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…
Kosny, J.; Christian, J.E.; Desjarlais, A.O.; Kossecka, E.; Berrenberg, L.
1998-06-01
At the last IEA Annex 32 meeting it was proposed that the annex develop the links between level 1 (the whole building performance) and level 2 (the envelope system). This paper provides a case study of just that type of connection. An exterior wall mockup is hot box tested and modeled in the laboratory. Measurements of the steady state and dynamic behavior of this mockup are used as the basis to define the thermal bridging, thermal mass benefit and air tightness of the whole wall system. These level two performance characteristics are related to the whole building performance. They can be analyzed by a finite difference modeling of the wall assembly. An equivalent wall theory is used to convert three dimensional heat flow to one dimensional terms that capture thermal mass effects, which in turn are used in a common whole building simulation model. This paper illustrates a performance check between the thermal performance of a Massive ICF (Insulating Concrete Form) wall system mocked up (level 2) and Whole Building Performance criteria (level 1) such as total space heating and cooling loads (thermal comfort).
Whole building design guide -- A Department of Defense resource
Talton, D.O.
1999-07-01
The Whole Building Design Guide (EBDG) is a resource that defines the whole building process for high quality buildings (e.g., energy efficient, sustainable, aesthetic, durable, cost effective), and organizes and provides access to design guidance. The resource is web-based and can be accessed from the Naval Facilities Engineering Command (NAVFAC) Criteria Office web site.
Whole Building Energy Diagnostician, version 3.0
Energy Science and Technology Software Center (ESTSC)
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 usemore » 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.« less
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.
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.
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.
Cantera Aerosol Dynamics Simulator
Moffat, Harry
2004-09-01
The Cantera Aerosol Dynamics Simulator (CADS) package is a general library for aerosol modeling to address aerosol general dynamics, including formation from gas phase reactions, surface chemistry (growth and oxidation), bulk particle chemistry, transport by Brownian diffusion, thermophoresis, and diffusiophoresis with linkage to DSMC studies, and thermal radiative transport. The library is based upon Cantera, a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. The method uses a discontinuous galerkin formulation for the condensation and coagulation operator that conserves particles, elements, and enthalpy up to round-off error. Both O-D and 1-D time dependent applications have been developed with the library. Multiple species in the solid phase are handled as well. The O-D application, called Tdcads (Time Dependent CADS) is distributed with the library. Tdcads can address both constant volume and constant pressure adiabatic homogeneous problems. An extensive set of sample problems for Tdcads is also provided.
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.
Energy Science and Technology Software Center (ESTSC)
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.
Molecular dynamics simulations
Alder, B.J.
1985-07-01
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs.
Bauman, Nathan N.; Carlon, Teresa A.
2003-08-29
This document describes how to set up the Whole-Building Energy (WBE) module of the Whole-Building Diagnostician (WBD) for use in monitoring whole-building and major end-use energy consumption. It is a companion to the Instructions for Installation of the Whole-Building Diagnostician Software Release 2.10-162. This document describes how to set up the WBE software to collect new data or process data in existing data bases.
Cantera Aerosol Dynamics Simulator
Energy Science and Technology Software Center (ESTSC)
2004-09-01
The Cantera Aerosol Dynamics Simulator (CADS) package is a general library for aerosol modeling to address aerosol general dynamics, including formation from gas phase reactions, surface chemistry (growth and oxidation), bulk particle chemistry, transport by Brownian diffusion, thