), and a permanent log of all runs and errors. The
Insights from molecular dynamics simulations for computational protein design.
Childers, Matthew Carter; Daggett, Valerie
2017-02-01
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
Enhanced sampling techniques in molecular dynamics simulations of biological systems.
Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus
2015-05-01
Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.
Dynamic computer simulations of electrophoresis: three decades of active research.
Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A
2009-06-01
Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.
Simulating Timescale Dynamics of Network Traffic Using Homogeneous Modeling
Yuan, Jian; Mills, Kevin L.
2006-01-01
Simulating and understanding traffic dynamics in large networks are difficult and challenging due to the complexity of such networks and the limitations inherent in simulation modeling. Typically, simulation models used to study traffic dynamics include substantial detail representing protocol mechanisms across several layers of functionality. Such models must be restricted in space and time in order to be computationally tractable. We propose an alternative simulation approach that uses homogeneous modeling with an increased level of abstraction, in order to explore networks at larger space-time scales than otherwise feasible and to develop intuition and insight about the space-time dynamics of large networks. To illustrate the utility of our approach, we examine some current understandings of the timescale dynamics of network traffic, and we discuss some speculative results obtained with homogeneous modeling. Using a wavelet-based technique, we show correlation structures, and changes in correlation structures, of network traffic under variations in traffic sources, transport mechanisms, and network structure. Our simulation results justify further investigation of our approach, which might benefit from cross-verifications against more detailed simulation models. PMID:27274931
Multiscale simulation of microbe structure and dynamics.
Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V; Cheluvaraja, Srinath C; Ortoleva, Peter J
2011-10-01
A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin.
Multiscale Simulation of Microbe Structure and Dynamics
Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.
2012-01-01
A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin. PMID:21802438
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver
2015-06-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Dynamic stall simulation including turbulence modeling
Allet, A.; Halle, S.; Paraschivoiu, I.
1995-09-01
The objective of this study is to investigate the two-dimensional unsteady flow around an airfoil undergoing a Darrieus motion in dynamic stall conditions. For this purpose, a numerical solver based on the solution of the Reynolds-averaged Navier-Stokes equations expressed in a streamfunction-vorticity formulation in a non-inertial frame of reference was developed. The governing equations are solved by the streamline upwind Petrov-Galerkin finite element method (FEM). Temporal discretization is achieved by second-order-accurate finite differences. The resulting global matrix system is linearized by the Newton method and solved by the generalized minimum residual method (GMRES) with an incomplete triangular factorization preconditioning (ILU). Turbulence effects are introduced in the solver by an eddy viscosity model. The investigation centers on an evaluation of the possibilities of several turbulence models, including the algebraic Cebeci-Smith model (CSM) and the nonequilibrium Johnson-King model (JKM). In an effort to predict dynamic stall features on rotating airfoils, first the authors present some testing results concerning the performance of both turbulence models for the flat plate case. Then, computed flow structure together with aerodynamic coefficients for a NACA 0015 airfoil in Darrieus motion under stall conditions are presented.
Numerical simulations of blobs with ion dynamics
NASA Astrophysics Data System (ADS)
Nielsen, A. H.; Rasmussen, J. Juul; Madsen, J.; Xu, G. S.; Naulin, V.; Olsen, J. M. B.; Løiten, M.; Hansen, S. K.; Yan, N.; Tophøj, L.; Wan, B. N.
2017-02-01
The transport of particles and energy into the scrape-off layer (SOL) region at the outboard midplane of medium-sized tokamaks, operating in low confinement mode, is investigated by applying the first-principle HESEL (hot edge-sol-electrostatic) model. HESEL is a four-field drift-fluid model including finite electron and ion temperature effects, drift wave dynamics on closed field lines, and sheath dynamics on open field lines. Particles and energy are mainly transported by intermittent blobs. Therefore, blobs have a significant influence on the corresponding profiles. The formation of a ‘shoulder’ in the SOL density profile can be obtained by increasing the collisionality or connection length, thus decreasing the efficiency of the SOL’s ability to remove plasma. As the ion pressure has a larger perpendicular but smaller parallel dissipation rate compared to the electron pressure, ion energy is transported far into the SOL. This implies that the ion temperature in the SOL exceeds the electron temperature by a factor of 2-4 and significantly broadens the power deposition profile.
Distortion and flow of nematics simulated by dissipative particle dynamics.
Zhao, Tongyang; Wang, Xiaogong
2014-05-14
In this study, we simulated distortion and flow of nematics by dissipative particle dynamics (DPD). The nematics were modeled by a binary mixture that contained rigid rods composed of DPD particles as mesogenic units and normal DPD particles as solvent. Elastic distortions were investigated by monitoring director orientation in space under influences of boundary anchoring and external fields. Static distortion demonstrated by the simulation is consistent with the prediction of Frank elastic theory. Spatial distortion profile of the director was examined to obtain static elastic constants. Rotational motions of the director under influence of the external field were simulated to understand the dynamic process. The rules revealed by the simulation are in a good agreement with those obtained from dynamical experiments and classical theories for nematics. Three Miesowicz viscosities were obtained by using external fields to hold the orientation of the rods in shear flows. The simulation showed that the Miesowicz viscosities have the order of ηc > ηa > ηb and the rotational viscosity γ1 is about two orders larger than the Miesowicz viscosity ηb. The DPD simulation correctly reproduced the non-monotonic concentration dependence of viscosity, which is a unique property of lyotropic nematic fluids. By comparing simulation results with classical theories for nematics and experiments, the DPD nematic fluids are proved to be a valid model to investigate the distortion and flow of lyotropic nematics.
Gas dynamic simulations of galaxy formation
NASA Technical Reports Server (NTRS)
Evrard, August E.
1993-01-01
Results are presented from a simulation modeling the formation of a group of galaxies in a 'standard' cold, dark matter universe with delta = 1, h sub 0 = 50 km/(s(Mpc)), baryon fraction omega sub b = 0.1 and spectrum normalization sigma sub 8 = 0.6 (bias parameter b = 1.7). Initial conditions are generated within a periodic box with comoving length 16 Mpc in a manner constrained to produce a small cluster of total mass approximately 10 exp 14 solar mass. Two sets of 643 particles are used to model the dark matter and baryon fluids. Each gas particle represents 1.08 x 10 exp -8 solar mass, implying an L* galaxy is resolved by approximately 1000 particles. The system is evolved self-consistently in three dimensions using the combined N-body/hydrodynamic scheme P3MSPH up to a final redshift z = 1. Evolving to the present is prohibited by the fact that the mean density in the simulated volume is above critical and the entire volume would be going nonlinear beyond this point, We are currently analyzing another run with somewhat poorer mass resolution which was evolved to the present.
New ways to boost molecular dynamics simulations.
Krieger, Elmar; Vriend, Gert
2015-05-15
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Modeling and simulation of consumer response to dynamic pricing.
Valenzuela, J.; Thimmapuram, P.; Kim, J
2012-08-01
Assessing the impacts of dynamic-pricing under the smart grid concept is becoming extremely important for deciding its full deployment. In this paper, we develop a model that represents the response of consumers to dynamic pricing. In the model, consumers use forecasted day-ahead prices to shift daily energy consumption from hours when the price is expected to be high to hours when the price is expected to be low while maintaining the total energy consumption as unchanged. We integrate the consumer response model into the Electricity Market Complex Adaptive System (EMCAS). EMCAS is an agent-based model that simulates restructured electricity markets. We explore the impacts of dynamic-pricing on price spikes, peak demand, consumer energy bills, power supplier profits, and congestion costs. A simulation of an 11-node test network that includes eight generation companies and five aggregated consumers is performed for a period of 1 month. In addition, we simulate the Korean power system.
Simulation of ceramics fracture due to high rate dynamic impact
NASA Astrophysics Data System (ADS)
Kazarinov, N. A.; Bratov, V. A.; Petrov, Y. V.
2015-11-01
In this paper dynamic fracture process due to high-speed impact of steel plunger into ceramic sample is simulated. The developed numerical model is based on finite element method and a concept of incubation time criterion, which is proven applicable in order to predict brittle fracture under high-rate deformation. Simulations were performed for ZrO2(Y2O3) ceramic plates. To characterize fracture process quantitatively fracture surface area parameter is introduced and controlled. This parameter gives the area of new surface created during dynamic fracture of a sample and is essentially connected to energetic peculiarities of fracture process. Multiple simulations with various parameters made it possible to explore dependencies of fracture area on plunger velocity and material properties. Energy required to create unit of fracture area at fracture initiation (dynamic analogue of Griffith surface energy) was evaluated and was found to be an order of magnitude higher as comparing to its static value.
Predicting protein interactions by Brownian dynamics simulations.
Meng, Xuan-Yu; Xu, Yu; Zhang, Hong-Xing; Mezei, Mihaly; Cui, Meng
2012-01-01
We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions.
Simulation of nanofractal dynamics with MBN Explorer
NASA Astrophysics Data System (ADS)
Solov'yov, Ilia A.; Solov'yov, Andrey V.
2013-06-01
One of the goals of nanotechnology is the development of controlled, reproducible, and industrially transposable nanostructured materials. In this context, controlling of the final architecture of such materials by tuneable parameters is one of the fundamental problems. Post-growth processes occurring in patterns grown on a surface were studied using a multi-purpose computer code MBN EXPLORER introduced in the present paper. The package allows to model molecular systems of varied level of complexity, and in the present paper was used, in particular, to study dynamics of silver nanofractal formation and fragmentation on graphite surface. We demonstrate that the detachment of particles from the fractal and their diffusion within the fractal and over the surface determines the shape of the islands remaining on a surface after the fractal fragmentation.
Symplectic molecular dynamics simulations on specially designed parallel computers.
Borstnik, Urban; Janezic, Dusanka
2005-01-01
We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.
Robotic Simulation of Flexible-Body Spacecraft Dynamics
NASA Technical Reports Server (NTRS)
Brannan, Justin C.; Carignan, Craig R.
2016-01-01
A robotic testbed has been developed to conduct hardware-in-the-loop simulations of a robotic servicer interacting with a client satellite on-orbit. By creating an analytical model of a satellite with flexible appendages, it is possible to simulate the system response to external force and torque inputs and compare the predicted system motion to a robot mass simulator outfitted with physical appendages. This validation effort includes multiple test cases that encompass the types of interaction forces a satellite might experience during a nominal on-orbit servicing mission and aims to show the simulation's ability to capture the physical system response. After incorporating the flexible-body dynamics into the robotic mass simulator at NASA Goddard Space Flight Center (GSFC), a hardware-in-the-loop simulation can be used to characterize the potential impact of structural flexibility on an end-to-end satellite servicing mission.
Molecular dynamics simulation of interfacial adhesion
Yarovsky, I.; Chaffee, A.L.
1996-12-31
Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.
Analytical Dynamics and Nonrigid Spacecraft Simulation
NASA Technical Reports Server (NTRS)
Likins, P. W.
1974-01-01
Application to the simulation of idealized spacecraft are considered both for multiple-rigid-body models and for models consisting of combination of rigid bodies and elastic bodies, with the elastic bodies being defined either as continua, as finite-element systems, or as a collection of given modal data. Several specific examples are developed in detail by alternative methods of analytical mechanics, and results are compared to a Newton-Euler formulation. The following methods are developed from d'Alembert's principle in vector form: (1) Lagrange's form of d'Alembert's principle for independent generalized coordinates; (2) Lagrange's form of d'Alembert's principle for simply constrained systems; (3) Kane's quasi-coordinate formulation of D'Alembert's principle; (4) Lagrange's equations for independent generalized coordinates; (5) Lagrange's equations for simply constrained systems; (6) Lagrangian quasi-coordinate equations (or the Boltzmann-Hamel equations); (7) Hamilton's equations for simply constrained systems; and (8) Hamilton's equations for independent generalized coordinates.
Molecular-dynamics simulation of thin-film growth
NASA Astrophysics Data System (ADS)
Schneider, M.; Schuller, I. K.; Rahman, A.
1987-01-01
The epitaxial growth of thin films has been studied by molecular-dynamics computer simulation. In these simulations atoms are projected towards a temperature-controlled substrate, and the equations of motion of all atoms are solved for a given interaction potential. The calculations give insight into the microscopic structure of thin films, the dynamics of the adsorption process, and they help answer the way in which substrate temperature, form of the substrate, flux of impinging atoms, and form of the interaction potential, affect epitaxial growth. Simulations were performed for monatomic and binary systems with spherically symmetric atomic interactions, and for systems in which the atoms are interacting via a three-body potential to simulate the epitaxial growth of silicon.
A dynamic skull model for simulation of cerebral cortex folding.
Chen, Hanbo; Guo, Lei; Nie, Jingxin; Zhang, Tuo; Hu, Xintao; Liu, Tianming
2010-01-01
The mechanisms of human cerebral cortex folding and their interactions during brain development are largely unknown, partly due to the difficulties in biological experiments and data acquisition for the developing fetus brain. Computational modeling and simulation provide a novel approach to the understanding of cortex folding processes in normal or aberrant neurodevelopment. Based on our recently developed computational model of the cerebral cortex folding using neuronal growth model and mechanical skull constraint, this paper presents a computational dynamic model of the brain skull that regulates the cortical folding simulation. Our simulation results show that the dynamic skull model is more biologically realistic and significantly improves our cortical folding simulation results. This work provides further computational support to the hypothesis that skull is an important regulator of cortical folding.
LINAC BEAM DYNAMICS SIMULATIONS WITH PY-ORBIT
Shishlo, Andrei P
2012-01-01
Linac dynamics simulation capabilities of the PyORBIT code are discussed. PyORBIT is an open source code and a further development of the original ORBIT code that was created and used for design, studies, and commissioning of the SNS ring. The PyORBIT code, like the original one, has a two-layer structure. C++ is used to perform time-consuming computations, and the program flow is controlled from a Python language shell. The flexible structure makes it possible to use PyORBIT also for linac dynamics simulations. A benchmark of PyORBIT with Parmila and the XAL Online model is presented.
Simulated dynamics and control of an extractive alcoholic fermentation.
Costa, A C; Dechechi, E C; Silva, F L; Maugeri, F; Maciel, R
2000-01-01
In this study, we investigated the dynamics of a computer simulation of a continuous alcoholic fermentation process combined with a flash column under vacuum. The alcohol was partially extracted in order to maintain its concentration at about 40 kg/m3 in the fermentor. The mathematical model of the fermentation was developed for industrial conditions and considers the effect of the temperature on the kinetic parameters. The performance of the dynamic matrix control algorithm, single input single output and multiple input multiple output, for the control of the extractive process was studied. The concepts of factorial design were used in a simulation study to determine the best control structures for the process.
Molecular Dynamics Simulations of Gas Transport in Polymer Films
NASA Astrophysics Data System (ADS)
Whitley, David; Butler, Simon; Adolf, David
2010-03-01
Parallel molecular dynamics simulations have been carried out to determine the permeability of O2 and N2 through polyethylene terephthalate, polypropylene and cis(1-4) polybutadiene. The permeability of both mixed and unmixed gas penetrants is studied within films of these well known gas barrier polymers. Results are obtained either through the solubility and diffusion (i.e. P=D*S) or via the permeability directly. Encouraging results are obtained. Additional analysis focuses on ``unmixed/mixed gas'' intracomparisons of the simulated permeability data in addition to corresponding penetrant and host polymer local dynamics.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
NASA Technical Reports Server (NTRS)
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
NASA Technical Reports Server (NTRS)
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
Numerical simulation of dynamic fracture and failure in solids
Chen, E.P.
1994-05-01
Numerical simulation of dynamic fracture and failure processes in solid continua using Lagrangian finite element techniques is the subject of discussion in this investigation. The specific configurations in this study include penetration of steel projectiles into aluminum blocks and concrete slabs. The failure mode in the aluminum block is excessive deformation while the concrete slab fails by hole growth, spallation, and scabbing. The transient dynamic finite element code LS-DYNA2D was used for the numerical analysis. The erosion capability in LS-DYNA2D was exercised to carry out the fracture and failure simulations. Calculated results were compared to the experimental data. Good correlations were obtained.
Simulation of Naval Guns' Breechblock System Dynamics Based on ADAMS
NASA Astrophysics Data System (ADS)
Tan, Bo; Liu, Hui-Min; Liu, Kai
In order to study the dynamical characteristics of the breechblock system during gun firing, a virtual prototype model was established based on ADAMS, in which motion and force transmission among mechanisms are realized by collision. By simulation, kinematics and dynamics properties of main components are obtained, and the relationships between the motion of breechblock and the position of breechblock opening plate are analyzed. According to the simulation results, the collision among the breechblock opening plate and the roller is discontinuous, which may make the breechblock system fail to hitch the breechblock reliably. And within allowable scope of the structure, the breechblock opening template should be installed near the upside as much as possible.
Lessons Learned From Dynamic Simulations of Advanced Fuel Cycles
Steven J. Piet; Brent W. Dixon; Jacob J. Jacobson; Gretchen E. Matthern; David E. Shropshire
2009-04-01
Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe “lessons learned” from dynamic simulations but attempt to answer the “so what” question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.
Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems
Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus
2014-01-01
Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171
Hybrid simulations with dynamical quarks: Spectra, screening and thermodynamics
Sinclair, D.K.
1987-11-18
We summarize simulations made by the Argonne/University of Illinois group using the Hybrid algorithm to include dynamical staggered fermions. Recent work on the mass spectrum and screening effects due to the inclusion of four light flavors of dynamical quarks is presented. We also present a brief overview of what we have learned about the finite temperature chiral phase transition. 5 refs., 4 figs., 1 tab.
Computer simulation and image guidance for individualised dynamic spinal stabilization.
Kantelhardt, S R; Hausen, U; Kosterhon, M; Amr, A N; Gruber, K; Giese, A
2015-08-01
Dynamic implants for the human spine are used to re-establish regular segmental motion. However, the results have often been unsatisfactory and complications such as screw loosening are common. Individualisation of appliances and precision implantation are needed to improve the outcome of this procedure. Computer simulation, virtual implant optimisation and image guidance were used to improve the technique. A human lumbar spine computer model was developed using multi-body simulation software. The model simulates spinal motion under load and degenerative changes. After virtual degeneration of a L4/5 segment, virtual pedicle screw-based implants were introduced. The implants' positions and properties were iteratively optimised. The resulting implant positions were used as operative plan for image guidance and finally implemented in a physical spine model. In the simulation, the introduction and optimisation of virtually designed dynamic implants could partly compensate for the effects of virtual lumbar segment degeneration. The optimised operative plan was exported to two different image-guidance systems for transfer to a physical spine model. Three-dimensional computer graphic simulation is a feasible means to develop operative plans for dynamic spinal stabilization. These operative plans can be transferred to commercially available image-guidance systems for use in implantation of physical implants in a spine model. This concept has important potential in the design of operative plans and implants for individualised dynamic spine stabilization surgery.
Dynamical QCD+QED simulation with staggered quarks
Zhou, Ran; Gottlieb, Steven
2014-11-15
Electromagnetic effects play an important role in many phenomena such as isospin-symmetry breaking in the hadron spectrum and the hadronic contributions to g-2. We have generalized the MILC QCD code to include the electromagnetic field. In this work, we focus on simulations including charged sea quarks using the RHMC algorithm. We show details of the dynamical QCD+QED simulation algorithm with compact QED. We analyze the code performance and results for hadron-spectrum observables.
Molecular dynamics simulation of carbon disulphide with a Gaussian correction
NASA Astrophysics Data System (ADS)
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2017-02-01
Molecular Dynamics (MD) simulations of liquid carbon disulphide (CS2) in the temperature range 164-318 K under normal pressure and at experimental density were performed using an expa-6 potential with a Gaussian correction plus electrostatic interactions. This correction allowed to modify the curvature of the potential. The results of the MD simulation are compared with available experimental data. The agreement is good.
Molecular dynamics simulation of a nanoscopic nematic twist cell
NASA Astrophysics Data System (ADS)
Mirantsev, Leonid V.; Virga, Epifanio G.
2007-08-01
We present molecular dynamics simulations of a nanoscopic nematic twist cell confined within two bounding substrates with conflicting anchoring conditions. The results of our simulations show that the torque transmitted through the cell drops significantly below a certain critical cell’s thickness, thus confirming the predictions of the continuum Landau theory extrapolated down to the nanoscopic scale [F. Bisi, E. G. Virga, and G. E. Durand, Phys. Rev. E 70, 042701 (2004)].
Combined molecular dynamics-spin dynamics simulations of bcc iron
Perera, Meewanage Dilina N; Yin, Junqi; Landau, David P; Nicholson, Don M; Stocks, George Malcolm; Eisenbach, Markus; Brown, Greg
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Simulating aggregate dynamics in ocean biogeochemical models
NASA Astrophysics Data System (ADS)
Jackson, George A.; Burd, Adrian B.
2015-04-01
The dynamics of elements in the water column is complex, depending on multiple biological and physical processes operating at very different physical scales. Coagulation of particulate material is important for transforming particles and moving them in the water column. Mechanistic models of coagulation processes provide a means to predict these processes, help interpret observations, and provide insight into the processes occurring. However, most model applications have focused on describing simple marine systems and mechanisms. We argue that further model development, in close collaboration with field and experimental scientists, is required in order to extend the models to describe the large-scale elemental distributions and interactions being studied as part of GEOTRACES. Models that provide a fundamental description of trace element-particle interactions are required as are experimental tests of the mechanisms involved and the predictions arising from models. However, a comparison between simple and complicated models of aggregation and trace metal provides a means for understanding the implications of simplifying assumptions and providing guidance as to which simplifications are needed.
Dissipative Particle Dynamics simulation of colloidal suspensions
NASA Astrophysics Data System (ADS)
Jamali, Safa; Boromand, Arman; Maia, Joao
2014-03-01
DPD as a mesoscale method was firstly proposed to study dynamics of suspensions under flow condition. However the proposed method failed to capture shear properties of suspensions because it lacked: first a potential to reproduce lubrication forces and second a clear definition for the colloid surface. Recently we reported a modified DPD method which defines colloidal particles as particles with hard core and a dissipative coat. An additional lubrication force was introduced to include the short-range hydrodynamics that are not captured in original DPD. The model was found to be able to reproduce shear properties of suspensions for a wide range of different systems, from monodisperse to bimodal with different volume fractions, compositions and size ratios. In present work our modified DPD method is employed to study both equilibrium and flow properties of colloidal suspension. Zero shear viscosity of suspension is measured using Green-Kubo expressions and the results are compared to theoretical predictions. Furthermore, structure formation in suspensions is studied in respect to energy landscape of the fluid both at rest and under flow.
Studies of thermal transport properties using molecular dynamics simulation techniques
NASA Astrophysics Data System (ADS)
Ratanapisit, Juraivan
The purpose of this research has been to investigate the transport properties of fluids using novel techniques in molecular dynamics simulations: symplectic integration algorithms for equations of motion, Baranyai's thermostatted fluid wall algorithm, and Rapaport's algorithm for hard chain fluids. In the symplectic integration study, an extensive series of equilibrium molecular dynamic simulations have been performed to investigate the accuracy, stability and efficiency of second order explicit symplectic integrators: position Verlet, velocity Verlet, and the McLauchlan-Atela algorithms. To our knowledge, previous studies of the symplectic integrators have only looked at the thermodynamic energy using a simple model fluid. Our work presents realistic but perhaps the simplest simulations possible to test the effect of the integrators on the three main transport properties. Our results suggest that if an algorithm fails to adequately conserve energy, it will also show significant uncertainties in transport property calculations. A large portion of the simulation study focused on a new algorithm for thermal conductivity based on Baranyai's fluid wall method. This algorithm is stable enough to perform simulations even using large time steps and provides reasonable values and uncertainties for the thermal conductivity. The investigation was conducted using two different thermostat algorithms: the Gaussian and Nosé-Hoover thermostats. The final part of this research focused on the viscosity of hard chain fluids. This study was initiated with an investigation of the equilibrium molecular dynamic simulations of pure hard-sphere molecules. The natural extension of that work was to hard chain fluids. (Abstract shortened by UMI.)
Molecular dynamics simulations: Parameter evaluation, application and development
NASA Astrophysics Data System (ADS)
Zhou, Jin
Molecular dynamics (MD) simulation is a theoretical technique for investigating the physical properties of a wide variety of molecules. This dissertation contains my studies on three important parts of the MD simulation: evaluation of parameters in empirical energy functions widely used in MD simulations, application of MD simulation on experimentally interested biological molecules and development of new methods for constraint dynamics simulations. All the work in this thesis made use of CHARMM as an MD simulation tool. The MD simulation uses empirical energy functions parameterized by a set of parameters. These parameters play an important role in the quality of the simulations. I evaluated nine parameter sets from Harvard University and Molecular Simulations, Inc. for protein simulations by the MD simulations of hydrated form of carboxy- myoglobin and interleukin-1/beta, which are rich in two typical protein structure motifs, helix and β sheet structures respectively. It is found that some sets are good at representing helical structure proteins while others are good at β sheet proteins. But all of them need improvement on representing motions at low temperature. Experimental evidence indicates that the 1A coiled-coil domains of the Intermediate Filament (IF) proteins consisting of coiled human keratins 1 and 10 (K1 and K10) are 'hot spots' for substitutional mutations. Some of these mutations are correlated to the human skin diseases-epidermolytic hyperkeratiosis (EH) and epidermolysis bullosa simplex (EBS). The MD simulation technique is used here for the first time to model and simulate these proteins to elucidate the molecular-level effects of these mutations. Lacking the experimental crystal structures, the initial structure of 1A domain of the wild type Intermediate Filament protein and its mutants were modeled from scratch to reproduce the well- known properties of the proteins of this kind followed by identical MD simulations. The important result is
Dynamic simulation of coronal mass ejections
NASA Technical Reports Server (NTRS)
Steinolfson, R. S.; Wu, S. T.
1980-01-01
A model is developed for the formation and propagation through the lower corona of the loop-like coronal transients in which mass is ejected from near the solar surface to the outer corona. It is assumed that the initial state for the transient is a coronal streamer. The initial state for the streamer is a polytropic, hydrodynamic solution to the steady-state radial equation of motion coupled with a force-free dipole magnetic field. The numerical solution of the complete time-dependent equations then gradually approaches a stationary coronal streamer configuration. The streamer configuration becomes the initial state for the coronal transient. The streamer and transient simulations are performed completely independent of each other. The transient is created by a sudden increase in the pressure at the base of the closed-field region in the streamer configuration. Both coronal streamers and coronal transients are calculated for values of the plasma beta (the ratio of thermal to magnetic pressure) varying from 0.1 to 100.
NASA Astrophysics Data System (ADS)
Kawamura, Kohei; Ueno, Yosuke; Nakamura, Yoshiaki
In the present study we have developed a numerical method to simulate the flight dynamics of a small flying body with unsteady motion, where both aerodynamics and flight dynamics are fully considered. A key point of this numerical code is to use computational fluid dynamics and computational flight dynamics at the same time, which is referred to as CFD2, or double CFDs, where several new ideas are adopted in the governing equations, the method to make each quantity nondimensional, and the coupling method between aerodynamics and flight dynamics. This numerical code can be applied to simulate the unsteady motion of small vehicles such as micro air vehicles (MAV). As a sample calculation, we take up Taketombo, or a bamboo dragonfly, and its free flight in the air is demonstrated. The eventual aim of this research is to virtually fly an aircraft with arbitrary motion to obtain aerodynamic and flight dynamic data, which cannot be taken in the conventional wind tunnel.
Papaleo, Elena
2015-01-01
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210
Papaleo, Elena
2015-01-01
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
Efficient dynamic simulation for multiple chain robotic mechanisms
NASA Technical Reports Server (NTRS)
Lilly, Kathryn W.; Orin, David E.
1989-01-01
An efficient O(mN) algorithm for dynamic simulation of simple closed-chain robotic mechanisms is presented, where m is the number of chains, and N is the number of degrees of freedom for each chain. It is based on computation of the operational space inertia matrix (6 x 6) for each chain as seen by the body, load, or object. Also, computation of the chain dynamics, when opened at one end, is required, and the most efficient algorithm is used for this purpose. Parallel implementation of the dynamics for each chain results in an O(N) + O(log sub 2 m+1) algorithm.
Selection of Solar Simulator for Solar Dynamic Ground Test
NASA Technical Reports Server (NTRS)
Tolbert, Carol M.
1994-01-01
The 2 kWe Solar Dynamic (SD) Ground Test Demonstration (GTD) experiment will be conducted in 1995 at NASA Lewis Research Center (LeRC). This solar dynamic power system test will be conducted in a simulated space environment and will require an artificial sun. To address the solar simulator requirements for the GTD, Arnold Engineering Development Center (AEDC) was hired under contract to review and visit four existing solar simulator facilities. The four facilities included, AEDC's Mark 1 Chamber, NASA-JSC Chamber A, AEDC's 12V Chamber, and NASA-JPL Space Simulator Chamber. Two design concepts were considered following several months of evaluating existing solar simulator facilities throughout the United States. To satisfy system requirements for the SD GTD experiment the solar simulator needs to provide a uniform light flux to the SD concentrator, provide the light within a subtense angle of one degree, and provide an intensity of one solar constant (1.37 kW/sq m) at airmass zero. Most solar simulators are designed for supplying heat loads to spacecraft where a cone angle as large as 3 degrees is acceptable. It was also concluded that a solar simulator, such like these considered in the AEDC study, would require major facility modifications for NASA LeRC and result in significant impacts to the program. The advanced solar simulator concept developed by NASA LeRC will meet the system requirements for the SD GTD experiment Since SD GTD solar simulator requirements could not be addressed by existing simulator, an advanced concept was considered.
Tethsim - A dynamics simulation software package for tethered system
NASA Astrophysics Data System (ADS)
Venditti, F.; Cibrario, B.; Origgi, G.
This paper presents the description of a dynamics simulation package, called Tethsim, devoted to the investigation of tethered systems behavior in space. The papers also analyzes specific problems related to tethered system simulation such as validation, varying-length tether growth model, and CPU time consumption and describes the approaches used to solve them. The system is modeled in Tethsim as composed by rigid bodies and point-masses connected by spring-dashpot, to form an open-line configuration. Strong emphasis has been placed on easing user interfaces with the program; in particular, the software can be flexibly adapted to the specific system to be simulated.
A Fault Evolution Model Including the Rupture Dynamic Simulation
NASA Astrophysics Data System (ADS)
Wu, Y.; Chen, X.
2011-12-01
We perform a preliminary numerical simulation of seismicity and stress evolution along a strike-slip fault in a 3D elastic half space. Following work of Ben-Zion (1996), the fault geometry is devised as a vertical plane which is about 70 km long and 17 km wide, comparable to the size of San Andreas Fault around Parkfield. The loading mechanism is described by "backslip" method. The fault failure is governed by a static/kinetic friction law, and induced stress transfer is calculated with Okada's static solution. In order to track the rupture propagation in detail, we allow induced stress to propagate through the medium at the shear wave velocity by introducing a distance-dependent time delay to responses to stress changes. Current simulation indicates small to moderate earthquakes following the Gutenberg-Richter law and quasi-periodical characteristic large earthquakes, which are consistent with previous work by others. Next we will consider introducing a more realistic friction law, namely, the laboratory-derived rate- and state- dependent law, which can simulate more realistic and complicated sliding behavior such as the stable and unstable slip, the aseismic sliding and the slip nucleation process. In addition, the long duration of aftershocks is expected to be reproduced due to this time-dependent friction law, which is not available in current seismicity simulation. The other difference from previous work is that we are trying to include the dynamic ruptures in this study. Most previous study on seismicity simulation is based on the static solution when dealing with failure induced stress changes. However, studies of numerical simulation of rupture dynamics have revealed lots of important details which are missing in the quasi-static/quasi- dynamic simulation. For example, dynamic simulations indicate that the slip on the ground surface becomes larger if the dynamic rupture process reaches the free surface. The concentration of stress on the propagating crack
Dynamic simulation and validation of a satellite docking system
NASA Astrophysics Data System (ADS)
Hays, Anthony B.; Tchoryk, Peter, Jr.; Pavlich, Jane C.; Wassick, Gregory
2003-08-01
In recent years, Michigan Aerospace has approached the problem of gentle autonomous spacecraft rendezvous and docking using a flexible soft-dock cable that is extended from the docking spacecraft to the target spacecraft. Because of the nature of a soft-dock cable, testing and validation of the technology is difficult in normal gravity. To properly emulate the behavior of this soft-dock cable, we have performed dynamic computer simulations so that the effects of micro-gravity could be simulated. The Autonomous Satellite Docking System (ASDS) was initially prototyped and tested at Marshall Space Flight Center"s air-bearing floor facility. The test data was compared to the simulations and used to validate the model. Once a good correlation between the simulation"s predicted results and the actual data was shown, the model was used to predict future performance of the ASDS mechanism on several potential spacecraft for the Orbital Express program. A new dynamic simulation model was created and compared to test data from a recent KC-135 flight test to further validate the modeling approach used. This paper will describe the methodology used in modeling and simulating the ASDS mechanism. Correlation between the models and the test data will be discussed.
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.
De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut
2011-07-15
With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.
Simulation Analysis of Helicopter Ground Resonance Nonlinear Dynamics
NASA Astrophysics Data System (ADS)
Zhu, Yan; Lu, Yu-hui; Ling, Ai-min
2017-07-01
In order to accurately predict the dynamic instability of helicopter ground resonance, a modeling and simulation method of helicopter ground resonance considering nonlinear dynamic characteristics of components (rotor lead-lag damper, landing gear wheel and absorber) is presented. The numerical integral method is used to calculate the transient responses of the body and rotor, simulating some disturbance. To obtain quantitative instabilities, Fast Fourier Transform (FFT) is conducted to estimate the modal frequencies, and the mobile rectangular window method is employed in the predictions of the modal damping in terms of the response time history. Simulation results show that ground resonance simulation test can exactly lead up the blade lead-lag regressing mode frequency, and the modal damping obtained according to attenuation curves are close to the test results. The simulation test results are in accordance with the actual accident situation, and prove the correctness of the simulation method. This analysis method used for ground resonance simulation test can give out the results according with real helicopter engineering tests.
Dynamic testing and simulation of the Mars Exploration Rover
NASA Technical Reports Server (NTRS)
Lindemann, Randel
2005-01-01
In January of 2004, NASA landed two mobile robotic spacecraft on the surface of Mars as part of the Mars Exploration Rover (MER) project. The results and lessons learned of the test and dynamic simulation of the MER vehicles is provided in this paper.
Simulating Poverty and Inequality Dynamics in Developing Countries
ERIC Educational Resources Information Center
Ansoms, An; Geenen, Sara
2012-01-01
This article considers how the simulation game of DEVELOPMENT MONOPOLY provides insight into poverty and inequality dynamics in a development context. It first discusses how the game is rooted in theoretical and conceptual frameworks on poverty and inequality. Subsequently, it reflects on selected playing experiences, with special focus on the…
Brownian dynamics simulation of the interactions between DNA and histones
NASA Astrophysics Data System (ADS)
Wang, Peng-Ye; Li, Wei; Dou, Shuo-Xing; Tong, Pei-Qing
2003-03-01
In eukaryotic cells, the basic structural unit of chromatin is a nucleosome which consists of 146bp of DNA and histones. The interaction between DNA and histone is one of the essential factors influencing the formation of chromosome structure. We have studied the dynamic process of the interaction of DNA and histones in the formation of nucleosome by Brownian dynamics simulation. The aim of our work is to search for important features in the formation of nucleosome by observing the snapshots of the dynamic process of DNA wrapping around histones. In the simulation, we have used the stochastic Runge-Kutta numerical method. It is found that, with proper parameter values, DNA can correctly wrap around the histone octamer about two turns as in the actual situations. The simulation shows that the interaction potential between DNA and histone plays the main rule for the wrapping of DNA, and the temperature is also an important parameter in the process. The stretching dynamics of the chromatin by an externally applied force has also been simulated.
Simulating Poverty and Inequality Dynamics in Developing Countries
ERIC Educational Resources Information Center
Ansoms, An; Geenen, Sara
2012-01-01
This article considers how the simulation game of DEVELOPMENT MONOPOLY provides insight into poverty and inequality dynamics in a development context. It first discusses how the game is rooted in theoretical and conceptual frameworks on poverty and inequality. Subsequently, it reflects on selected playing experiences, with special focus on the…
Molecular dynamics simulations on PGLa using NMR orientational constraints.
Sternberg, Ulrich; Witter, Raiker
2015-11-01
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
Protocols for Molecular Dynamics Simulations of RNA Nanostructures.
Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A
2017-01-01
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.
Molecular dynamics simulation of aqueous solutions of glycine betaine
NASA Astrophysics Data System (ADS)
Civera, Monica; Fornili, Arianna; Sironi, Maurizio; Fornili, Sandro L.
2003-01-01
Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine- N-oxide, a bioprotectant closely related to glycine betaine.
The 3-axis Dynamic Motion Simulator (DMS) system
NASA Technical Reports Server (NTRS)
1975-01-01
A three-axis dynamic motion simulator (DMS) consisting of a test table with three degrees of freedom and an electronics control system was designed, constructed, delivered, and tested. Documentation, as required in the Data Requirements List (DRL), was also provided.
Evaluating the Accuracy of Hessian Approximations for Direct Dynamics Simulations.
Zhuang, Yu; Siebert, Matthew R; Hase, William L; Kay, Kenneth G; Ceotto, Michele
2013-01-08
Direct dynamics simulations are a very useful and general approach for studying the atomistic properties of complex chemical systems, since an electronic structure theory representation of a system's potential energy surface is possible without the need for fitting an analytic potential energy function. In this paper, recently introduced compact finite difference (CFD) schemes for approximating the Hessian [J. Chem. Phys.2010, 133, 074101] are tested by employing the monodromy matrix equations of motion. Several systems, including carbon dioxide and benzene, are simulated, using both analytic potential energy surfaces and on-the-fly direct dynamics. The results show, depending on the molecular system, that electronic structure theory Hessian direct dynamics can be accelerated up to 2 orders of magnitude. The CFD approximation is found to be robust enough to deal with chaotic motion, concomitant with floppy and stiff mode dynamics, Fermi resonances, and other kinds of molecular couplings. Finally, the CFD approximations allow parametrical tuning of different CFD parameters to attain the best possible accuracy for different molecular systems. Thus, a direct dynamics simulation requiring the Hessian at every integration step may be replaced with an approximate Hessian updating by tuning the appropriate accuracy.
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter
2015-12-07
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
Molecular dynamics simulation: A tool for exploration and discovery
NASA Astrophysics Data System (ADS)
Rapaport, Dennis C.
2009-03-01
The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).
Ion Move Brownian Dynamics (IMBD)--simulations of ion transport.
Kurczynska, Monika; Kotulska, Malgorzata
2014-01-01
Comparison of the computed characteristics and physiological measurement of ion transport through transmembrane proteins could be a useful method to assess the quality of protein structures. Simulations of ion transport should be detailed but also timeefficient. The most accurate method could be Molecular Dynamics (MD), which is very time-consuming, hence is not used for this purpose. The model which includes ion-ion interactions and reduces the simulation time by excluding water, protein and lipid molecules is Brownian Dynamics (BD). In this paper a new computer program for BD simulation of the ion transport is presented. We evaluate two methods for calculating the pore accessibility (round and irregular shape) and two representations of ion sizes (van der Waals diameter and one voxel). Ion Move Brownian Dynamics (IMBD) was tested with two nanopores: alpha-hemolysin and potassium channel KcsA. In both cases during the simulation an ion passed through the pore in less than 32 ns. Although two types of ions were in solution (potassium and chloride), only ions which agreed with the selectivity properties of the channels passed through the pores. IMBD is a new tool for the ion transport modelling, which can be used in the simulations of wide and narrow pores.
Acoustic properties in glycerol glass-former: Molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Busselez, Remi; Pezeril, Thomas; Institut des Materiaux et Molecules du Mans Team
2013-03-01
Study of high-frequency collective dynamics around TeraHertz region in glass former has been a subject of intense investigations and debates over the past decade. In particular, the presence of the Boson peak characteristic of glassy material and its relation to other glass anomalies. Recently, experiments and simulations have underlined possible relation between Boson peak and transverse acoustic modes in glassy materials. In particular, simulations of simple Lennard Jones glass former have shown a relation between Ioffe-Regel criterion in transverse modes and Boson peak. We present here molecular dynamics simulation on high frequency dynamics of glycerol. In order to study mesoscopic order (0.5-5nm-1), we made use of large simulation box containing 80000 atoms. Analysis of collective longitudinal and transverse acoustic modes shows striking similarities in comparison with simulation of Lennard-Jones particles. In particular, it seems that a connection may exist between Ioffe-Regel criterion for transverse modes and Bose Peak frequency. However,in our case we show that this connection may be related with structural correlation arising from molecular clusters.
Understanding Diabetes Population Dynamics Through Simulation Modeling and Experimentation
Jones, Andrew P.; Homer, Jack B.; Murphy, Dara L.; Essien, Joyce D. K.; Milstein, Bobby; Seville, Donald A.
2006-01-01
Health planners in the Division of Diabetes Translation and others from the National Center for Chronic Disease Prevention and Health Promotion of the Centers for Disease Control and Prevention used system dynamics simulation modeling to gain a better understanding of diabetes population dynamics and to explore implications for public health strategy. A model was developed to explain the growth of diabetes since 1980 and portray possible futures through 2050. The model simulations suggest characteristic dynamics of the diabetes population, including unintended increases in diabetes prevalence due to diabetes control, the inability of diabetes control efforts alone to reduce diabetes-related deaths in the long term, and significant delays between primary prevention efforts and downstream improvements in diabetes outcomes. PMID:16449587
Understanding diabetes population dynamics through simulation modeling and experimentation.
Jones, Andrew P; Homer, Jack B; Murphy, Dara L; Essien, Joyce D K; Milstein, Bobby; Seville, Donald A
2006-03-01
Health planners in the Division of Diabetes Translation and others from the National Center for Chronic Disease Prevention and Health Promotion of the Centers for Disease Control and Prevention used system dynamics simulation modeling to gain a better understanding of diabetes population dynamics and to explore implications for public health strategy. A model was developed to explain the growth of diabetes since 1980 and portray possible futures through 2050. The model simulations suggest characteristic dynamics of the diabetes population, including unintended increases in diabetes prevalence due to diabetes control, the inability of diabetes control efforts alone to reduce diabetes-related deaths in the long term, and significant delays between primary prevention efforts and downstream improvements in diabetes outcomes.
Quantum Dynamics Simulations for Modeling Experimental Pump-Probe Measurements
NASA Astrophysics Data System (ADS)
Pearson, Brett; Nayyar, Sahil; Liss, Kyle; Weinacht, Thomas
2016-05-01
Time-resolved studies of quantum dynamics have benefited greatly from developments in ultrafast table-top and free electron lasers. Advances in computer software and hardware have lowered the barrier for performing calculations such that relatively simple simulations allow for direct comparison with experimental results. We describe here a set of quantum dynamics calculations in low-dimensional molecular systems. The calculations incorporate coupled electronic-nuclear dynamics, including two interactions with an applied field and nuclear wave packet propagation. The simulations were written and carried out by undergraduates as part of a senior research project, with the specific goal of allowing for detailed interpretation of experimental pump-probe data (in additional to the pedagogical value).
Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.
Markegard, Cade B; Mazaheripour, Amir; Jocson, Jonah-Micah; Burke, Anthony M; Dickson, Mary N; Gorodetsky, Alon A; Nguyen, Hung D
2015-09-03
Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks.
The effect of simulator dynamics on pilot response
NASA Technical Reports Server (NTRS)
Weener, E. F.
1974-01-01
The effects of visual display dynamics on the altitude tracking performance of a subject in a fixed base flight simulator are considered. The subject, flying the linearized longitudinal equations of motion, attempts to maintain the same altitude as two airplanes positioned three hundred feet ahead, as in level formation flying. The horizon together with the two leading aircraft are represented symbolically on a CRT display. The subject's aircraft is disturbed by atmospheric turbulence. The data indicate a relationship between the bandwidth of the display dynamics and the short period characteristics of the simulated airplane. For an airplane with a relatively fast pitch response the presence of altitude display dynamics, with a bandwidth as high as five times the short period natural frequency, causes significant degradation of altitude tracking performance.
4D simulation of explosive eruption dynamics at Vesuvius
NASA Astrophysics Data System (ADS)
Neri, Augusto; Esposti Ongaro, Tomaso; Menconi, Gianluca; De'Michieli Vitturi, Mattia; Cavazzoni, Carlo; Erbacci, Giovanni; Baxter, Peter J.
2007-02-01
We applied a new simulation model, based on multiphase transport laws, to describe the 4D (3D spatial coordinates plus time) dynamics of explosive eruptions. Numerical experiments, carried out on a parallel supercomputer, describe the collapse of the volcanic eruption column and the propagation of pyroclastic density currents (PDCs), for selected medium scale (sub-Plinian) eruptive scenarios at Vesuvius, Italy. Simulations provide crucial insights into the effects of the generation mechanism of the flows - partial collapse vs boiling-over - on their evolution and hazard potential, the unstable dynamics of the fountain, and the influence of Mount Somma on the propagation of PDCs into the circum-Vesuvian area, one of the world's most hazardous volcanic settings. Results also show that it is possible to characterize the volcanic column behavior in terms of percentage of the mass of pyroclasts collapsed to the ground and how this parameter strongly influences the dynamics and hazard of the associated PDCs.
Simulation of Screw Dislocation Motion in Iron by Molecular Dynamics Simulations
Domain, Christophe; Monnet, Ghiath
2005-11-18
Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations.
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
Wei Gu; Garcia, A.E.; Schoenborn, B.P.
1994-12-31
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.
Software life cycle dynamic simulation model: The organizational performance submodel
NASA Technical Reports Server (NTRS)
Tausworthe, Robert C.
1985-01-01
The submodel structure of a software life cycle dynamic simulation model is described. The software process is divided into seven phases, each with product, staff, and funding flows. The model is subdivided into an organizational response submodel, a management submodel, a management influence interface, and a model analyst interface. The concentration here is on the organizational response model, which simulates the performance characteristics of a software development subject to external and internal influences. These influences emanate from two sources: the model analyst interface, which configures the model to simulate the response of an implementing organization subject to its own internal influences, and the management submodel that exerts external dynamic control over the production process. A complete characterization is given of the organizational response submodel in the form of parameterized differential equations governing product, staffing, and funding levels. The parameter values and functions are allocated to the two interfaces.
Numerical simulations of complex fluid-fluid interface dynamics
NASA Astrophysics Data System (ADS)
Krüger, T.; Frijters, S.; Günther, F.; Kaoui, B.; Harting, J.
2013-05-01
Interfaces between two fluids are ubiquitous and of special importance for industrial applications, e.g., stabilisation of emulsions. The dynamics of fluid-fluid interfaces is difficult to study because these interfaces are usually deformable and their shapes are not known a priori. Since experiments do not provide access to all observables of interest, computer simulations pose attractive alternatives to gain insight into the physics of interfaces. In the present article, we restrict ourselves to systems with dimensions comparable to the lateral interface extensions. We provide a critical discussion of three numerical schemes coupled to the lattice Boltzmann method as a solver for the hydrodynamics of the problem: (a) the immersed boundary method for the simulation of vesicles and capsules, the Shan-Chen pseudopotential approach for multi-component fluids in combination with (b) an additional advection-diffusion component for surfactant modelling and (c) a molecular dynamics algorithm for the simulation of nanoparticles acting as emulsifiers.
Linear Optics Simulation of Quantum Non-Markovian Dynamics
Chiuri, Andrea; Greganti, Chiara; Mazzola, Laura; Paternostro, Mauro; Mataloni, Paolo
2012-01-01
The simulation of open quantum dynamics has recently allowed the direct investigation of the features of system-environment interaction and of their consequences on the evolution of a quantum system. Such interaction threatens the quantum properties of the system, spoiling them and causing the phenomenon of decoherence. Sometimes however a coherent exchange of information takes place between system and environment, memory effects arise and the dynamics of the system becomes non-Markovian. Here we report the experimental realisation of a non-Markovian process where system and environment are coupled through a simulated transverse Ising model. By engineering the evolution in a photonic quantum simulator, we demonstrate the role played by system-environment correlations in the emergence of memory effects. PMID:23236588
Linear Optics Simulation of Quantum Non-Markovian Dynamics
NASA Astrophysics Data System (ADS)
Chiuri, Andrea; Greganti, Chiara; Mazzola, Laura; Paternostro, Mauro; Mataloni, Paolo
2012-12-01
The simulation of open quantum dynamics has recently allowed the direct investigation of the features of system-environment interaction and of their consequences on the evolution of a quantum system. Such interaction threatens the quantum properties of the system, spoiling them and causing the phenomenon of decoherence. Sometimes however a coherent exchange of information takes place between system and environment, memory effects arise and the dynamics of the system becomes non-Markovian. Here we report the experimental realisation of a non-Markovian process where system and environment are coupled through a simulated transverse Ising model. By engineering the evolution in a photonic quantum simulator, we demonstrate the role played by system-environment correlations in the emergence of memory effects.
Ultrascale simulations of non-smooth granular dynamics
NASA Astrophysics Data System (ADS)
Preclik, Tobias; Rüde, Ulrich
2015-06-01
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their micro-dynamics and thus to extend the time and length scales that can be simulated. The global multi-contact problem is solved using a non-linear block Gauss-Seidel method that is conforming to the subdomain structure. The parallel algorithms employ a sophisticated protocol between processors that delegate algorithmic tasks such as contact treatment and position integration uniquely and robustly to the processors. Communication overhead is minimized through aggressive message aggregation, leading to excellent strong and weak scaling. The robustness and scalability is assessed on three clusters including two peta-scale supercomputers with up to 458,752 processor cores. The simulations can reach unprecedented resolution of up to ten billion () non-spherical particles and contacts.
Multiscale and multimodel simulation of Bloch-point dynamics
NASA Astrophysics Data System (ADS)
Andreas, Christian; Kákay, Attila; Hertel, Riccardo
2014-04-01
We present simulation results on the structure and dynamics of micromagnetic point singularities with atomistic resolution. This is achieved by embedding an atomistic computational region into a standard micromagnetic algorithm. Several length scales are bridged by means of an adaptive mesh refinement and a seamless coupling between the continuum theory and a Heisenberg formulation for the atomistic region. The code operates on graphical processing units and is able to detect and track the position of strongly inhomogeneous magnetic regions. This enables us to reliably simulate the dynamics of Bloch points, which means that a fundamental class of micromagnetic switching processes can be analyzed with unprecedented accuracy. We test the code by comparing it with established results and present its functionality with the example of a simulated field-driven Bloch-point motion in a soft-magnetic cylinder.
ParaDiS-FEM dislocation dynamics simulation code primer
Tang, M; Hommes, G; Aubry, S; Arsenlis, A
2011-09-27
The ParaDiS code is developed to study bulk systems with periodic boundary conditions. When we try to perform discrete dislocation dynamics simulations for finite systems such as thin films or cylinders, the ParaDiS code must be extended. First, dislocations need to be contained inside the finite simulation box; Second, dislocations inside the finite box experience image stresses due to the free surfaces. We have developed in-house FEM subroutines to couple with the ParaDiS code to deal with free surface related issues in the dislocation dynamics simulations. This primer explains how the coupled code was developed, the main changes from the ParaDiS code, and the functions of the new FEM subroutines.
Molecular dynamics simulation of friction of hydrocarbon thin films
Tamura, Hiroyuki; Yoshida, Muneo; Kusakabe, Kenichi
1999-10-26
Molecular Dynamics (MD) simulations were performed to investigate the dynamic behavior of hydrocarbon molecules under shear conditions. Frictional properties of cyclohexane, n-hexane, and iso-hexane thin films confirmed between two solid surfaces were calculated. Because the affinity of the solid surfaces in these simulations is strong, slippages occurred at inner parts of the confined films, whereas no slippages were observed at the solid boundaries. The hexagonal closest packing structure was observed for the adsorbed cyclohexane molecular layers. The branched methyl groups in the iso-hexane molecules increase the shear stress between the molecular layers. For the n-hexane monolayer, molecules were observed to roll during the sliding simulations. Rolling of the n-hexane molecules decreased the shear stress.
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.
Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A
2016-01-01
Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics. © 2015 The Protein Society.
Information diversity in structure and dynamics of simulated neuronal networks.
Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena
2011-01-01
Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.
Simulating Field-Scale Soil Organic Carbon Dynamics Using EPIC
Causarano, Hector J.; Shaw, Joey N.; Franzluebbers, A. J.; reeves, D. W.; Raper, Randy L.; Balkcom, Kipling S.; Norfleet, M. L.; Izaurralde, R Cesar
2007-07-01
Simulation models integrate our knowledge of soil organic C (SOC) dynamics and are useful tools for evaluating impacts of crop management on soil C sequestration; yet, they require local calibration. Our objectives were to calibrate the Environmental Policy Integrated Climate (EPIC) model, and evaluate its performance for simulating SOC fractions as affected by soil landscape and management. An automated parameter optimization procedure was used to calibrate the model for a site-specific experiment in the Coastal Plain of central Alabama. The ability of EPIC to predict corn (Zea mays L.) and cotton (Gossypium hirsutum L.) yields and SOC dynamics on different soil landscape positions (summit, sideslope and drainageway) during the initial period of conservation tillage adoption (5 years) was evaluated using regression and mean squared deviations. Simulated yield explained 88% of measured yield variation, with greatest disagreement on the sideslope position and highest agreement in the drainageway. Simulations explained approximately 1, 34 and 40% of the total variation in microbial biomass C (MBC), particulate organic C (POC) and total organic C (TOC), respectively. Lowest errors on TOC simulations (0-20 cm) were found on the sideslope and summit. We conclude that the automated parameterization was generally successful, although further work is needed to refine the MBC and POC fractions, and to improve EPIC predictions of SOC dynamics with depth. Overall, EPIC was sensitive to spatial differences in C fractions that resulted from differing soil landscape positions. The model needs additional refinement for accurate simulations of field-scale SOC dynamics affected by short-term management decisions.
Dynamic simulation for distortion image with turbulence atmospheric transmission effects
NASA Astrophysics Data System (ADS)
Du, Huijie; Fei, Jindong; Qing, Duzheng; Zhao, Hongming; Yu, Hong; Cheng, Chen
2013-09-01
The imaging through atmospheric turbulence is an inevitable problem encountered by infrared imaging sensors working in the turbulence atmospheric environment. Before light-rays enter the window of the imaging sensors, the atmospheric turbulence will randomly interfere with the transmission of the light waves came from the objects, causing the distribution of image intensity values on the focal plane to diffuse, the peak value to decrease, the image to get blurred, and the pixels to deviate, and making image identification very difficult. Owing to the fact of the long processing time and that the atmospheric turbulent flow field is unknown and hard to be described by mathematical models, dynamic simulation for distortion Image with turbulence atmospheric transmission effects is much more difficult and challenging in the world. This paper discusses the dynamic simulation for distortion Image of turbulence atmospheric transmission effect. First of all, with the data and the optical transmission model of the turbulence atmospheric, the ray-tracing method is applied to obtain the propagation path of optical ray which propagates through the high-speed turbulent flow field, and then to calculate the OPD from the reference wave to the reconverted wave front and obtain the point spread function (PSF). Secondly, infrared characteristics models of typical scene were established according to the theory of infrared physics and heat conduction, and then the dynamic infrared image was generated by OpenGL. The last step is to obtain the distortion Image with turbulence atmospheric transmission effects .With the data of atmospheric transmission computation, infrared simulation image of every frame was processed according to the theory of image processing and the real-time image simulation, and then the dynamic distortion simulation images with effects of blurring, jitter and shifting were obtained. Above-mentioned simulation method can provide the theoretical bases for recovering
The molecular dynamics simulation of ion-induced ripple growth
NASA Astrophysics Data System (ADS)
Süle, P.; Heinig, K.-H.
2009-11-01
The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength (λ) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths (λ <35 nm) the adatom yield drops hence no surface diffusion takes place which is sufficient for ripple growth. The MD simulations predict that the growth of ripples with λ >35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in λ long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for λ >35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.
Human Sensibility Ergonomics Approach to Vehicle Simulator Based on Dynamics
NASA Astrophysics Data System (ADS)
Son, Kwon; Choi, Kyung-Hyun; Yoon, Ji-Sup
Simulators have been used to evaluate drivers' reactions to various transportation products. Most research, however, has concentrated on their technical performance. This paper considers driver's motion perception on a vehicle simulator through the analysis of human sensibility ergonomics. A sensibility ergonomic method is proposed in order to improve the reliability of vehicle simulators. A simulator in a passenger vehicle consists of three main modules such as vehicle dynamics, virtual environment, and motion representation modules. To evaluate drivers' feedback, human perceptions are categorized into a set verbal expressions collected and investigated to find the most appropriate ones for translation and angular accelerations of the simulator. The cut-off frequency of the washout filter in the representation module is selected as one sensibility factor. Sensibility experiments were carried out to find a correlation between the expressions and the cut-off frequency of the filter. This study suggests a methodology to obtain an ergonomic database that can be applied to the sensibility evaluation of dynamic simulators.
Molecular Dynamics of Dense Fluids: Simulation-Theory Symbiosis
NASA Astrophysics Data System (ADS)
Yip, Sidney
35 years ago Berni J. Alder showed the Boltzmann-Enskog kinetic theory failed to adequately account for the viscosity of fluids near solid density as determined by molecular dynamics simulation. This work, along with other notable simulation findings, provided great stimulus to the statistical mechanical studies of transport phenomena, particularly in dealing with collective effects in the time correlation functions of liquids. An extended theoretical challenge that remains partially resolved at best is the shear viscosity of supercooled liquids. How can one give a unified explanation of the so-called fragile and strong characteristic temperature behavior, with implications for the dynamics of glass transition? In this tribute on the occasion of his 90th birthday symposium, we recount a recent study where simulation, combined with heuristic (transition-state) and first principles (linear response) theories, identifies the molecular mechanisms governing glassy-state relaxation. Such an interplay between simulation and theory is progress from the early days; instead of simulation challenging theory, now simulation and theory complement each other.
Dynamic Simulation of a Wave Rotor Topped Turboshaft Engine
NASA Technical Reports Server (NTRS)
Greendyke, R. B.; Paxson, D. E.; Schobeiri, M. T.
1997-01-01
The dynamic behavior of a wave rotor topped turboshaft engine is examined using a numerical simulation. The simulation utilizes an explicit, one-dimensional, multi-passage, CFD based wave rotor code in combination with an implicit, one-dimensional, component level dynamic engine simulation code. Transient responses to rapid fuel flow rate changes and compressor inlet pressure changes are simulated and compared with those of a similarly sized, untopped, turboshaft engine. Results indicate that the wave rotor topped engine responds in a stable, and rapid manner. Furthermore, during certain transient operations, the wave rotor actually tends to enhance engine stability. In particular, there is no tendency toward surge in the compressor of the wave rotor topped engine during rapid acceleration. In fact, the compressor actually moves slightly away from the surge line during this transient. This behavior is precisely the opposite to that of an untopped engine. The simulation is described. Issues associated with integrating CFD and component level codes are discussed. Results from several transient simulations are presented and discussed.
Research on hyperspectral dynamic scene and image sequence simulation
NASA Astrophysics Data System (ADS)
Sun, Dandan; Gao, Jiaobo; Sun, Kefeng; Hu, Yu; Li, Yu; Xie, Junhu; Zhang, Lei
2016-10-01
This paper presents a simulation method of hyper-spectral dynamic scene and image sequence for hyper-spectral equipment evaluation and target detection algorithm. Because of high spectral resolution, strong band continuity, anti-interference and other advantages, in recent years, hyper-spectral imaging technology has been rapidly developed and is widely used in many areas such as optoelectronic target detection, military defense and remote sensing systems. Digital imaging simulation, as a crucial part of hardware in loop simulation, can be applied to testing and evaluation hyper-spectral imaging equipment with lower development cost and shorter development period. Meanwhile, visual simulation can produce a lot of original image data under various conditions for hyper-spectral image feature extraction and classification algorithm. Based on radiation physic model and material characteristic parameters this paper proposes a generation method of digital scene. By building multiple sensor models under different bands and different bandwidths, hyper-spectral scenes in visible, MWIR, LWIR band, with spectral resolution 0.01μm, 0.05μm and 0.1μm have been simulated in this paper. The final dynamic scenes have high real-time and realistic, with frequency up to 100 HZ. By means of saving all the scene gray data in the same viewpoint image sequence is obtained. The analysis results show whether in the infrared band or the visible band, the grayscale variations of simulated hyper-spectral images are consistent with the theoretical analysis results.
Research on hyperspectral dynamic scene and image sequence simulation
NASA Astrophysics Data System (ADS)
Sun, Dandan; Liu, Fang; Gao, Jiaobo; Sun, Kefeng; Hu, Yu; Li, Yu; Xie, Junhu; Zhang, Lei
2016-10-01
This paper presents a simulation method of hyperspectral dynamic scene and image sequence for hyperspectral equipment evaluation and target detection algorithm. Because of high spectral resolution, strong band continuity, anti-interference and other advantages, in recent years, hyperspectral imaging technology has been rapidly developed and is widely used in many areas such as optoelectronic target detection, military defense and remote sensing systems. Digital imaging simulation, as a crucial part of hardware in loop simulation, can be applied to testing and evaluation hyperspectral imaging equipment with lower development cost and shorter development period. Meanwhile, visual simulation can produce a lot of original image data under various conditions for hyperspectral image feature extraction and classification algorithm. Based on radiation physic model and material characteristic parameters this paper proposes a generation method of digital scene. By building multiple sensor models under different bands and different bandwidths, hyperspectral scenes in visible, MWIR, LWIR band, with spectral resolution 0.01μm, 0.05μm and 0.1μm have been simulated in this paper. The final dynamic scenes have high real-time and realistic, with frequency up to 100 HZ. By means of saving all the scene gray data in the same viewpoint image sequence is obtained. The analysis results show whether in the infrared band or the visible band, the grayscale variations of simulated hyperspectral images are consistent with the theoretical analysis results.
Fast Simulation of Dynamic Ultrasound Images Using the GPU.
Storve, Sigurd; Torp, Hans
2017-10-01
Simulated ultrasound data is a valuable tool for development and validation of quantitative image analysis methods in echocardiography. Unfortunately, simulation time can become prohibitive for phantoms consisting of a large number of point scatterers. The COLE algorithm by Gao et al. is a fast convolution-based simulator that trades simulation accuracy for improved speed. We present highly efficient parallelized CPU and GPU implementations of the COLE algorithm with an emphasis on dynamic simulations involving moving point scatterers. We argue that it is crucial to minimize the amount of data transfers from the CPU to achieve good performance on the GPU. We achieve this by storing the complete trajectories of the dynamic point scatterers as spline curves in the GPU memory. This leads to good efficiency when simulating sequences consisting of a large number of frames, such as B-mode and tissue Doppler data for a full cardiac cycle. In addition, we propose a phase-based subsample delay technique that efficiently eliminates flickering artifacts seen in B-mode sequences when COLE is used without enough temporal oversampling. To assess the performance, we used a laptop computer and a desktop computer, each equipped with a multicore Intel CPU and an NVIDIA GPU. Running the simulator on a high-end TITAN X GPU, we observed two orders of magnitude speedup compared to the parallel CPU version, three orders of magnitude speedup compared to simulation times reported by Gao et al. in their paper on COLE, and a speedup of 27000 times compared to the multithreaded version of Field II, using numbers reported in a paper by Jensen. We hope that by releasing the simulator as an open-source project we will encourage its use and further development.
The Fermi-Pasta-Ulam problem: Simulation and modern dynamics
Weissert, T.P.
1992-01-01
In 1952, Enrico Fermi, John Pasta and Stanislaw Ulam (FPU) simulated the loaded string model, perturbed with small, nonlinear interaction terms. Because Poincare's theorem guarantees the non-existence of a complete set of integrals for three-body problem, they expected to see the diffusion of energy from its single-mode initial condition to all other modes of the string. But for every combination of initial conditions, the energy remained bounded within the lowest few modes. No theoretical explanation existed for this failure of the underlying hypothesis that erogidicity follows from the lack of a complete set of integrals of the motion in a Hamiltonian model. The author traces the history of this problem from the FPU simulation to the point that a consensus was reached concerning its solution twenty years later. During this period, the simulation of nonlinearly-perturbed integral models became the methodology for a new era in dynamics. Through the use of simulation, dynamicists discovered deterministic chaos, in which the exponential separation of pair orbits generate randomness in deterministic macroscopic systems, and a new kind of structure-related to the KAM theorem-that provides limited order in the absence of analytic integrals of the motions. The author maps the set of conceptually-related journal articles into a chronological inference topology that tracks the understanding of this problem of dynamics. Simulating non-integrable models on a digital computer requires the discretization of time and space. These approximations affect what the simulation can reveal about the model, and the model about reality. Simulations play the role of experiments on mathematical models. A discussion is presented of the issues that emerge with the use of simulation as a heuristic device and the groundwork is laid for an epistemology of simulation.
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.
Erban, Radek
2016-02-01
Molecular dynamics (MD) simulations of ions (K(+), Na(+), Ca(2+) 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.
Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams
NASA Astrophysics Data System (ADS)
Ohya, Kaoru
2017-03-01
The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.
Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control
Zhang, Xingwu; Chen, Xuefeng; You, Shangqin; He, Zhengjia; Li, Bing
2012-01-01
In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC) is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results. PMID:22666072
The fractional-nonlinear robotic manipulator: Modeling and dynamic simulations
NASA Astrophysics Data System (ADS)
David, S. A.; Balthazar, J. M.; Julio, B. H. S.; Oliveira, C.
2012-11-01
In this paper, we applied the Riemann-Liouville approach and the fractional Euler-Lagrange equations in order to obtain the fractional-order nonlinear dynamics equations of a two link robotic manipulator. The aformentioned equations have been simulated for several cases involving: integer and non-integer order analysis, with and without external forcing acting and some different initial conditions. The fractional nonlinear governing equations of motion are coupled and the time evolution of the angular positions and the phase diagrams have been plotted to visualize the effect of fractional order approach. The new contribution of this work arises from the fact that the dynamics equations of a two link robotic manipulator have been modeled with the fractional Euler-Lagrange dynamics approach. The results reveal that the fractional-nonlinear robotic manipulator can exhibit different and curious behavior from those obtained with the standard dynamical system and can be useful for a better understanding and control of such nonlinear systems.
Digital dynamics and the simulation of magnetic systems
NASA Astrophysics Data System (ADS)
Choi, M. Y.; Huberman, B. A.
1983-09-01
This paper investigates the problems associated with simulating many-body systems with finite-state machines such as computers. It is shown that the digital (discrete) character of time brings in features which are not encountered in the usual analytical studies using continuous time. This is illustrated with a thorough study of the dynamics of simple magnetic systems with competing interactions. Whereas continuous dynamics, as derived from the usual master-equation approach, yields asymptotic behavior which is time independent, dynamics in digital time can lead to complex behavior characterized by the existence of multiple basins of attraction, broken symmetries, oscillations, and chaos. These results might provide a dynamical explanation for the breakdown of ergodicity which has been reported in Monte Carlo studies of spin-glasses.
Generic solar photovoltaic system dynamic simulation model specification
Ellis, Abraham; Behnke, Michael Robert; Elliott, Ryan Thomas
2013-10-01
This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intended to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.
Noe, F; Diadone, Isabella; Lollmann, Marc; Sauer, Marcus; Chondera, John D; Smith, Jeremy C
2011-01-01
There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is dynamical fingerprints which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.
Lin, Yuqing; Pan, Dingyi; Li, Jiaming; Zhang, Lingxin; Shao, Xueming
2017-03-28
The Berendsen barostat from molecular dynamics simulation is applied in both standard dissipative particle dynamics (DPD) and many-body dissipative particle dynamics (MDPD) simulations. The original Berendsen barostat works well in (M)DPD simulation of a single-component system under constant pressure condition and in nonequilibrium dynamic processes. The partial Berendsen barostat is proposed for multi-component system simulation with (M)DPD. The displacement rescaling process of the Berendsen barostat is only applied on the particles outside the center region, acting as a pressure "boundary condition." The center part forms the free zone, in which the interface shape and nonequilibrium dynamic behavior between different phases can be captured properly. An immiscible bubble in the second fluid under constant pressure condition is studied, and the oscillation of the bubble radius and fluctuation of systempressure can be obtained by the current barostat. Preliminary models for bubble growing and collapsing under square pressure wave and bubble oscillation under harmonic pressure wave are also reported in the current simulation. It shows that the partial Berendsen barostat is suitable for the modeling of nonequilibrium process of single or few droplets/bubbles in multi-component systems.
An alamethicin channel in a lipid bilayer: molecular dynamics simulations.
Tieleman, D P; Berendsen, H J; Sansom, M S
1999-01-01
We present the results of 2-ns molecular dynamics (MD) simulations of a hexameric bundle of Alm helices in a 1-palmitoyl-2-oleoylphosphatidylcholine bilayer. These simulations explore the dynamic properties of a model of a helix bundle channel in a complete phospholipid bilayer in an aqueous environment. We explore the stability and conformational dynamics of the bundle in a phospholipid bilayer. We also investigate the effect on bundle stability of the ionization state of the ring of Glu18 side chains. If all of the Glu18 side chains are ionised, the bundle is unstable; if none of the Glu18 side chains are ionized, the bundle is stable. pKA calculations suggest that either zero or one ionized Glu18 is present at neutral pH, correlating with the stable form of the helix bundle. The structural and dynamic properties of water in this model channel were examined. As in earlier in vacuo simulations (Breed et al., 1996 .Biophys. J. 70:1643-1661), the dipole moments of water molecules within the pore were aligned antiparallel to the helix dipoles. This contributes to the stability of the helix bundle. PMID:10096876
Dynamic simulation of structural phase transitions in magnetic iron
NASA Astrophysics Data System (ADS)
Ma, Pui-Wai; Dudarev, S. L.; Wróbel, Jan S.
2017-09-01
The occurrence of bcc-fcc (α -γ ) and fcc-bcc (γ -δ ) phase transitions in magnetic iron stems from the interplay between magnetic excitations and lattice vibrations. However, this fact has never been confirmed by a direct dynamic simulation, treating noncollinear magnetic fluctuations and dynamics of atoms, and their coupling at a finite temperature. Starting from a large set of data generated by ab initio simulations, we derive noncollinear magnetic many-body potentials for bcc and fcc iron, describing fluctuations of atomic coordinates in the vicinity of near perfect lattice positions. We then use spin-lattice dynamic simulations to evaluate the difference between the free energies of bcc and fcc phases, assessing their relative stability within a unified dynamic picture. We find two intersections between the bcc and fcc free energy curves, which correspond to the α -γ bcc-fcc and γ -δ fcc-bcc phase transitions. The maximum bcc-fcc free energy difference over the temperature interval between the two phase transitions is 2 meV per atom, in agreement with other experimental and theoretical estimates.
Climate Simulations with an Isentropic Finite Volume Dynamical Core
Chen, Chih-Chieh; Rasch, Philip J.
2012-04-15
This paper discusses the impact of changing the vertical coordinate from a hybrid pressure to a hybrid-isentropic coordinate within the finite volume dynamical core of the Community Atmosphere Model (CAM). Results from a 20-year climate simulation using the new model coordinate configuration are compared to control simulations produced by the Eulerian spectral and FV dynamical cores of CAM which both use a pressure-based ({sigma}-p) coordinate. The same physical parameterization package is employed in all three dynamical cores. The isentropic modeling framework significantly alters the simulated climatology and has several desirable features. The revised model produces a better representation of heat transport processes in the atmosphere leading to much improved atmospheric temperatures. We show that the isentropic model is very effective in reducing the long standing cold temperature bias in the upper troposphere and lower stratosphere, a deficiency shared among most climate models. The warmer upper troposphere and stratosphere seen in the isentropic model reduces the global coverage of high clouds which is in better agreement with observations. The isentropic model also shows improvements in the simulated wintertime mean sea-level pressure field in the northern hemisphere.
Structural dynamics test simulation and optimization for aerospace components
Klenke, S.E.; Baca, T.J.
1996-06-01
This paper initially describes an innovative approach to product realization called Knowledge Based Testing (KBT). This research program integrates test simulation and optimization software, rapid fabrication techniques and computational model validation to support a new experimentally-based design concept. This design concept implements well defined tests earlier in the design cycle enabling the realization of highly reliable aerospace components. A test simulation and optimization software environment provides engineers with an essential tool needed to support this KBT approach. This software environment, called the Virtual Environment for Test Optimization (VETO), integrates analysis and test based models to support optimal structural dynamic test design. A goal in developing this software tool is to provide test and analysis engineers with a capability of mathematically simulating the complete structural dynamics test environment within a computer. A developed computational model of an aerospace component can be combined with analytical and/or experimentally derived models of typical structural dynamic test instrumentation within the VETO to determine an optimal test design. The VETO provides the user with a unique analysis and visualization environment to evaluate new and existing test methods in addition to simulating specific experiments designed to maximize test based information needed to validate computational models. The results of both a modal and a vibration test design are presented for a reentry vehicle and a space truss structure.
Ab-Initio Molecular Dynamics Simulation of Graphene Sheet
NASA Astrophysics Data System (ADS)
Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.
2017-01-01
The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.
NETIMIS: Dynamic Simulation of Health Economics Outcomes Using Big Data.
Johnson, Owen A; Hall, Peter S; Hulme, Claire
2016-02-01
Many healthcare organizations are now making good use of electronic health record (EHR) systems to record clinical information about their patients and the details of their healthcare. Electronic data in EHRs is generated by people engaged in complex processes within complex environments, and their human input, albeit shaped by computer systems, is compromised by many human factors. These data are potentially valuable to health economists and outcomes researchers but are sufficiently large and complex enough to be considered part of the new frontier of 'big data'. This paper describes emerging methods that draw together data mining, process modelling, activity-based costing and dynamic simulation models. Our research infrastructure includes safe links to Leeds hospital's EHRs with 3 million secondary and tertiary care patients. We created a multidisciplinary team of health economists, clinical specialists, and data and computer scientists, and developed a dynamic simulation tool called NETIMIS (Network Tools for Intervention Modelling with Intelligent Simulation; http://www.netimis.com ) suitable for visualization of both human-designed and data-mined processes which can then be used for 'what-if' analysis by stakeholders interested in costing, designing and evaluating healthcare interventions. We present two examples of model development to illustrate how dynamic simulation can be informed by big data from an EHR. We found the tool provided a focal point for multidisciplinary team work to help them iteratively and collaboratively 'deep dive' into big data.
Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.
Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao
2017-08-24
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Copyright © 2017. Published by Elsevier Ltd.
Simulation of plume dynamics by the Lattice Boltzmann Method
NASA Astrophysics Data System (ADS)
Mora, Peter; Yuen, David A.
2017-09-01
The Lattice Boltzmann Method (LBM) is a semi-microscopic method to simulate fluid mechanics by modelling distributions of particles moving and colliding on a lattice. We present 2-D simulations using the LBM of a fluid in a rectangular box being heated from below, and cooled from above, with a Rayleigh of Ra = 108, similar to current estimates of the Earth's mantle, and a Prandtl number of 5000. At this Prandtl number, the flow is found to be in the non-inertial regime where the inertial terms denoted I ≪ 1. Hence, the simulations presented lie within the regime of relevance for geodynamical problems. We obtain narrow upwelling plumes with mushroom heads and chutes of downwelling fluid as expected of a flow in the non-inertial regime. The method developed demonstrates that the LBM has great potential for simulating thermal convection and plume dynamics relevant to geodynamics, albeit with some limitations.
Molecular dynamics simulation of amplitude modulation atomic force microscopy.
Hu, Xiaoli; Egberts, Philip; Dong, Yalin; Martini, Ashlie
2015-06-12
Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip-substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip-sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement.
Molecular Dynamics Simulations of Carbon Nanotubes in Water
NASA Technical Reports Server (NTRS)
Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.
2000-01-01
We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.
Molecular Dynamics Simulations of Carbon Nanotubes in Water
NASA Technical Reports Server (NTRS)
Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.
2000-01-01
We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.
Molecular-dynamics simulation of a ceramide bilayer
NASA Astrophysics Data System (ADS)
Pandit, Sagar A.; Scott, H. Larry
2006-01-01
Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368K (5° above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall "dipole potential," when ceramide is compared to sphingomyelin.
Survey of Dynamic Simulation Programs for Nuclear Fuel Reprocessing
Troy J. Tranter; Daryl R. Haefner
2008-06-01
The absence of any industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other industries. Modeling programs to simulate the dynamic behavior of nuclear fuel separations and processing were originally developed to support the US government’s mission of weapons production and defense fuel recovery. Consequently there has been little effort is the US devoted towards improving this specific process simulation capability during the last two or three decades. More recent work has been focused on elucidating chemical thermodynamics and developing better models of predicting equilibrium in actinide solvent extraction systems. These equilibrium models have been used to augment flowsheet development and testing primarily at laboratory scales. The development of more robust and complete process models has not kept pace with the vast improvements in computational power and user interface and is significantly behind simulation capability in other chemical processing and separation fields.
Advanced beam-dynamics simulation tools for RIA.
Garnett, R. W.; Wangler, T. P.; Billen, J. H.; Qiang, J.; Ryne, R.; Crandall, K. R.; Ostroumov, P.; York, R.; Zhao, Q.; Physics; LANL; LBNL; Tech Source; Michigan State Univ.
2005-01-01
We are developing multi-particle beam-dynamics simulation codes for RIA driver-linac simulations extending from the low-energy beam transport (LEBT) line to the end of the linac. These codes run on the NERSC parallel supercomputing platforms at LBNL, which allow us to run simulations with large numbers of macroparticles. The codes have the physics capabilities needed for RIA, including transport and acceleration of multiple-charge-state beams, beam-line elements such as high-voltage platforms within the linac, interdigital accelerating structures, charge-stripper foils, and capabilities for handling the effects of machine errors and other off-normal conditions. This year will mark the end of our project. In this paper we present the status of the work, describe some recent additions to the codes, and show some preliminary simulation results.
Lattice Boltzmann simulations of multiple-droplet interaction dynamics
NASA Astrophysics Data System (ADS)
Zhou, Wenchao; Loney, Drew; Fedorov, Andrei G.; Degertekin, F. Levent; Rosen, David W.
2014-03-01
A lattice Boltzmann (LB) formulation, which is consistent with the phase-field model for two-phase incompressible fluid, is proposed to model the interface dynamics of droplet impingement. The interparticle force is derived by comparing the macroscopic transport equations recovered from LB equations with the governing equations of the continuous phase-field model. The inconsistency between the existing LB implementations and the phase-field model in calculating the relaxation time at the phase interface is identified and an approximation is proposed to ensure the consistency with the phase-field model. It is also shown that the commonly used equilibrium velocity boundary for the binary fluid LB scheme does not conserve momentum at the wall boundary and a modified scheme is developed to ensure the momentum conservation at the boundary. In addition, a geometric formulation of the wetting boundary condition is proposed to replace the popular surface energy formulation and results show that the geometric approach enforces the prescribed contact angle better than the surface energy formulation in both static and dynamic wetting. The proposed LB formulation is applied to simulating droplet impingement dynamics in three dimensions and results are compared to those obtained with the continuous phase-field model, the LB simulations reported in the literature, and experimental data from the literature. The results show that the proposed LB simulation approach yields not only a significant speed improvement over the phase-field model in simulating droplet impingement dynamics on a submillimeter length scale, but also better accuracy than both the phase-field model and the previously reported LB techniques when compared to experimental data. Upon validation, the proposed LB modeling methodology is applied to the study of multiple-droplet impingement and interactions in three dimensions, which demonstrates its powerful capability of simulating extremely complex interface
Simulating soil phosphorus dynamics for a phosphorus loss quantification tool.
Vadas, Peter A; Joern, Brad C; Moore, Philip A
2012-01-01
Pollution of fresh waters by agricultural phosphorus (P) is a water quality concern. Because soils can contribute significantly to P loss in runoff, it is important to assess how management affects soil P status over time, which is often done with models. Our objective was to describe and validate soil P dynamics in the Annual P Loss Estimator (APLE) model. APLE is a user-friendly spreadsheet model that simulates P loss in runoff and soil P dynamics over 10 yr for a given set of runoff, erosion, and management conditions. For soil P dynamics, APLE simulates two layers in the topsoil, each with three inorganic P pools and one organic P pool. It simulates P additions to soil from manure and fertilizer, distribution among pools, mixing between layers due to tillage and bioturbation, leaching between and out of layers, crop P removal, and loss by surface runoff and erosion. We used soil P data from 25 published studies to validate APLE's soil P processes. Our results show that APLE reliably simulated soil P dynamics for a wide range of soil properties, soil depths, P application sources and rates, durations, soil P contents, and management practices. We validated APLE specifically for situations where soil P was increasing from excessive P inputs, where soil P was decreasing due to greater outputs than inputs, and where soil P stratification occurred in no-till and pasture soils. Successful simulations demonstrate APLE's potential to be applied to major management scenarios related to soil P loss in runoff and erosion. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.
2016-04-01
AMOS) , ISSN-Print 2199-1928 Angewandte Mathematik und Optimierung Schriftenreihe (AMOS) , ISSN- Internet 2199-1936 REPORT DOCUMENTATION PAGE I Form...Konflikte: Gesch ichte, D ynamik, Simulation und Analyse (Armed Conflict: History , Dynamics, Simulation and Analysis) 6 . AUTHOR(S) Armin Fi.igenschuh...Machine assisted translation. 14. SUBJECT TERMS UN1BW , Gennan, anned conflict, history , simu lation , wargami ng, games 17. S ECURITY CLASS IFI CATION
A reliable simulator for dynamic flux balance analysis.
Höffner, K; Harwood, S M; Barton, P I
2013-03-01
Dynamic flux balance analysis (DFBA) provides a platform for detailed design, control and optimization of biochemical process technologies. It is a promising modeling framework that combines genome-scale metabolic network analysis with dynamic simulation of the extracellular environment. Dynamic flux balance analysis assumes that the intracellular species concentrations are in equilibrium with the extracellular environment. The resulting underdetermined stoichiometric model is solved under the assumption of a biochemical objective such as growth rate maximization. The model of the metabolism is coupled with the dynamic mass balance equations of the extracellular environment via expressions for the rates of substrate uptake and product excretion, which imposes additional constraints on the linear program (LP) defined by growth rate maximization of the metabolism. The linear program is embedded into the dynamic model of the bioreactor, and together with the additional constraints this provides an accurate model of the substrate consumption, product secretion, and biomass production during operation. A DFBA model consists of a system of ordinary differential equations for which the evaluation of the right-hand side requires not only function evaluations, but also the solution of one or more linear programs. The numerical tool presented here accurately and efficiently simulates large-scale dynamic flux balance models. The main advantages that this approach has over existing implementation are that the integration scheme has a variable step size, that the linear program only has to be solved when qualitative changes in the optimal flux distribution of the metabolic network occur, and that it can reliably simulate behavior near the boundary of the domain where the model is defined. This is illustrated through large-scale examples taken from the literature.
Spectral Element Simulations of Rupture Dynamics along kinked faults
NASA Astrophysics Data System (ADS)
Vilotte, J.; Festa, G.; Madariaga, R.
2005-12-01
Numerical simulation of earthquake source dynamics provides key elements for ground-motion prediction and insights into the physics of dynamic rupture propagation. Faulting is controlled by non-linear frictional interactions and damage within the fault zone. Important features of the earthquakes dynamics, such as rupture velocity, arrest phase and high-frequency radiation are believed to be strongly influenced by the geometry of the faults (kinks, jogs and forks). Data analysis as well as kinematic inversions have pointed out potential links between super-shear and geometry, as in the case of the Denali and Izmit earthquakes. Finally, recent laboratory experiments of sub- and super-shear rupture propagation along kink interfaces have shed new lights on these phenomena. We present here spectral element simulations of the dynamic rupture propagation along kinked and curved fault interfaces, a problem that has been experimentally investigated by Rousseau and Rosakis (2003). Depending on the state of the initial stress, we numerically analyze the mechanics of the dynamical fault branching for sub- and super-shear rupture propagation. Special interest is devoted to source directivity effects and high frequency generation related to the branching process. Implications for strong motion analysis will be discussed. This work was supported by the SPICE - Research and Training project
Trotter-based simulation of quantum-classical dynamics.
Kernan, Dónal Mac; Ciccotti, Giovanni; Kapral, Raymond
2008-01-17
Quantum rate processes in condensed phase systems are often computed by combining quantum and classical descriptions of the dynamics. An algorithm for simulating the quantum-classical Liouville equation, which describes the dynamics of a quantum subsystem coupled to a classical bath, is presented in this paper. The algorithm is based on a Trotter decomposition of the quantum-classical propagator, in conjunction with Monte Carlo sampling of quantum transitions, to yield a surface-hopping representation of the dynamics. An expression for the nonadiabatic propagator that is responsible for quantum transitions and associated bath momentum changes is derived in a form that is convenient for Monte Carlo sampling and exactly conserves the total energy of the system in individual trajectories. The expectation values of operators or quantum correlation functions can be evaluated by initial sampling of quantum states and use of quantum-classical Liouville dynamics for the time evolution. The algorithm is tested by calculations on the spin-boson model, for which exact quantum results are available, and is shown to reproduce the exact results for stronger nonadiabatic coupling and much longer times using fewer trajectories than other schemes for simulating quantum-classical Liouville dynamics.
Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Lu, Yan; Salsbury, Freddie R.
2015-01-01
ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.
Multi-Scale Dynamics, Control, and Simulation of Granular Spacecraft
NASA Technical Reports Server (NTRS)
Quadrelli, Marco B.; Basinger, Scott; Swartzlander, Grover
2013-01-01
In this paper, we present some ideas regarding the modeling, dynamics and control aspects of granular spacecraft. Granular spacecraft are complex multibody systems composed of a spatially disordered distribution of a large number of elements, for instance a cloud of grains in orbit. An example of application is a spaceborne observatory for exoplanet imaging, where the primary aperture is a cloud instead of a monolithic aperture. A model is proposed of a multi-scale dynamics of the grains and cloud in orbit, as well as a control approach for cloud shape maintenance and alignment, and preliminary simulation studies are carried out for the representative imaging system.
Nonholonomic Hamiltonian method for molecular dynamics simulations of reacting shocks
NASA Astrophysics Data System (ADS)
Bass, Joseph; Fahrenthold, Eric P.
2017-01-01
Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general the potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new nonholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations, and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted parameters.
3D vesicle dynamics simulations with a linearly triangulated surface
NASA Astrophysics Data System (ADS)
Boedec, G.; Leonetti, M.; Jaeger, M.
2011-02-01
Simulations of biomembranes have gained an increasing interest in the past years. Specificities of these membranes propose new challenges for the numerics. In particular, vesicle dynamics are governed by bending forces as well as a surface incompressibility constraint. A method to compute the bending force density resultant onto piecewise linearly triangulated surface meshes is described. This method is coupled with a boundary element method solver for inner and outer fluids, to compute vesicle dynamics under external flows. The surface incompressibility constraint is satisfied by the construction of a projection operator.
Molecular dynamical simulations of melting behaviors of metal clusters
Hamid, Ilyar; Fang, Meng; Duan, Haiming
2015-04-15
The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures.
Dynamic load balancing for simulations of biological aging
Meisgen, F.
1997-06-01
The efficient usage of parallel computers and workstation clusters for biologically motivated simulations depends first of all on a dynamic redistribution of the workload. For the development of a parallel algorithm for the Perma model of aging we have used a dynamic load balancing library, called PLB. It turns out that PLB manages a nearly balanced load situation during runtime taking only a low communication overhead. We compare different architectures like parallel computers and nondedicated heterogeneous networks, and give some results for large populations.
Investigation of Ribosomes Using Molecular Dynamics Simulation Methods.
Makarov, G I; Makarova, T M; Sumbatyan, N V; Bogdanov, A A
2016-12-01
The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.
Beam Dynamics Design and Simulation in Ion Linear Accelerators (
Ostroumov, Peter N.; Asseev, Vladislav N.; Mustapha, and Brahim
2006-08-01
Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modern ion linear accelerators and beam transport systems.
Multi-Scale Dynamics, Control, and Simulation of Granular Spacecraft
NASA Technical Reports Server (NTRS)
Quadrelli, Marco B.; Basinger, Scott; Swartzlander, Grover
2013-01-01
In this paper, we present some ideas regarding the modeling, dynamics and control aspects of granular spacecraft. Granular spacecraft are complex multibody systems composed of a spatially disordered distribution of a large number of elements, for instance a cloud of grains in orbit. An example of application is a spaceborne observatory for exoplanet imaging, where the primary aperture is a cloud instead of a monolithic aperture. A model is proposed of a multi-scale dynamics of the grains and cloud in orbit, as well as a control approach for cloud shape maintenance and alignment, and preliminary simulation studies are carried out for the representative imaging system.
Nonlinear dynamics of turbulence driven magnetic islands. II. Numerical simulations
NASA Astrophysics Data System (ADS)
Agullo, O.; Muraglia, M.; Benkadda, S.; Poyé, A.; Dubuit, N.; Garbet, X.; Sen, A.
2017-04-01
The nonlinear dynamics of a turbulence driven magnetic island (TDMI) is investigated numerically in a reduced magnetohydrodynamic fluid model. The significance of identifying a characteristic signature of a TDMI for its experimental observation is discussed. The principal focus of our simulations is on the nature of the pressure profile flattening inside a TDMI, and we show that, in agreement with analytical predictions, a partial flattening occurs when the island size exceeds a critical value that is a function of the small scale interchange dynamics. We also present a model and test it numerically, which links explicitly the interchange turbulence and the island pressure flattening.
Petascale Molecular Dynamics Simulations of Polymers and Liquid Crystals
NASA Astrophysics Data System (ADS)
Nguyen, Trung Dac; Carrillo, Jan-Michael; Brown, W. Michael
2014-03-01
The availability of faster and larger supercomputers and more efficient parallel algorithms now enable us to perform unprecedented simulations approaching experimental scales. Here we present two examples of our latest large-scale molecular dynamics simulations using the Titan supercomputer in the Oak Ridge Leadership Computing Facility (OLCF). In the first study, we address the rupture origin of liquid crystal thin films wetting a solid substrate. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation. Importantly, we found evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. In the second study, we used coarse-grained molecular dynamics to simulate the thermal annealing of poly(3-hexylthiophene) (P3HT) and Phenyl-C61-butyric acid methyl ester (PCBM) blends in the presence of a silicon substrate found in organic solar cells. Our simulations show different phase segregated morphologies dependent on the P3HT chain length and PCBM volume fraction in the blend. Furthermore, the ternary blend of short and long P3HT chains with PCBM affects the vertical phase segregation of PCBM decreasing its concentration in the vicinity of the substrate. U.S. DOE Contract No. DE-AC05-00OR22725.
Quantum dynamical simulations of local field enhancement in metal nanoparticles.
Negre, Christian F A; Perassi, Eduardo M; Coronado, Eduardo A; Sánchez, Cristián G
2013-03-27
Field enhancements (Γ) around small Ag nanoparticles (NPs) are calculated using a quantum dynamical simulation formalism and the results are compared with electrodynamic simulations using the discrete dipole approximation (DDA) in order to address the important issue of the intrinsic atomistic structure of NPs. Quite remarkably, in both quantum and classical approaches the highest values of Γ are located in the same regions around single NPs. However, by introducing a complete atomistic description of the metallic NPs in optical simulations, a different pattern of the Γ distribution is obtained. Knowing the correct pattern of the Γ distribution around NPs is crucial for understanding the spectroscopic features of molecules inside hot spots. The enhancement produced by surface plasmon coupling is studied by using both approaches in NP dimers for different inter-particle distances. The results show that the trend of the variation of Γ versus inter-particle distance is different for classical and quantum simulations. This difference is explained in terms of a charge transfer mechanism that cannot be obtained with classical electrodynamics. Finally, time dependent distribution of the enhancement factor is simulated by introducing a time dependent field perturbation into the Hamiltonian, allowing an assessment of the localized surface plasmon resonance quantum dynamics.
Process Modeling and Dynamic Simulation for EAST Helium Refrigerator
NASA Astrophysics Data System (ADS)
Lu, Xiaofei; Fu, Peng; Zhuang, Ming; Qiu, Lilong; Hu, Liangbing
2016-06-01
In this paper, the process modeling and dynamic simulation for the EAST helium refrigerator has been completed. The cryogenic process model is described and the main components are customized in detail. The process model is controlled by the PLC simulator, and the realtime communication between the process model and the controllers is achieved by a customized interface. Validation of the process model has been confirmed based on EAST experimental data during the cool down process of 300-80 K. Simulation results indicate that this process simulator is able to reproduce dynamic behaviors of the EAST helium refrigerator very well for the operation of long pulsed plasma discharge. The cryogenic process simulator based on control architecture is available for operation optimization and control design of EAST cryogenic systems to cope with the long pulsed heat loads in the future. supported by National Natural Science Foundation of China (No. 51306195) and Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, CAS (No. CRYO201408)
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2015-01-28
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.
Petsev, Nikolai D; Leal, L Gary; Shell, M Scott
2015-01-28
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
Methods for simulating the dynamics of complex biological processes.
Schilstra, Maria J; Martin, Stephen R; Keating, Sarah M
2008-01-01
In this chapter, we provide the basic information required to understand the central concepts in the modeling and simulation of complex biochemical processes. We underline the fact that most biochemical processes involve sequences of interactions between distinct entities (molecules, molecular assemblies), and also stress that models must adhere to the laws of thermodynamics. Therefore, we discuss the principles of mass-action reaction kinetics, the dynamics of equilibrium and steady state, and enzyme kinetics, and explain how to assess transition probabilities and reactant lifetime distributions for first-order reactions. Stochastic simulation of reaction systems in well-stirred containers is introduced using a relatively simple, phenomenological model of microtubule dynamic instability in vitro. We demonstrate that deterministic simulation [by numerical integration of coupled ordinary differential equations (ODE)] produces trajectories that would be observed if the results of many rounds of stochastic simulation of the same system were averaged. In Section V, we highlight several practical issues with regard to the assessment of parameter values. We draw some attention to the development of a standard format for model storage and exchange, and provide a list of selected software tools that may facilitate the model building process, and can be used to simulate the modeled systems.
Dislocation dynamics simulations of plasticity at small scales
Zhou, Caizhi
2010-01-01
As metallic structures and devices are being created on a dimension comparable to the length scales of the underlying dislocation microstructures, the mechanical properties of them change drastically. Since such small structures are increasingly common in modern technologies, there is an emergent need to understand the critical roles of elasticity, plasticity, and fracture in small structures. Dislocation dynamics (DD) simulations, in which the dislocations are the simulated entities, offer a way to extend length scales beyond those of atomistic simulations and the results from DD simulations can be directly compared with the micromechanical tests. The primary objective of this research is to use 3-D DD simulations to study the plastic deformation of nano- and micro-scale materials and understand the correlation between dislocation motion, interactions and the mechanical response. Specifically, to identify what critical events (i.e., dislocation multiplication, cross-slip, storage, nucleation, junction and dipole formation, pinning etc.) determine the deformation response and how these change from bulk behavior as the system decreases in size and correlate and improve our current knowledge of bulk plasticity with the knowledge gained from the direct observations of small-scale plasticity. Our simulation results on single crystal micropillars and polycrystalline thin films can march the experiment results well and capture the essential features in small-scale plasticity. Furthermore, several simple and accurate models have been developed following our simulation results and can reasonably predict the plastic behavior of small scale materials.
Molecular dynamics simulation of dipalmitoylphosphatidylserine bilayer with Na+ counterions.
Pandit, Sagar A; Berkowitz, Max L
2002-01-01
We performed a molecular dynamics simulation of dipalmitoylphosphatidylserine (DPPS) bilayer with Na+ counterions. We found that hydrogen bonding between the NH group and the phosphate group leads to a reduction in the area per headgroup when compared to the area in dipalmitoylphosphatidylcholine bilayer. The Na+ ions bind to the oxygen in the carboxyl group of serine, thus giving rise to a dipolar bilayer similar to dipalmitoylphosphatidylethanolamine bilayer. The results of the simulation show that counterions play a crucial role in determining the structural and electrostatic properties of DPPS bilayer. PMID:11916841
Numerical simulation of vehicle dynamics for virtual reality
NASA Astrophysics Data System (ADS)
Belyaev, Sergey Y.; Aranov, Vladislav Y.
2001-02-01
The paper is devoted to snowmobile and car dynamics simulation in real time mode. This task is typical for trainers and computer games, where a model of moving vehicle is handled interactively. The challenge of real time is to recalculate values of a moving model on each frame, that is, at least 30 times per second and take for this not more than 5% processor time on an ordinary personal computer. We describe the minimal mathematical model and numerical method sufficient to simulate a snowmobile quite realistically. The approach proposed may be applied for various vehicle models.
Numerical simulation of vehicle dynamics for virtual reality
NASA Astrophysics Data System (ADS)
Belyaev, Sergey Y.; Aranov, Vladislav Y.
2000-02-01
The paper is devoted to snowmobile and car dynamics simulation in real time mode. This task is typical for trainers and computer games, where a model of moving vehicle is handled interactively. The challenge of real time is to recalculate values of a moving model on each frame, that is, at least 30 times per second and take for this not more than 5% processor time on an ordinary personal computer. We describe the minimal mathematical model and numerical method sufficient to simulate a snowmobile quite realistically. The approach proposed may be applied for various vehicle models.
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.
Superionicity in Na3 PO4 : A molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Yin, Wei-Guo; Liu, Jianjun; Duan, Chun-Gang; Mei, W. N.; Smith, R. W.; Hardy, J. R.
2004-08-01
Fast ionic conduction in solid Na3PO4 is studied by use of molecular dynamics simulation based on the modified Lu -Hardy approach. We obtain reasonable agreement with experiment for the structural transition and diffusion of the sodium ions. All the sodium ions are found to contribute comparably to the high ionic conductivity. The results of the simulation are discussed in terms of the relative magnitude of the two proposed transport mechanisms: percolation and paddle-wheel. It appears to us that the percolation mechanism dominates the sodium diffusion.
Structural considerations for a software life cycle dynamic simulation model
NASA Technical Reports Server (NTRS)
Tausworthe, R. C.; Mckenzie, M.; Lin, C. Y.
1983-01-01
This paper presents the results of a preliminary study into the prospects for simulating the software implementation and maintenance life cycle process, with the aim of producing a computerized tool for use by management and software engineering personnel in project planning, tradeoff studies involving product, environmental, situational, and technological factors, and training. The approach taken is the modular application of a 'flow of resource' concept to the systems dynamics simulation modeling technique. The software life cycle process is represented as a number of stochastic, time-varying, interacting work tasks that each achieves one of the project milestones. Each task is characterized by the item produced, the personnel applied, and the budgetary profile.
Using collective variables to drive molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme
2013-12-01
A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.
Structural considerations for a software life cycle dynamic simulation model
NASA Technical Reports Server (NTRS)
Tausworthe, R. C.; Mckenzie, M.; Lin, C. Y.
1983-01-01
This paper presents the results of a preliminary study into the prospects for simulating the software implementation and maintenance life cycle process, with the aim of producing a computerized tool for use by management and software engineering personnel in project planning, tradeoff studies involving product, environmental, situational, and technological factors, and training. The approach taken is the modular application of a 'flow of resource' concept to the systems dynamics simulation modeling technique. The software life cycle process is represented as a number of stochastic, time-varying, interacting work tasks that each achieves one of the project milestones. Each task is characterized by the item produced, the personnel applied, and the budgetary profile.
The architecture of Newton, a general-purpose dynamics simulator
NASA Technical Reports Server (NTRS)
Cremer, James F.; Stewart, A. James
1989-01-01
The architecture for Newton, a general-purpose system for simulating the dynamics of complex physical objects, is described. The system automatically formulates and analyzes equations of motion, and performs automatic modification of this system equations when necessitated by changes in kinematic relationships between objects. Impact and temporary contact are handled, although only using simple models. User-directed influence of simulations is achieved using Newton's module, which can be used to experiment with the control of many-degree-of-freedom articulated objects.
Research of TREETOPS Structural Dynamics Controls Simulation Upgrade
NASA Technical Reports Server (NTRS)
Yates, Rose M.
1996-01-01
Under the provisions of contract number NAS8-40194, which was entitled 'TREETOPS Structural Dynamics and Controls Simulation System Upgrade', Oakwood College contracted to produce an upgrade to the existing TREETOPS suite of analysis tools. This suite includes the main simulation program, TREETOPS, two interactive preprocessors, TREESET and TREEFLX, an interactive post processor, TREEPLOT, and an adjunct program, TREESEL. A 'Software Design Document', which provides descriptions of the argument lists and internal variables for each subroutine in the TREETOPS suite, was established. Additionally, installation guides for both DOS and UNIX platforms were developed. Finally, updated User's Manuals, as well as a Theory Manual, were generated.
Molecular dynamics simulation of threshold displacement energies in zircon
Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.
2009-10-15
Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different interatomic potentials. For each sublattice, the simulation was repeated from different initial conditions to estimate the uncertainty in the calculated value of Ed. The displacement threshold energies vary considerably with crystallographic direction and sublattice. The average displacement energy calculated with a recently developed transferable potential is about 120 and 60 eV for cations and anions, respectively. The oxygen displacement energy shows good agreement with experimental estimates in ceramics.
Frank, Martin
2015-01-01
Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).
Periodic boundary conditions for dislocation dynamics simulations in three dimensions
Bulatov, V V; Rhee, M; Cai, W
2000-11-20
This article presents an implementation of periodic boundary conditions (PBC) for Dislocation Dynamics (DD) simulations in three dimensions (3D). We discuss fundamental aspects of PBC development, including preservation of translational invariance and line connectivity, the choice of initial configurations compatible with PBC and a consistent treatment of image stress. On the practical side, our approach reduces to manageable proportions the computational burden of updating the long-range elastic interactions among dislocation segments. The timing data confirms feasibility and practicality of PBC for large-scale DD simulations in 3D.
The architecture of Newton, a general-purpose dynamics simulator
NASA Technical Reports Server (NTRS)
Cremer, James F.; Stewart, A. James
1989-01-01
The architecture for Newton, a general-purpose system for simulating the dynamics of complex physical objects, is described. The system automatically formulates and analyzes equations of motion, and performs automatic modification of this system equations when necessitated by changes in kinematic relationships between objects. Impact and temporary contact are handled, although only using simple models. User-directed influence of simulations is achieved using Newton's module, which can be used to experiment with the control of many-degree-of-freedom articulated objects.
Dynamic focusing approach to mixed-level simulation
NASA Astrophysics Data System (ADS)
Fall, Thomas C.
1997-06-01
The dynamic focusing approach (DFA) has been under development for several years. Its intent is to address several of the issues of mixed level simulations, particularly the aggregational issues. Though the approach requires that the system be able to be modeled within certain constraints, many systems of interest fit well within them. This approach combines a hierarchical representation of knowledge with a stochastic propagation mechanism; this provides capability to gracefully move from coarse granularity to fine granularity under user guidance. Prototype tools have been developed for engineering analysis, combat simulation and TQM process implementation. This paper gives an overview of the approach and its current status.
Classical molecular dynamics simulations for non-equilibrium correlated plasmas
NASA Astrophysics Data System (ADS)
Ferri, S.; Calisti, A.; Talin, B.
2017-03-01
A classical molecular dynamics model was recently extended to simulate neutral multi-component plasmas where various charge states of the same atom and electrons coexist. It is used to investigate the plasma effects on the ion charge and on the ionization potential in dense plasmas. Different simulated statistical properties will show that the concept of isolated particles is lost in such correlated plasmas. The charge equilibration is discussed for a carbon plasma at solid density and investigation on the charge distribution and on the ionization potential depression (IPD) for aluminum plasmas is discussed with reference to existing experiments.
Grain-level simulation of dynamic failure in ceramic materials
NASA Astrophysics Data System (ADS)
Maiti, Spandan
2002-04-01
Advanced ceramic materials are finding increasing use in different adverse mechanical and chemical situations due to their good mechanical properties, corrosion resistance and thermal stability. Their wider use is however impeded by their brittleness, especially in applications involving dynamic loads, in which dynamic fracture and fragmentation events are often observed. Most of the research aimed at the understanding of dynamic crack initiation and propagation mechanisms in this class of materials do not take into account the inherent granular microstructure of ceramics. In this project, we develop a grain-based finite element scheme that allows for the mesoscale study of a range of dynamic failure events in granular media, including propagation and branching of inter-granular cracks and fragmentation. The scheme relies on Voronoi tessellation to generate the granular microstructure and on a 2-D explicit cohesive/volumetric finite element (CVFE) scheme to simulate the constitutive and failure response of the material under dynamic loads. A non-linear kinematics description is used in our analysis to account for the possible large deformations and/or rotations of the grains during the fracture event. A viscoplastic update algorithm is also introduced to model problems (such as dynamic indentation and grinding) for which localized plasticity plays a key role. The numerical scheme finally relies on robust contact search and enforcement algorithms to capture the complex contact events between fracture surfaces, between individual grains and between the impactor/tool and the ceramic specimen. To demonstrate the capabilities and versatility of the grain-based CVFE code, we investigate four dynamic fracture problems. The first one is concerned with the propagation of dynamic intergranular cracks under mode I loading, with special emphasis on the effect of the microstructure on the branching instability of the crack motion. The second problem is that of dynamic fracture
Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field
2015-01-01
Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein–water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance. PMID:24955078
Molecular dynamics simulation of radiation damage cascades in diamond
Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.
2015-06-28
Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.
Dislocation dynamics: simulation of plastic flow of bcc metals
Lassila, D H
2001-02-20
This is the final report for the LDRD strategic initiative entitled ''Dislocation Dynamic: Simulation of Plastic Flow of bcc Metals'' (tracking code: 00-SI-011). This report is comprised of 6 individual sections. The first is an executive summary of the project and describes the overall project goal, which is to establish an experimentally validated 3D dislocation dynamics simulation. This first section also gives some information of LLNL's multi-scale modeling efforts associated with the plasticity of bcc metals, and the role of this LDRD project in the multiscale modeling program. The last five sections of this report are journal articles that were produced during the course of the FY-2000 efforts.
Homogeneous Nucleation of Methane Hydrate in Microsecond Molecular Dynamics Simulations.
Sarupria, Sapna; Debenedetti, Pablo G
2012-10-18
We report atomistically detailed molecular dynamics simulations of homogeneous nucleation of methane hydrate in bulk aqueous phase in the absence of any interface. Subcritical clusters of water and methane molecules are formed in the initial segment of the simulations, which then aggregate to give the critical hydrate nucleus. This occurs over time scales of several hundred nanoseconds, indicating that the formation and aggregation of subcritical clusters can contribute significantly to the overall rate of hydrate nucleation. The clusters have elements of sI hydrate structure, such as 5(12) and 5(12)6(2) cages as well as other uncommon 5(12)6(3) and 5(12)6(4) cages, but do not possess long-range order. Clusters are dynamic in nature and undergo continuous structural rearrangements.
Description of ferrocenylalkylthiol SAMs on gold by molecular dynamics simulations.
Goujon, F; Bonal, C; Limoges, B; Malfreyt, P
2009-08-18
Molecular dynamics simulations of mixed monolayers consisting of Fc(CH2)12S-/C10S-Au SAMs are carried out to calculate structural (density profiles, angular distributions, positions of atoms) and energetic properties. The purpose of this paper is to explore the possible inhomogeneity of the neutral ferrocene moieties within the monolayer. Five systems have been studied using different grafting densities for the ferrocenylalkylthiolates. The angular distributions are described in terms of the relative contributions from isolated and clustered ferrocene moieties in the binary SAMs. It is shown that the energetic contributions strongly depend on the state of the ferrocene. The ability of molecular dynamics simulations to enable better understanding the SAM structure is illustrated in this work.
Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2016-02-01
Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales.
Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.
Omelyan, I P
2006-09-01
A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations.
Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics
Alekseeva, Uliana; Winkler, Roland G.; Sutmann, Godehard
2016-06-01
A new adaptive resolution technique for particle-based multi-level simulations of fluids is presented. In the approach, the representation of fluid and solvent particles is changed on the fly between an atomistic and a coarse-grained description. The present approach is based on a hybrid coupling of the multiparticle collision dynamics (MPC) method and molecular dynamics (MD), thereby coupling stochastic and deterministic particle-based methods. Hydrodynamics is examined by calculating velocity and current correlation functions for various mixed and coupled systems. We demonstrate that hydrodynamic properties of the mixed fluid are conserved by a suitable coupling of the two particle methods, and that the simulation results agree well with theoretical expectations.
Spin dynamics simulations for a nanoscale Heisenberg antiferromagnet
NASA Astrophysics Data System (ADS)
Hou, Zhuofei; Landau, D. P.; Brown, G.; Stocks, G. M.
2010-03-01
Thermoinduced magnetization(TiM) is a novel response which was predicted to occur in nanoscale antiferromagnetic materials. Extensive Monte Carlo simulations footnotetextG. Brown, A. Janotti, M. Eisenbach, and G. M. Stocks, Phys.Rev.B 72, 140405(2005) have shown that TiM is an intrinsic property of the antiferromagnetic classical Heisenberg model below the Neel temperature. To obtain a fundamental understanding of TiM, spin dynamics(SD) simulations are performed to study the spin wave behavior, which seems to be the cause of TiM. A classical Heisenberg model with an antiferromagnetic nearest-neighbor exchange interaction and uniaxial single-site anisotropy is studied. Simple-cubic lattices with free boundary conditions are used. We employed the fast spin dynamics algorithms with fourth-order Suzuki-Trotter decompositions of the exponential operator. Additional small excitation peaks due to surface effects are found in transverse S(q,w).
A review of the analytical simulation of aircraft crash dynamics
NASA Technical Reports Server (NTRS)
Fasanella, Edwin L.; Carden, Huey D.; Boitnott, Richard L.; Hayduk, Robert J.
1990-01-01
A large number of full scale tests of general aviation aircraft, helicopters, and one unique air-to-ground controlled impact of a transport aircraft were performed. Additionally, research was also conducted on seat dynamic performance, load-limiting seats, load limiting subfloor designs, and emergency-locator-transmitters (ELTs). Computer programs were developed to provide designers with methods for predicting accelerations, velocities, and displacements of collapsing structure and for estimating the human response to crash loads. The results of full scale aircraft and component tests were used to verify and guide the development of analytical simulation tools and to demonstrate impact load attenuating concepts. Analytical simulation of metal and composite aircraft crash dynamics are addressed. Finite element models are examined to determine their degree of corroboration by experimental data and to reveal deficiencies requiring further development.
A dynamical formulation for multiflexible controlled spacecraft simulation
NASA Astrophysics Data System (ADS)
Corrado, G.; Ravazzotti, M. T.
1981-09-01
The dynamic behavior of highly flexible, rotating spacecraft is described by a method which does not require any particular approximation and is not limited to any particular arrangement of the bodies constituting the system. The analytical technique is based on the formalism of the DISCOS computer program (Bodley, 1978), a powerful tool for the dynamic simulation of complex spacecraft. The state equations, described in a general format, are applicable to any complex spacecraft under any environmental load. The approach takes into account the distributed flexibility, the relative motion of the bodies, the automatic coupling of the momentum wheels, the system control laws, and their interaction with the structure. Synthesis and analysis of the linearized system are used to solve time and frequency equations. The required computing times for different program options are listed, along with the number of equations and the integration step size. A block diagram of the DISCOS package structure is given, showing the development from problem definition to simulation results.
Molecular Dynamics Simulation of Membranes and a Transmembrane Helix
NASA Astrophysics Data System (ADS)
Duong, Tap Ha; Mehler, Ernest L.; Weinstein, Harel
1999-05-01
Three molecular dynamics (MD) simulations of 1.5-ns length were carried out on fully hydrated patches of dimyristoyl phosphatidylcholine (DMPC) bilayers in the liquid-crystalline phase. The simulations were performed using different ensembles and electrostatic conditions: a microcanonical ensemble or constant pressure-temperature ensemble, with or without truncated electrostatic interactions. Calculated properties of the membrane patches from the three different protocols were compared to available data from experiments. These data include the resulting overall geometrical dimensions, the order characteristics of the lipid hydrocarbon chains, as well as various measures of the conformations of the polar head groups. The comparisons indicate that the simulation carried out within the microcanonical ensemble with truncated electrostatic interactions yielded results closest to the experimental data, provided that the initial equilibration phase preceding the production run was sufficiently long. The effects of embedding a non-ideal helical protein domain in the membrane patch were studied with the same MD protocols. This simulation was carried out for 2.5 ns. The protein domain corresponds to the seventh transmembrane segment (TMS7) of the human serotonin 5HT 2Areceptor. The peptide is composed of two α-helical segments linked by a hinge domain around a perturbing Asn-Pro motif that produces at the end of the simulation a kink angle of nearly 80° between the two helices. Several aspects of the TMS7 structure, such as the bending angle, backbone Φ and Ψ torsion angles, the intramolecular hydrogen bonds, and the overall conformation, were found to be very similar to those determined by NMR for the corresponding transmembrane segment of the tachykinin NK-1 receptor. In general, the simulations were found to yield structural and dynamic characteristics that are in good agreement with experiment. These findings support the application of simulation methods to the study
The Dynamics of Simulated Convective Storms in Hurricane Environments.
NASA Astrophysics Data System (ADS)
McCaul, Eugene Williamson, Jr.
Numerical simulations of convection in selected hurricane environments show that supercell storms are possible, even when buoyancy is relatively small. In one simulated supercell, the dynamic pressure force is found to reach a maximum about three times as strong as that of buoyancy in the late stages of the simulation. Updrafts reach peak intensity at low levels, often around 2-3 km AGL, and may exceed magnitudes expected from consideration of moist CAPE alone. Interactions between updraft and ambient vertical shear, and, later, growing contributions from vorticity, appear to dominate the development of the dynamic pressure field. Although the weak buoyancy tends to restrict storm intensity, a favorable matching of the vertical distribution of buoyancy with that of the vertical shear allows the pressure forces to become strong enough to take up the slack. Terms in the disturbance kinetic energy budget are correspondingly more strongly influenced by pressure effects than by buoyancy. Although the simulated supercells display the very strong, organized rotation characteristic of tornadic storms, many of the multicell storms which appear in the simulations also contain local concentrations of vorticity intense enough to suggest tornado potential. Simulations with differing background rotation (Coriolis) rates "f" show that convection which was multicellular at low f can become supercellular at higher f. The enhanced vertical vorticity that develops naturally in decaying tropical cyclones when angular momentum disperses under the influence of weakening pressure gradients may, by analogy, help explain why dissipating tropical cyclones are an especially fertile breeding ground for tornadic storms. Test simulations in which surface drag and a slightly modified subgrid mixing formulation were used show that the details of storm behavior can be quite sensitive to changes in these model parameters, although updraft and vorticity statistics are not altered greatly. In general
Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining
Khasin, M.; Kosloff, R.
2010-04-15
An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables--the elements of the spectrum-generating algebra--is simulated by a surrogate open-system dynamics, which can be interpreted as weak measurement of the target observables, performed on the evolving system. The open-system state can be represented by a mixture of pure states, localized in the phase space. The localization reduces the scaling of the computational resources with the Hilbert-space dimension n by factor n{sup 3/2}(ln n){sup -1} compared to conventional sparse-matrix methods. The guidelines for the choice of parameters for the simulation are presented and the scaling of the computational resources with the Hilbert-space dimension of the system is estimated. The algorithm is applied to the simulation of the dynamics of systems of 2x10{sup 4} and 2x10{sup 6} cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.
Mild Traumatic Brain Injury and Dynamic Simulated Shooting Performance
2016-02-01
USAARL Report No. 2016-16 Mild Traumatic Brain Injury and Dynamic Simulated Shooting Performance By Ben Lawson1, Bethany Ranes1, Amanda...Kelley1, Bradley Erickson1, Lana Milam1, Melody King1, Catherine Wrobel1, Jim Chiaramonte1, Timothy Cho1, Brain Laskowski1, John Campbell1,2, Linda... Human Use The USAARL Determination Official determined that the USAARL studies did not constitute research as defined under the human subjects
Improved Pyrolysis Micro reactor Design via Computational Fluid Dynamics Simulations
2017-05-23
NUMBER (Include area code) 23 May 2017 Briefing Charts 25 April 2017 - 23 May 2017 Improved Pyrolysis Micro-reactor Design via Computational Fluid... PYROLYSIS MICRO-REACTOR DESIGN VIA COMPUTATIONAL FLUID DYNAMICS SIMULATIONS Ghanshyam L. Vaghjiani* DISTRIBUTION A: Approved for public release...Approved for public release, distribution unlimited. PA Clearance 17247 Chen-Source (>240 references from SciFinder as of 5/1/17): Flash pyrolysis
The Architecture of Newton, a General-Purpose Dynamics Simulator
1989-01-01
11 N The Architecture of Newton, a General-Purpose Dynamics 0 Simulator OTIC James F. Cremer ELECTE A. James Stewart JUL 141989f l Computer Science...173SS, ONR grant N00t4.SK-0281 and DARPA grant N0014-OOK.0S91 Support for James Stewart is provided in part by U.S. Army Math-4.3 Control matica Sciences
Simulated dynamic response of a servovalve controlled hydraulic actuator
NASA Technical Reports Server (NTRS)
Babcock, Dale A.
1990-01-01
A general purpose math model of a servovalve controlled hydraulic actuator system is derived. The system consists of a linear actuator with unequal piston areas, a single stage servovalve, a gas charged hydraulic accumulator, and the interconnecting piping. The state equations are integrated using the Advanced Continuous Simulation Language (ACSL) for determining the system's dynamic response characteristics. Using this generalized hydraulic actuator system model, response characteristics were determined for various servovalve commands.
Using Soft Computing Technologies for the Simulation of LCAC Dynamics
2011-09-01
real-time, time-domain predictions of the vehicle’s dynamics as a function of the control signals given by the driver. Results are presented...free- running LCAC model, faster-than-real-time simulation, soft computing technology 1.0 INTRODUCTION The Maneuvering and Control Division (MCD...like all hovercraft , rides on a cushion of air. The air is supplied to the cushion by four centrifugal fans driven by the craft’s gas turbine
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
NASA Astrophysics Data System (ADS)
Rapaport, D. C.
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Applying Parallel Processing Techniques to Tether Dynamics Simulation
NASA Technical Reports Server (NTRS)
Wells, B. Earl
1996-01-01
The focus of this research has been to determine the effectiveness of applying parallel processing techniques to a sizable real-world problem, the simulation of the dynamics associated with a tether which connects two objects in low earth orbit, and to explore the degree to which the parallelization process can be automated through the creation of new software tools. The goal has been to utilize this specific application problem as a base to develop more generally applicable techniques.
Simulation of dynamic material response with the PAGOSA code
Holian, K.S.; Adams, T.F.
1993-08-01
The 3D Eulerian PAGOSA hydrocode is being run on the massively parallel Connection Machine (CM) to simulate the response of materials to dynamic loading, such as by high explosives or high velocity impact. The code has a variety of equation of state forms, plastic yield models, and fracture and fragmentation models. The numerical algorithms in PAGOSA and the implementation of material models are discussed briefly.
Molecular dynamics simulations of ordering of polydimethylsiloxane under uniaxial extension
Lacevic, N M; Gee, R H
2005-03-11
Molecular dynamics simulations of a bulk melts of polydimethylsiloxane (PDMS) are utilized to study chain conformation and ordering under constant uniaxial tension. We find that large extensions induce chain ordering in the direction of applied tension. We also find that voids are created via a cavitation mechanism. This study represents a validation of the current model for PDMS and benchmark for the future study of mechanical properties of PDMS melts enriched with fillers under tension.
Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations
2008-07-17
membrane-insertion process. Structure and dynamics of membrane- bound peptides have been partly investigated experimentally with carefully designed small...been experimentally determined [6], and characterizing large conformational changes of small, membrane- bound peptides during the membrane-insertion...solid- state NMR techniques [22], were prepared after brief energy minimizations. A time step of 2 fs has been used in the MD simulations. Langevin
Simulating market dynamics: interactions between consumer psychology and social networks.
Janssen, Marco A; Jager, Wander
2003-01-01
Markets can show different types of dynamics, from quiet markets dominated by one or a few products, to markets with continual penetration of new and reintroduced products. In a previous article we explored the dynamics of markets from a psychological perspective using a multi-agent simulation model. The main results indicated that the behavioral rules dominating the artificial consumer's decision making determine the resulting market dynamics, such as fashions, lock-in, and unstable renewal. Results also show the importance of psychological variables like social networks, preferences, and the need for identity to explain the dynamics of markets. In this article we extend this work in two directions. First, we will focus on a more systematic investigation of the effects of different network structures. The previous article was based on Watts and Strogatz's approach, which describes the small-world and clustering characteristics in networks. More recent research demonstrated that many large networks display a scale-free power-law distribution for node connectivity. In terms of market dynamics this may imply that a small proportion of consumers may have an exceptional influence on the consumptive behavior of others (hubs, or early adapters). We show that market dynamics is a self-organized property depending on the interaction between the agents' decision-making process (heuristics), the product characteristics (degree of satisfaction of unit of consumption, visibility), and the structure of interactions between agents (size of network and hubs in a social network).
Molecular dynamics simulation of liquid water: Hybrid density functionals
Todorova, T; Seitsonen, A; Hutter, J; Kuo, W; Mundy, C
2005-09-12
The structure, dynamical and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta functional, four gradient corrected functionals, the local density and Hartree-Fock approximation. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and under-structured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller averaged numbers of hydrogen bonds and similar hydrogen bond populations as pure density functionals. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than from the corresponding pure density functionals.
Direct identification of predator-prey dynamics in gyrokinetic simulations
NASA Astrophysics Data System (ADS)
Kobayashi, Sumire; Gürcan, Özgür D.; Diamond, Patrick H.
2015-09-01
The interaction between spontaneously formed zonal flows and small-scale turbulence in nonlinear gyrokinetic simulations is explored in a shearless closed field line geometry. It is found that when clear limit cycle oscillations prevail, the observed turbulent dynamics can be quantitatively captured by a simple Lotka-Volterra type predator-prey model. Fitting the time traces of full gyrokinetic simulations by such a reduced model allows extraction of the model coefficients. Scanning physical plasma parameters, such as collisionality and density gradient, it was observed that the effective growth rates of turbulence (i.e., the prey) remain roughly constant, in spite of the higher and varying level of primary mode linear growth rates. The effective growth rate that was extracted corresponds roughly to the zonal-flow-modified primary mode growth rate. It was also observed that the effective damping of zonal flows (i.e., the predator) in the parameter range, where clear predator-prey dynamics is observed, (i.e., near marginal stability) agrees with the collisional damping expected in these simulations. This implies that the Kelvin-Helmholtz-like instability may be negligible in this range. The results imply that when the tertiary instability plays a role, the dynamics becomes more complex than a simple Lotka-Volterra predator prey.
Direct identification of predator-prey dynamics in gyrokinetic simulations
Kobayashi, Sumire Gürcan, Özgür D; Diamond, Patrick H.
2015-09-15
The interaction between spontaneously formed zonal flows and small-scale turbulence in nonlinear gyrokinetic simulations is explored in a shearless closed field line geometry. It is found that when clear limit cycle oscillations prevail, the observed turbulent dynamics can be quantitatively captured by a simple Lotka-Volterra type predator-prey model. Fitting the time traces of full gyrokinetic simulations by such a reduced model allows extraction of the model coefficients. Scanning physical plasma parameters, such as collisionality and density gradient, it was observed that the effective growth rates of turbulence (i.e., the prey) remain roughly constant, in spite of the higher and varying level of primary mode linear growth rates. The effective growth rate that was extracted corresponds roughly to the zonal-flow-modified primary mode growth rate. It was also observed that the effective damping of zonal flows (i.e., the predator) in the parameter range, where clear predator-prey dynamics is observed, (i.e., near marginal stability) agrees with the collisional damping expected in these simulations. This implies that the Kelvin-Helmholtz-like instability may be negligible in this range. The results imply that when the tertiary instability plays a role, the dynamics becomes more complex than a simple Lotka-Volterra predator prey.
4D Simulation of Explosive Eruption Dynamics at Vesuvius
NASA Astrophysics Data System (ADS)
Neri, A.; Esposti Ongaro, T.; Menconi, G.; de'Michieli Vitturi, M.; Cavazzoni, C.; Erbacci, G.; Baxter, P. J.
2006-12-01
We applied, using a supercomputer, a new simulation model based on fundamental transport laws to describe the 4D (3D spatial co-ordinates plus time) multiphase flow dynamics of explosive eruptions. The model solves the fundamental transport equations for a multiphase mixture formed by a continuous multi-component gas phase and n solid particulate phases representative of magma fragments (such as ash, crystals, and lapilli). Numerical simulations describe the collapse of the volcanic eruption column and the propagation of pyroclastic density currents, for selected medium scale (sub-Plinian) eruptive scenarios at Vesuvius, Italy. The study shows that 4D multiphase numerical models can illuminate the non-intuitive and internal dynamics of explosive eruptions that cannot otherwise be studied by direct observation or using previous models. In particular, simulations provide crucial insights into the effects of the generation mechanism of the flows - partial collapse vs boiling-over - on their hazard potential, the complex dynamics of the collapsing column, and the influence of Mount Somma on the propagation of PDCs into the circum-Vesuvian area, one of the world's most hazardous volcanic settings.
NETL's IGCC Dynamic Simulator Reserach and Training Center
Erbes, M.; Zitney, S.
2008-01-01
The National Energy Technology Laboratory (NETL) is collaborating with software, industry, and university partners to establish a world-class Dynamic Simulator Research and Training (DSR&T) Center dedicated to the operation and control of advanced energy plants with carbon capture capabilities. The DSR&T Center will offer a collaborative R&D program and comprehensive hands-on training built around a portfolio of non-proprietary, high-fidelity, real-time dynamic simulators. The simulators will provide full-scope operator training system (OTS) capabilities for normal and faulted operations, as well as plant start-up, shutdown, and load following. Immersive three-dimensional (3-D) virtual reality will add another dimension of realism to the dynamic OTS systems and extend the training scope to both control room and outside operators, allowing them to work as a team. The benefits of high-fidelity immersive training systems (ITS) include more realistic training scenarios, improved communication and collaboration among work crews, off-line evaluations of procedures, and training for safety-critical tasks and rare abnormal situations.
Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.
Tavernelli, Ivano
2015-03-17
Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics
Real-world predictions from ab initio molecular dynamics simulations.
Kirchner, Barbara; di Dio, Philipp J; Hutter, Jürg
2012-01-01
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
Reweighted ensemble dynamics simulations: Theory, improvement, and application
NASA Astrophysics Data System (ADS)
Gong, Lin-Chen; Zhou, Xin; Ouyang, Zhong-Can
2015-06-01
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provide schemes on selection of basis functions, and determination of the free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enables us to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in an entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems. Project supported by the National Natural Science Foundation of China (Grant No. 11175250).
Molecular dynamics simulation of shock melting of aluminum single crystal
NASA Astrophysics Data System (ADS)
Ju, Yuanyuan; Zhang, Qingming; Gong, Zizheng; Ji, Guangfu; Zhou, Lin
2013-09-01
Molecular dynamics method in conjunction with multi-scale shock technique is employed to study the melting characteristics of aluminum single crystal under dynamic conditions. The simulated results show that a linear relationship exists between the shock wave velocity and particle velocity, in good agreement with the experimental data. Comparing the Lindemann melting curve with the two Hugoniot curves for the solid and liquid phases, the Hugoniot melting is found to begin at 93.6 GPa and end at 140 GPa, which is consistent with the theoretical calculations. The impact of crystal defects on the melting characteristics of aluminum single crystal is also studied, and the results indicate that the pressure and temperature increase slightly for the system experiencing the same dynamic loading due to the crystal defects.
Pavement nondestructive evaluation using finite-element dynamic simulation
NASA Astrophysics Data System (ADS)
Uddin, W.; Hackett, R. M.
1996-11-01
This paper describes the nondestructive evaluation devices, visual distress survey and coring used to investigate jointed concrete pavement performance in northern Mississippi. 3D finite-element models were developed to simulate in-service conditions and to characterize in-situ material properties. Reasonable good agreement is found between in-situ moduli backcalculated from the dynamic analysis of falling weight deflectometer (FWD) deflections measured on selected pavements and laboratory moduli. Effects of load pulse shape, cracking, and discontinuities on the surface deflection response of pavements subjected to FWD load wee also investigated. It is shown that 3D analysis of temperature distribution and resulting thermal stresses play a significant role int he performance of concrete pavements. The study results demonstrated the extensive usefulness of the finite-element dynamic analysis and limitations of the static multilayered analysis and other pavement analysis programs which do not allow for crack modeling and dynamic analysis.
Simulating fast and slow dynamic effects in power systems
de Mello, F.P.; Feltes, J.W.; Laskowski, T.F.; Oppel, L.J. )
1992-07-01
Electric power systems comprise a nearly infinite number of devices, exhibiting dynamic characteristics in a wide range of bandwidths and with significant nonlinear effects. Historically, the nature of these devices, the robust configuration of the electric power system, and its loading were such that the interaction between devices became relatively unimportant in system performance several seconds after disturbances. Greater utilization of electric plant, through heavier system loadings, interconnections, and increasing use of controls, has at times necessitated predictions of system performance through simulation extending over a time range of tens of seconds to several minutes. The phenomena occurring over this extended time frame has been referred to as long-term dynamics. There are basically two classes of problems involving long-term dynamics. One is the problem of islanding with significant imbalances between load and generation where prime mover action in response to frequency deviations is significant. The other concerns problems of insufficient damping and/or synchronizing power, and voltage collapse.
Reveal protein dynamics by combining computer simulation and neutron scattering
NASA Astrophysics Data System (ADS)
Hong, Liang; Smith, Jeremy; CenterMolecular Biophysics Team
2014-03-01
Protein carries out most functions in living things on the earth through characteristic modulation of its three-dimensional structure over time. Understanding the microscopic nature of the protein internal motion and its connection to the function and structure of the biomolecule is a central topic in biophysics, and of great practical importance for drug design, study of diseases, and the development of renewable energy, etc. Under physiological conditions, protein exhibits a complex dynamics landscape, i.e., a variety of diffusive and conformational motions occur on similar time and length scales. This variety renders difficult the derivation of a simplified description of protein internal motions in terms of a small number of distinct, additive components. This difficulty is overcome by our work using a combined approach of Molecular Dynamics (MD) simulations and the Neutron Scattering experiments. Our approach enables distinct protein motions to be characterized separately, furnishing an in-depth understanding of the connection between protein structure, dynamics and function.
Molecular dynamics simulations of lysozyme in water/sugar solutions
NASA Astrophysics Data System (ADS)
Lerbret, A.; Affouard, F.; Bordat, P.; Hédoux, A.; Guinet, Y.; Descamps, M.
2008-04-01
Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.
The dynamic response of a viscoelastic biological tissue simulant
NASA Astrophysics Data System (ADS)
Shepherd, Christopher; Appleby-Thomas, Gareth; Hazell, Paul; Allsop, Derek
2009-06-01
The development and optimisation of new projectiles requires comparative techniques to assess ballistic performance. Porcine gelatin has found a substantial niche in the ballistics community as a tissue mimic. Primarily due to its elasticity, gelatin has been shown to deform in a similar manner to biological tissues. Bullet impacts typically occur in the 350-850 m/s range and consequently, knowledge of the high strain rate dynamic properties of both the projectile constituents and target materials is desirable if simulations are to allow the optimisation of projectile design. A large body of knowledge exists on the dynamic properties of projectiles, however relatively little data exists in the literature on the dynamic response of flesh simulants. The Hugoniot for a 20 wt% porcine gelatin, which exhibits a ballistic response similar to that of human tissues at room temperature, is determined in this paper using the plate impact technique. Up-Us and Up-P relationships are determined for impact velocities in the range of 200-900 m/s. Good agreement with the limited available data from the literature for similar concentrations is found and the dynamic response established at impact stresses up to 3 times higher than that observed elsewhere. Additionally, high frequency elastic properties are investigated using ultrasound and compared to those observed elsewhere.
Dynamic regulation of phenylalanine hydroxylase by simulated redox manipulation.
Fuchs, Julian E; Huber, Roland G; von Grafenstein, Susanne; Wallnoefer, Hannes G; Spitzer, Gudrun M; Fuchs, Dietmar; Liedl, Klaus R
2012-01-01
Recent clinical studies revealed increased phenylalanine levels and phenylalanine to tyrosine ratios in patients suffering from infection, inflammation and general immune activity. These data implicated down-regulation of activity of phenylalanine hydroxylase by oxidative stress upon in vivo immune activation. Though the structural damage of oxidative stress is expected to be comparably small, a structural rationale for this experimental finding was lacking. Hence, we investigated the impact of side chain oxidation at two vicinal cysteine residues on local conformational flexibility in the protein by comparative molecular dynamics simulations. Analysis of backbone dynamics revealed a highly flexible loop region (Tyr138-loop) in proximity to the active center of phenylalanine hydroxylase. We observed elevated loop dynamics in connection with a loop movement towards the active site in the oxidized state, thereby partially blocking access for the substrate phenylalanine. These findings were confirmed by extensive replica exchange molecular dynamics simulations and serve as a first structural explanation for decreased enzyme turnover in situations of oxidative stress.
Two-Speed Gearbox Dynamic Simulation Predictions and Test Validation
NASA Technical Reports Server (NTRS)
Lewicki, David G.; DeSmidt, Hans; Smith, Edward C.; Bauman, Steven W.
2010-01-01
Dynamic simulations and experimental validation tests were performed on a two-stage, two-speed gearbox as part of the drive system research activities of the NASA Fundamental Aeronautics Subsonics Rotary Wing Project. The gearbox was driven by two electromagnetic motors and had two electromagnetic, multi-disk clutches to control output speed. A dynamic model of the system was created which included a direct current electric motor with proportional-integral-derivative (PID) speed control, a two-speed gearbox with dual electromagnetically actuated clutches, and an eddy current dynamometer. A six degree-of-freedom model of the gearbox accounted for the system torsional dynamics and included gear, clutch, shaft, and load inertias as well as shaft flexibilities and a dry clutch stick-slip friction model. Experimental validation tests were performed on the gearbox in the NASA Glenn gear noise test facility. Gearbox output speed and torque as well as drive motor speed and current were compared to those from the analytical predictions. The experiments correlate very well with the predictions, thus validating the dynamic simulation methodologies.
King, Sharla; Carbonaro, Michael; Greidanus, Elaine; Ansell, Dawn; Foisy-Doll, Colette; Magus, Sam
2014-08-01
The purpose of this study was to develop, deliver, and assess relevant interprofessional (IP) simulation experiences for prelicensure students from multiple disciplines in certificate, diploma, and degree programs. Seventy-eight students from four post-secondary institutions participated in either a high-fidelity mannequin postoperative simulation experience (dynamic simulation) or a standardized patient homecare simulation experience (routine simulation). The University of West England Questionnaire was used pre- and post-simulation experience to determine the change in communication and teamwork. Overall, students' perceptions of their communication and teamwork skills increased after completing either simulation. Students from certificate, diploma, and degree programs participating in the same simulations demonstrated improvements on self-report measures of communication and teamwork. The key was creating a simulation learning experience that reflected the realities of practice, rather than the participants' credentials. Placing students in teams that are relevant for practice, rather than grouping them by academic credentials, is necessary and can provide positive learning experiences for all participants, as demonstrated by these results.
Molecular dynamics simulation of pervaporation in zeolite membranes
NASA Astrophysics Data System (ADS)
Jia, W.; Murad, S.
The pervaporation separation of liquid mixtures of water/ethanol and water/methanol using three zeolite (Silicalite, NaA and Chabazite) membranes has been examined using the method of molecular dynamics. The main goal of this study was to identify intermolecular interactions between water, methanol, ethanol and the membrane surface that play a critical role in the separations. This would then allow better membranes to be designed more efficiently and systematically than the trial-and-error procedures often being used. Our simulations correctly exhibited all the qualitative experimental observations for these systems, including the hydrophobic or hydrophilic behaviour of zeolite membranes. The simulations showed that, for Silicalite zeolite, the separation is strongly influenced by the selective adsorption of ethanol. The separation factor, as a consequence, increases almost exponentially as the ethanol composition decreases. For ethanol dehydration in NaA and Chabazite, pore size was found to play a very important role in the separation; very high separation factors were therefore possible. Simulations were also used to investigate the effect of pore structure, feed compositions and operating conditions on the pervaporation efficiency. Finally, our simulations also demonstrated that molecular simulations could serve as a useful screening tool to determine the suitability of a membrane for potential pervaporation separation applications. Simulations can cost only a small fraction of an experiment, and can therefore be used to design experiments most likely to be successful.
Numerical simulation of landfill aeration using computational fluid dynamics.
Fytanidis, Dimitrios K; Voudrias, Evangelos A
2014-04-01
The present study is an application of Computational Fluid Dynamics (CFD) to the numerical simulation of landfill aeration systems. Specifically, the CFD algorithms provided by the commercial solver ANSYS Fluent 14.0, combined with an in-house source code developed to modify the main solver, were used. The unsaturated multiphase flow of air and liquid phases and the biochemical processes for aerobic biodegradation of the organic fraction of municipal solid waste were simulated taking into consideration their temporal and spatial evolution, as well as complex effects, such as oxygen mass transfer across phases, unsaturated flow effects (capillary suction and unsaturated hydraulic conductivity), temperature variations due to biochemical processes and environmental correction factors for the applied kinetics (Monod and 1st order kinetics). The developed model results were compared with literature experimental data. Also, pilot scale simulations and sensitivity analysis were implemented. Moreover, simulation results of a hypothetical single aeration well were shown, while its zone of influence was estimated using both the pressure and oxygen distribution. Finally, a case study was simulated for a hypothetical landfill aeration system. Both a static (steadily positive or negative relative pressure with time) and a hybrid (following a square wave pattern of positive and negative values of relative pressure with time) scenarios for the aeration wells were examined. The results showed that the present model is capable of simulating landfill aeration and the obtained results were in good agreement with corresponding previous experimental and numerical investigations.
Parallel Stochastic discrete event simulation of calcium dynamics in neuron.
Ishlam Patoary, Mohammad Nazrul; Tropper, Carl; McDougal, Robert A; Zhongwei, Lin; Lytton, William W
2017-09-26
The intra-cellular calcium signaling pathways of a neuron depends on both biochemical reactions and diffusions. Some quasi-isolated compartments (e.g. spines) are so small and calcium concentrations are so low that one extra molecule diffusing in by chance can make a nontrivial difference in its concentration (percentage-wise). These rare events can affect dynamics discretely in such way that they cannot be evaluated by a deterministic simulation. Stochastic models of such a system provide a more detailed understanding of these systems than existing deterministic models because they capture their behavior at a molecular level. Our research focuses on the development of a high performance parallel discrete event simulation environment, Neuron Time Warp (NTW), which is intended for use in the parallel simulation of stochastic reaction-diffusion systems such as intra-calcium signaling. NTW is integrated with NEURON, a simulator which is widely used within the neuroscience community. We simulate two models, a calcium buffer and a calcium wave model. The calcium buffer model is employed in order to verify the correctness and performance of NTW by comparing it to a serial deterministic simulation in NEURON. We also derived a discrete event calcium wave model from a deterministic model using the stochastic IP3R structure.
Hybrid molecular dynamics simulation for plasma induced damage analysis
NASA Astrophysics Data System (ADS)
Matsukuma, Masaaki
2016-09-01
In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam
Simulated impacts of insect defoliation on forest carbon dynamics
NASA Astrophysics Data System (ADS)
Medvigy, D.; Clark, K. L.; Skowronski, N. S.; Schäfer, K. V. R.
2012-12-01
Many temperate and boreal forests are subject to insect epidemics. In the eastern US, over 41 million meters squared of tree basal area are thought to be at risk of gypsy moth defoliation. However, the decadal-to-century scale implications of defoliation events for ecosystem carbon dynamics are not well understood. In this study, the effects of defoliation intensity, periodicity and spatial pattern on the carbon cycle are investigated in a set of idealized model simulations. A mechanistic terrestrial biosphere model, ecosystem demography model 2, is driven with observations from a xeric oak-pine forest located in the New Jersey Pine Barrens. Simulations indicate that net ecosystem productivity (equal to photosynthesis minus respiration) decreases linearly with increasing defoliation intensity. However, because of interactions between defoliation and drought effects, aboveground biomass exhibits a nonlinear decrease with increasing defoliation intensity. The ecosystem responds strongly with both reduced productivity and biomass loss when defoliation periodicity varies from 5 to 15 yr, but exhibits a relatively weak response when defoliation periodicity varies from 15 to 60 yr. Simulations of spatially heterogeneous defoliation resulted in markedly smaller carbon stocks than simulations with spatially homogeneous defoliation. These results show that gypsy moth defoliation has a large effect on oak-pine forest biomass dynamics, functioning and its capacity to act as a carbon sink.
An undergraduate laboratory activity on molecular dynamics simulations.
Spitznagel, Benjamin; Pritchett, Paige R; Messina, Troy C; Goadrich, Mark; Rodriguez, Juan
2016-01-01
Vision and Change [AAAS, 2011] outlines a blueprint for modernizing biology education by addressing conceptual understanding of key concepts, such as the relationship between structure and function. The document also highlights skills necessary for student success in 21st century Biology, such as the use of modeling and simulation. Here we describe a laboratory activity that allows students to investigate the dynamic nature of protein structure and function through the use of a modeling technique known as molecular dynamics (MD). The activity takes place over two lab periods that are 3 hr each. The first lab period unpacks the basic approach behind MD simulations, beginning with the kinematic equations that all bioscience students learn in an introductory physics course. During this period students are taught rudimentary programming skills in Python while guided through simple modeling exercises that lead up to the simulation of the motion of a single atom. In the second lab period students extend concepts learned in the first period to develop skills in the use of expert MD software. Here students simulate and analyze changes in protein conformation resulting from temperature change, solvation, and phosphorylation. The article will describe how these activities can be carried out using free software packages, including Abalone and VMD/NAMD. © 2016 The International Union of Biochemistry and Molecular Biology.
Massively Parallel Reactive and Quantum Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Vashishta, Priya
2015-03-01
In this talk I will discuss two simulations: Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. Quantum molecular dynamics (QMD) simulations are performed on 786,432-processor Blue Gene/Q to study on-demand production of hydrogen gas from water using Al nanoclusters. QMD simulations reveal rapid hydrogen production from water by an Al nanocluster. We find a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production. I will also discuss on-demand production of hydrogen gas from water using and LiAl alloy particles. Research reported in this lecture was carried in collaboration with Rajiv Kalia, Aiichiro Nakano and Ken-ichi Nomura from the University of Southern California, and Fuyuki Shimojo and Kohei Shimamura from Kumamoto University, Japan.
Simulation of dynamic processes with adaptive neural networks.
Tzanos, C. P.
1998-02-03
Many industrial processes are highly non-linear and complex. Their simulation with first-principle or conventional input-output correlation models is not satisfactory, either because the process physics is not well understood, or it is so complex that direct simulation is either not adequately accurate, or it requires excessive computation time, especially for on-line applications. Artificial intelligence techniques (neural networks, expert systems, fuzzy logic) or their combination with simple process-physics models can be effectively used for the simulation of such processes. Feedforward (static) neural networks (FNNs) can be used effectively to model steady-state processes. They have also been used to model dynamic (time-varying) processes by adding to the network input layer input nodes that represent values of input variables at previous time steps. The number of previous time steps is problem dependent and, in general, can be determined after extensive testing. This work demonstrates that for dynamic processes that do not vary fast with respect to the retraining time of the neural network, an adaptive feedforward neural network can be an effective simulator that is free of the complexities introduced by the use of input values at previous time steps.
Brownian Dynamics Simulations of Ion Transport through the VDAC
Lee, Kyu Il; Rui, Huan; Pastor, Richard W.; Im, Wonpil
2011-01-01
It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions. PMID:21281575
How to identify dislocations in molecular dynamics simulations?
NASA Astrophysics Data System (ADS)
Li, Duo; Wang, FengChao; Yang, ZhenYu; Zhao, YaPu
2014-12-01
Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals. With the development of computational facilities and technologies, the observations of dislocations at atomic level through numerical simulations are permitted. Molecular dynamics (MD) simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects. However, the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures. Thus, it is a big challenge for the beginners in this community to choose a proper method to start their investigations. In this review, we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids. A comprehensive comparison was made between the advantages and disadvantages of these typical techniques. We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing. It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.
Stochastic Simulation of Biomolecular Networks in Dynamic Environments
Voliotis, Margaritis; Thomas, Philipp; Grima, Ramon; Bowsher, Clive G.
2016-01-01
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate—using decision-making by a large population of quorum sensing bacteria—that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits. PMID:27248512
Stochastic Simulation of Biomolecular Networks in Dynamic Environments.
Voliotis, Margaritis; Thomas, Philipp; Grima, Ramon; Bowsher, Clive G
2016-06-01
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits.
Lightweight computational steering of very large scale molecular dynamics simulations
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.
A molecular dynamics simulation study of coaxial stacking in RNA.
Schneider, C; Sühnel, J
2000-12-01
We report on unrestrained molecular dynamics simulations of an RNA tetramer binding to a tetra-nucleotide overhang at the 5'-end of an RNA hairpin (nicked structure) and of the corresponding continuous hairpin with Na+ as counterions. The simulations lead to stable structures and in this way a structural model for the coaxially stacked RNA hairpin is generated. The stacking interface in the coaxially stacked nicked hairpin structure is characterized by a reduced twist and shift and a slightly increased propeller twist as compared to the continuous system. This leads to an increased overlap between C22 and G23 in the stacking interface of the nicked structure. In the simulations the continuous RNA hairpin has an almost straight helical axis. On the other hand, the corresponding axis for the nicked structure exhibits a marked kink of 39 degrees. The stacking interface exhibits no increased flexibility as compared to the corresponding base pair step in the continuous structure.
Molecular Dynamics Simulations of Acoustic Properties of Colloidal Suspensions
NASA Astrophysics Data System (ADS)
Noguez, Cecilia; Esquivel-Sirvent, Raul; Ramírez-Santiago, Guillermo
1998-03-01
Recent experiments of ultrasound waves in colloidal suspensions [1] have found that the acoustic velocity and attenuation exhibit an anomalous behavior close to the solid volume concentration of 40%. Currently, there appears that there is no clear understanding of these results. Motivated by these observations we have carried out extensive non-equilibrium molecular dynamics simulations to study the propagation of pressure waves through a colloidal suspension. The simulations consider the far from equilibrium corrections and calculate the viscosity and attenuation of sound waves traveling in the suspension. These quantities are studied as functions of frecuency and volume fraction. The possible relation between the results from the simulations and the experimental observatios is briefly discussed. [1] R. Esquivel-Sirvent and D. H. Green, Appl. Phys. Lett. 67, 3087 (1995); ibid, Mat. Res. Soc. Symp. 407, p. 99 (1996).
Dispersion analysis techniques within the space vehicle dynamics simulation program
NASA Technical Reports Server (NTRS)
Snow, L. S.; Kuhn, A. E.
1975-01-01
The Space Vehicle Dynamics Simulation (SVDS) program was evaluated as a dispersion analysis tool. The Linear Error Analysis (LEA) post processor was examined in detail and simulation techniques relative to conducting a dispersion analysis using the SVDS were considered. The LEA processor is a tool for correlating trajectory dispersion data developed by simulating 3 sigma uncertainties as single error source cases. The processor combines trajectory and performance deviations by a root-sum-square (RSS process) and develops a covariance matrix for the deviations. Results are used in dispersion analyses for the baseline reference and orbiter flight test missions. As a part of this study, LEA results were verified as follows: (A) Hand calculating the RSS data and the elements of the covariance matrix for comparison with the LEA processor computed data. (B) Comparing results with previous error analyses. The LEA comparisons and verification are made at main engine cutoff (MECO).
Molecular dynamics simulation of gold cluster growth during sputter deposition
NASA Astrophysics Data System (ADS)
Abraham, J. W.; Strunskus, T.; Faupel, F.; Bonitz, M.
2016-05-01
We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.
Comment on molecular dynamics simulations of monolayers of fluorinated amphiphiles
NASA Astrophysics Data System (ADS)
Shin, Seokmin; Collazo, Nancy; Rice, Stuart A.
1993-02-01
We report the results of new molecular dynamics simulations of liquid-supported monolayers of perfluorinated and partially fluorinated amphiphiles such as F(CF2)11COOH and F(CF2)10CH2COOH. The new simulations include a representation of the superhelical structure of the perfluoroalkane portion of the amphiphile chain in the intramolecular potential energy; in addition, the calculation of the collective tilt angle of the monolayer is improved to include the effect of the azimuthal distribution of individual molecular tilt angles. The results of the simulations are in agreement with the available experimental data. In particular, the packing structure and the observed breakup of the homogeneous ordered monolayer into ordered islands with the same collective tilt of the molecules are correctly predicted as are the very small collective tilt angles. These new results remove the discrepancy between predicted and observed collective tilt angles reported in our previous papers [J. Chem. Phys. 96, 1352, 4735 (1992)].
Molecular dynamics simulation of gold cluster growth during sputter deposition
Abraham, J. W. Bonitz, M.; Strunskus, T.; Faupel, F.
2016-05-14
We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.
Network Visualization of Conformational Sampling during Molecular Dynamics Simulation
Ahlstrom, Logan S.; Baker, Joseph Lee; Ehrlich, Kent; Campbell, Zachary T.; Patel, Sunita; Vorontsov, Ivan I.; Tama, Florence; Miyashita, Osamu
2013-01-01
Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions. PMID:24211466
Simulation of Tailrace Hydrodynamics Using Computational Fluid Dynamics Models
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.
A hybrid algorithm for parallel molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Mangiardi, Chris M.; Meyer, R.
2017-10-01
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.
Molecular Dynamics Simulation of Iron — A Review
NASA Astrophysics Data System (ADS)
Chui, C. P.; Liu, Wenqing; Xu, Yongbing; Zhou, Yan
2015-12-01
Molecular dynamics (MD) is a technique of atomistic simulation which has facilitated scientific discovery of interactions among particles since its advent in the late 1950s. Its merit lies in incorporating statistical mechanics to allow for examination of varying atomic configurations at finite temperatures. Its contributions to materials science from modeling pure metal properties to designing nanowires is also remarkable. This review paper focuses on the progress of MD in understanding the behavior of iron — in pure metal form, in alloys, and in composite nanomaterials. It also discusses the interatomic potentials and the integration algorithms used for simulating iron in the literature. Furthermore, it reveals the current progress of MD in simulating iron by exhibiting some results in the literature. Finally, the review paper briefly mentions the development of the hardware and software tools for such large-scale computations.
Hybrid simulation theory for a classical nonlinear dynamical system
NASA Astrophysics Data System (ADS)
Drazin, Paul L.; Govindjee, Sanjay
2017-03-01
Hybrid simulation is an experimental and computational technique which allows one to study the time evolution of a system by physically testing a subset of it while the remainder is represented by a numerical model that is attached to the physical portion via sensors and actuators. The technique allows one to study large or complicated mechanical systems while only requiring a subset of the complete system to be present in the laboratory. This results in vast cost savings as well as the ability to study systems that simply can not be tested due to scale. However, the errors that arise from splitting the system in two requires careful attention, if a valid simulation is to be guaranteed. To date, efforts to understand the theoretical limitations of hybrid simulation have been restricted to linear dynamical systems. In this work we consider the behavior of hybrid simulation when applied to nonlinear dynamical systems. As a model problem, we focus on the damped, harmonically-driven nonlinear pendulum. This system offers complex nonlinear characteristics, in particular periodic and chaotic motions. We are able to show that the application of hybrid simulation to nonlinear systems requires a careful understanding of what one expects from such an experiment. In particular, when system response is chaotic we advocate the need for the use of multiple metrics to characterize the difference between two chaotic systems via Lyapunov exponents and Lyapunov dimensions, as well as correlation exponents. When system response is periodic we advocate the use of L2 norms. Further, we are able to show that hybrid simulation can falsely predict chaotic or periodic response when the true system has the opposite characteristic. In certain cases, we are able to show that control system parameters can mitigate this issue.
An Evaluative Review of Simulated Dynamic Smart 3d Objects
NASA Astrophysics Data System (ADS)
Romeijn, H.; Sheth, F.; Pettit, C. J.
2012-07-01
Three-dimensional (3D) modelling of plants can be an asset for creating agricultural based visualisation products. The continuum of 3D plants models ranges from static to dynamic objects, also known as smart 3D objects. There is an increasing requirement for smarter simulated 3D objects that are attributed mathematically and/or from biological inputs. A systematic approach to plant simulation offers significant advantages to applications in agricultural research, particularly in simulating plant behaviour and the influences of external environmental factors. This approach of 3D plant object visualisation is primarily evident from the visualisation of plants using photographed billboarded images, to more advanced procedural models that come closer to simulating realistic virtual plants. However, few programs model physical reactions of plants to external factors and even fewer are able to grow plants based on mathematical and/or biological parameters. In this paper, we undertake an evaluation of plant-based object simulation programs currently available, with a focus upon the components and techniques involved in producing these objects. Through an analytical review process we consider the strengths and weaknesses of several program packages, the features and use of these programs and the possible opportunities in deploying these for creating smart 3D plant-based objects to support agricultural research and natural resource management. In creating smart 3D objects the model needs to be informed by both plant physiology and phenology. Expert knowledge will frame the parameters and procedures that will attribute the object and allow the simulation of dynamic virtual plants. Ultimately, biologically smart 3D virtual plants that react to changes within an environment could be an effective medium to visually represent landscapes and communicate land management scenarios and practices to planners and decision-makers.
cellGPU: Massively parallel simulations of dynamic vertex models
NASA Astrophysics Data System (ADS)
Sussman, Daniel M.
2017-10-01
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cells interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. This article discusses its implementation for a pair of two-dimensional models, and compares the typical performance that can be expected between running cellGPU entirely on the CPU versus its performance when running on a range of commercial and server-grade graphics cards. By implementing the calculation of topological changes and forces on cells in a highly parallelizable fashion, cellGPU enables researchers to simulate time- and length-scales previously inaccessible via existing single-threaded CPU implementations. Program Files doi:http://dx.doi.org/10.17632/6j2cj29t3r.1 Licensing provisions: MIT Programming language: CUDA/C++ Nature of problem: Simulations of off-lattice "vertex models" of cells, in which the interaction forces depend on both the geometry and the topology of the cellular aggregate. Solution method: Highly parallelized GPU-accelerated dynamical simulations in which the force calculations and the topological features can be handled on either the CPU or GPU. Additional comments: The code is hosted at https://gitlab.com/dmsussman/cellGPU, with documentation additionally maintained at http://dmsussman.gitlab.io/cellGPUdocumentation
Atomic dynamics in molecular dynamics simulations of glassy CuTi thin films
NASA Astrophysics Data System (ADS)
Vauth, Sebastian; Mayr, S. G.
2005-02-01
We present results on atomic dynamics in metallic glass thin films below the glass transition temperature using molecular dynamics simulations. Thin CuTi films of different compositions are prepared by quenching the liquid to an amorphous state. The atomic dynamics on the amorphous surface and inside the bulk of the samples are quantitatively compared by calculating diffusion constants and jump length distributions. Here, we focus on the collective or single particle character of the diffusion mechanism in dependence of the atom type. In addition, single atom exemplifications are analyzed for the different kinds of atomic dynamics. We find that Cu surface atoms diffuse with a single atom jump dynamics, whereas inside the bulk collective behavior dominates for both species.
NASA Astrophysics Data System (ADS)
Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.
2017-03-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.
Lee, Kyoung O; Holmes, Thomas W; Calderon, Adan F; Gardner, Robin P
2012-05-01
Using a Monte Carlo (MC) simulation, random walks were used for pebble tracking in a two-dimensional geometry in the presence of a biased gravity field. We investigated the effect of viscosity damping in the presence of random Gaussian fluctuations. The particle tracks were generated by Molecular Dynamics (MD) simulation for a Pebble Bed Reactor. The MD simulations were conducted in the interaction of noncohesive Hertz-Mindlin theory where the random walk MC simulation has a correlation with the MD simulation. This treatment can easily be extended to include the generation of transient gamma-ray spectra from a single pebble that contains a radioactive tracer. Then the inverse analysis thereof could be made to determine the uncertainty of the realistic measurement of transient positions of that pebble by any given radiation detection system designed for that purpose.
Monte Carlo-based simulation of dynamic jaws tomotherapy
Sterpin, E.; Chen, Y.; Chen, Q.; Lu, W.; Mackie, T. R.; Vynckier, S.
2011-09-15
Purpose: Original TomoTherapy systems may involve a trade-off between conformity and treatment speed, the user being limited to three slice widths (1.0, 2.5, and 5.0 cm). This could be overcome by allowing the jaws to define arbitrary fields, including very small slice widths (<1 cm), which are challenging for a beam model. The aim of this work was to incorporate the dynamic jaws feature into a Monte Carlo (MC) model called TomoPen, based on the MC code PENELOPE, previously validated for the original TomoTherapy system. Methods: To keep the general structure of TomoPen and its efficiency, the simulation strategy introduces several techniques: (1) weight modifiers to account for any jaw settings using only the 5 cm phase-space file; (2) a simplified MC based model called FastStatic to compute the modifiers faster than pure MC; (3) actual simulation of dynamic jaws. Weight modifiers computed with both FastStatic and pure MC were compared. Dynamic jaws simulations were compared with the convolution/superposition (C/S) of TomoTherapy in the ''cheese'' phantom for a plan with two targets longitudinally separated by a gap of 3 cm. Optimization was performed in two modes: asymmetric jaws-constant couch speed (''running start stop,'' RSS) and symmetric jaws-variable couch speed (''symmetric running start stop,'' SRSS). Measurements with EDR2 films were also performed for RSS for the formal validation of TomoPen with dynamic jaws. Results: Weight modifiers computed with FastStatic were equivalent to pure MC within statistical uncertainties (0.5% for three standard deviations). Excellent agreement was achieved between TomoPen and C/S for both asymmetric jaw opening/constant couch speed and symmetric jaw opening/variable couch speed, with deviations well within 2%/2 mm. For RSS procedure, agreement between C/S and measurements was within 2%/2 mm for 95% of the points and 3%/3 mm for 98% of the points, where dose is greater than 30% of the prescription dose (gamma analysis
Coupling a geodynamic seismic cycling model to rupture dynamic simulations
NASA Astrophysics Data System (ADS)
Gabriel, Alice; van Dinther, Ylona
2014-05-01
The relevance and results of dynamic rupture scenarios are implicitly linked to the geometry and pre-existing stress and strength state on a fault. The absolute stresses stored along faults during interseismic periods, are largely unquantifiable. They are, however, pivotal in defining coseismic rupture styles, near-field ground motion, and macroscopic source properties (Gabriel et al., 2012). Obtaining these in a physically consistent manner requires seismic cycling models, which directly couple long-term deformation processes (over 1000 year periods), the self-consistent development of faults, and the resulting dynamic ruptures. One promising approach to study seismic cycling enables both the generation of spontaneous fault geometries and the development of thermo-mechanically consistent fault stresses. This seismo-thermo-mechanical model has been developed using a methodology similar to that employed to study long-term lithospheric deformation (van Dinther et al., 2013a,b, using I2ELVIS of Gerya and Yuen, 2007). We will innovatively include the absolute stress and strength values along physically consistent evolving non-finite fault zones (regions of strain accumulation) from the geodynamic model into dynamic rupture simulations as an initial condition. The dynamic rupture simulations will be performed using SeisSol, an arbitrary high-order derivative Discontinuous Galerkin (ADER-DG) scheme (Pelties et al., 2012). The dynamic rupture models are able to incorporate the large degree of fault geometry complexity arising in naturally evolving geodynamic models. We focus on subduction zone settings with and without a splay fault. Due to the novelty of the coupling, we first focus on methodological challenges, e.g. the synchronization of both methods regarding the nucleation of events, the localization of fault planes, and the incorporation of similar frictional constitutive relations. We then study the importance of physically consistent fault stress, strength, and
Spin Dynamics simulations of the dynamic properties of classical models for magnetic materials
NASA Astrophysics Data System (ADS)
Bunker, Alex; Landau, D. P.
1998-03-01
The Spin Dynamics simulation technique, which has had considerable success for the study of critical properties of classical Heisenberg antiferromagnets(A. Bunker, K. Chen, and D. P. Landau Phys. Rev. B) \\underline54, 9259 (1996), has been used to determine more general properties for a wider range of materials. A general spin dynamics program has been developed which can determine the dynamic structure factor, S(q,ω), in the [100], [110], and [111] directions for a wide range of classical magnetic models at any temperature desired. We have simulated the magnetic dynamics in the ordered phase of the isotropic Heisenberg model with both ferromagnetic and antiferromagnetic coupling on L×L×L BCC and SC lattices. Outside of the critical regime relatively small lattice sizes of L = 12, 24 could be used. From our simulation we have determined the stiffness coefficient and the spin relaxation rate which were compared to both experimental(J. Als-Nielsen in Phase Transitions and Critical Phenomena), ed. C. Domb, M. S. Green, Academic Press, (1976) and theoretical results. We have performed the same simulation with anisotropy appropriate for MnF2 and FeF_2. Research supported in part by the NSF
Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation
NASA Astrophysics Data System (ADS)
Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting
2017-07-01
To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project
Isotopic hydration of cellobiose: vibrational spectroscopy and dynamical simulations.
Pincu, Madeleine; Cocinero, Emilio J; Mayorkas, Nitzan; Brauer, Brina; Davis, Benjamin G; Gerber, R Benny; Simons, John P
2011-09-01
The conformation and structural dynamics of cellobiose, one of the fundamental building blocks in nature, its C4' epimer, lactose, and their microhydrated complexes, isolated in the gas phase, have been explored through a combination of experiment and theory. Their structures at low temperature have been determined through double resonance, IR-UV vibrational spectroscopy conducted under molecular beam conditions, substituting D(2)O for H(2)O to separate isotopically, the carbohydrate (OH) bands from the hydration (OD) bands. Car-Parrinello (CP2K) simulations, employing dispersion corrected density functional potentials and conducted "on-the-fly" from ∼20 to ∼300 K, have been used to explore the consequences of raising the temperature. Comparisons between the experimental data, anharmonic vibrational self-consistent field calculations based upon ab initio potentials, and the CP2K simulations have established the role of anharmonicity; the reliability of classical molecular dynamics predictions of the vibrational spectra of carbohydrates and the accuracy of the dispersion corrected (BLYP-D) force fields employed; the structural consequences of increasing hydration; and the dynamical consequences of increasing temperature. The isolated and hydrated cellobiose and lactose units both present remarkably rigid structures: their glycosidic linkages adopt a "cis" (anti-ϕ and syn-ψ) conformation bound by inter-ring hydrogen bonds. This conformation is maintained when the temperature is increased to ∼300 K and it continues to be maintained when the cellobiose (or lactose) unit is hydrated by one or two explicitly bound water molecules. Despite individual fluctuations in the intra- and intermolecular hydrogen bonding pattern and some local structural motions, the water molecules remain locally bound and the isolated carbohydrates remain trapped within the cis potential well. The Car-Parrinello dynamical simulations do not suggest any accessible pathway to the trans
Recovering position-dependent diffusion from biased molecular dynamics simulations
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-28
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.
Recovering position-dependent diffusion from biased molecular dynamics simulations.
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-28
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica(®) package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics. Given known free energy and D, the package can also generate diffusive trajectories.
Simulation of all-scale atmospheric dynamics on unstructured meshes
NASA Astrophysics Data System (ADS)
Smolarkiewicz, Piotr K.; Szmelter, Joanna; Xiao, Feng
2016-10-01
The advance of massively parallel computing in the nineteen nineties and beyond encouraged finer grid intervals in numerical weather-prediction models. This has improved resolution of weather systems and enhanced the accuracy of forecasts, while setting the trend for development of unified all-scale atmospheric models. This paper first outlines the historical background to a wide range of numerical methods advanced in the process. Next, the trend is illustrated with a technical review of a versatile nonoscillatory forward-in-time finite-volume (NFTFV) approach, proven effective in simulations of atmospheric flows from small-scale dynamics to global circulations and climate. The outlined approach exploits the synergy of two specific ingredients: the MPDATA methods for the simulation of fluid flows based on the sign-preserving properties of upstream differencing; and the flexible finite-volume median-dual unstructured-mesh discretisation of the spatial differential operators comprising PDEs of atmospheric dynamics. The paper consolidates the concepts leading to a family of generalised nonhydrostatic NFTFV flow solvers that include soundproof PDEs of incompressible Boussinesq, anelastic and pseudo-incompressible systems, common in large-eddy simulation of small- and meso-scale dynamics, as well as all-scale compressible Euler equations. Such a framework naturally extends predictive skills of large-eddy simulation to the global atmosphere, providing a bottom-up alternative to the reverse approach pursued in the weather-prediction models. Theoretical considerations are substantiated by calculations attesting to the versatility and efficacy of the NFTFV approach. Some prospective developments are also discussed.
Simulation of in vivo dynamics during robot assisted joint movement.
Bobrowitsch, Evgenij; Lorenz, Andrea; Wülker, Nikolaus; Walter, Christian
2014-12-16
Robots are very useful tools in orthopedic research. They can provide force/torque controlled specimen motion with high repeatability and precision. A method to analyze dissipative energy outcome in an entire joint was developed in our group. In a previous study, a sheep knee was flexed while axial load remained constant during the measurement of dissipated energy. We intend to apply this method for the investigation of osteoarthritis. Additionally, the method should be improved by simulation of in vivo knee dynamics. Thus, a new biomechanical testing tool will be developed for analyzing in vitro joint properties after different treatments. Discretization of passive knee flexion was used to construct a complex flexion movement by a robot and simulate altering axial load similar to in vivo sheep knee dynamics described in a previous experimental study. The robot applied an in vivo like axial force profile with high reproducibility during the corresponding knee flexion (total standard deviation of 0.025 body weight (BW)). A total residual error between the in vivo and simulated axial force was 0.16 BW. Posterior-anterior and medio-lateral forces were detected by the robot as a backlash of joint structures. Their curve forms were similar to curve forms of corresponding in vivo measured forces, but in contrast to the axial force, they showed higher total standard deviation of 0.118 and 0.203 BW and higher total residual error of 0.79 and 0.21 BW for posterior-anterior and medio-lateral forces respectively. We developed and evaluated an algorithm for the robotic simulation of complex in vivo joint dynamics using a joint specimen. This should be a new biomechanical testing tool for analyzing joint properties after different treatments.
Preliminary analysis of the dynamic heliosphere by MHD simulations
Washimi, H.; Zank, G. P.; Tanaka, T.
2006-09-26
A preliminary analysis of the dynamic heliosphere to estimate the termination shock (TS) distance from the sun around the time when Voyager 1 passed the termination shock at December 16, 2004 is performed by using MHD simulations. For input to this simulation, we use the Voyager 2 solar-wind data. We first find a stationary solution of the 3-D outer heliosphere by assigning a set of LISM parameters as our outer boundary conditions and then the dynamical analysis is performed. The model TS crossing is within 6 months of the observed date. The TS is pushed outward every time a high ram-pressure solar wind pulse arrives. After the end of the high ram-pressure wind, the TS shock shrinks inward. When the last Halloween event passed through the TS at DOY 250, 2004, the TS began to shrink inward very quickly and the TS crossed V1. The highest inward speed of the TS is over 400 km/s. The high ram-pressure solar wind transmitted through the TS becomes a high thermal-pressure plasma in the heliosheath, acting to push the TS inward. This suggests that the position of the TS is determined not only by the steady-state pressure balance condition between the solar wind ram-pressure and the LISM pressure, but by the dynamical ram pressure too. The period when the high ram-pressure solar wind arrives at the TS shock seems to correspond to the period of the TS particle event (Stone et al, 2005, Decker et al., 2005). The TS crossing date will be revised in future simulations using a more appropriate set of parameters for the LISM. This will enable us to undertake a detailed comparison of the simulation results with the TS particle events.
Ice formation on kaolinite: Insights from molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos
2016-12-01
The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.
Merchant, Kusai A.; Noid, W. G.; Akiyama, Ryo; Finkelstein, Ilya J.; Goun, Alexei; McClain, Brian L.; Loring, Roger F.; Fayer, M. D.
2008-01-01
Spectrally resolved infrared stimulated vibrational echo data were obtained for sperm whale carbonmonoxymyoglobin (MbCO) at 300 K. The measured dephasing dynamics of the CO ligand are in agreement with dephasing dynamics calculated with molecular dynamics (MD) simulations for MbCO with the residue histidine-64 (His64) having its imidazole ε nitrogen protonated (Nε–H). The two conformational substate structures Bε and Rε observed in the MD simulations are assigned to the spectroscopic A1 and A3 conformational substates of MbCO, respectively, based on the agreement between the experimentally measured and calculated dephasing dynamics for these substates. In the A1 substate, the Nε–H proton and Nδ of His64 are approximately equidistant from the CO ligand, while in the A3 substate, the Nε–H of His64 is oriented toward the CO, and the Nδ is on the surface of the protein. The MD simulations show that dynamics of His64 represent the major source of vibrational dephasing of the CO ligand in the A3 state on both femtosecond and picosecond time scales. Dephasing in the A1 state is controlled by His64 on femtosecond time scales, and by the rest of the protein and the water solvent on longer time scales. PMID:14599220
Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
Paquet, Eric; Viktor, Herna L.
2015-01-01
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262
NASA Astrophysics Data System (ADS)
Ito, Hiroaki; Higuchi, Yuji; Shimokawa, Naofumi
2016-10-01
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the prior disturbance of the local molecular orientation in the domain.
Validation of Bubble Dynamics Equation for a Nano-scale Bubble via Molecular Dynamics Simulation
NASA Astrophysics Data System (ADS)
Tsuda, S.; Hyodo, H.; Watanabe, S.
2015-12-01
For a validation of the application of conventional bubble dynamics to a nano-scale bubble behaviour, we simulated a nano-scale bubble collapsing or vibration by Molecular Dynamics (MD) method and compared the result with the solution of Rayleigh-Plesset (RP) equation and that of Confined RP (CRP) equation, whose boundary condition was corrected to be consistent with that of MD simulation. As a result, a good coincidence was obtained between MD, RP, and CRP in the case of one-component fluid. In addition, also a good correspondence was obtained particularly in the comparison between MD and CRP in the case of two-component fluid containing non-condensable gas. The present results indicate that conventional bubble dynamics equation can be applied even to a nano-scale tiny bubble.
Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.
Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C; Roux, Benoît
2013-10-01
A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific β-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26-27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K(+) channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K(+) and Na(+) concentration gradients and the electrostatic potential difference of living cells.
Integrated Turbine-Based Combined Cycle Dynamic Simulation Model
NASA Technical Reports Server (NTRS)
Haid, Daniel A.; Gamble, Eric J.
2011-01-01
A Turbine-Based Combined Cycle (TBCC) dynamic simulation model has been developed to demonstrate all modes of operation, including mode transition, for a turbine-based combined cycle propulsion system. The High Mach Transient Engine Cycle Code (HiTECC) is a highly integrated tool comprised of modules for modeling each of the TBCC systems whose interactions and controllability affect the TBCC propulsion system thrust and operability during its modes of operation. By structuring the simulation modeling tools around the major TBCC functional modes of operation (Dry Turbojet, Afterburning Turbojet, Transition, and Dual Mode Scramjet) the TBCC mode transition and all necessary intermediate events over its entire mission may be developed, modeled, and validated. The reported work details the use of the completed model to simulate a TBCC propulsion system as it accelerates from Mach 2.5, through mode transition, to Mach 7. The completion of this model and its subsequent use to simulate TBCC mode transition significantly extends the state-of-the-art for all TBCC modes of operation by providing a numerical simulation of the systems, interactions, and transient responses affecting the ability of the propulsion system to transition from turbine-based to ramjet/scramjet-based propulsion while maintaining constant thrust.
Molecular dynamic simulations on TKX-50/RDX cocrystal.
Xiong, Shuling; Chen, Shusen; Jin, Shaohua
2017-06-01
Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) is a newly synthesized energetic material with excellent comprehensive properties. Cyclotrimethylenetrinitramine (RDX) is currently one of the most widely used energetic materials in the world. TKX-50 and RDX supercell models and TKX-50/RDX cocrystal model were constructed based on their crystal cell parameters and the formation mechanism of cocrystal, respectively, then they were simulated by molecular dynamics (MD) simulations. The maximum trigger bond (NNO2) length(Lmax), binding energy (Ebind), radial distribution function (RDF), cohesive energy density(CED) and mechanical properties were simulated at different temperatures based on the simulated equilibrium structures of the models. The simulated results indicate that hydrogen bond and van der Waals force interactions exist in the cocrystal system and the hydrogen bonds are mainly derived from the hydrogen atom of TKX-50 with the oxygen or nitrogen atom of RDX. Moreover, TKX-50/RDX cocrystal structure significantly reduces the sensitivity and improves the thermodynamic stability of RDX, and it also shows better mechanical properties than pure TKX-50 and RDX, indicating that it will vastly expand the application scope of the single compound explosives. Copyright © 2017 Elsevier Inc. All rights reserved.
Measurement of human pilot dynamic characteristics in flight simulation
NASA Technical Reports Server (NTRS)
Reedy, James T.
1987-01-01
Fast Fourier Transform (FFT) and Least Square Error (LSE) estimation techniques were applied to the problem of identifying pilot-vehicle dynamic characteristics in flight simulation. A brief investigation of the effects of noise, input bandwidth and system delay upon the FFT and LSE techniques was undertaken using synthetic data. Data from a piloted simulation conducted at NASA Ames Research Center was then analyzed. The simulation was performed in the NASA Ames Research Center Variable Stability CH-47B helicopter operating in fixed-basis simulator mode. The piloting task consisted of maintaining the simulated vehicle over a moving hover pad whose motion was described by a random-appearing sum of sinusoids. The two test subjects used a head-down, color cathode ray tube (CRT) display for guidance and control information. Test configurations differed in the number of axes being controlled by the pilot (longitudinal only versus longitudinal and lateral), and in the presence or absence of an important display indicator called an 'acceleration ball'. A number of different pilot-vehicle transfer functions were measured, and where appropriate, qualitatively compared with theoretical pilot- vehicle models. Some indirect evidence suggesting pursuit behavior on the part of the test subjects is discussed.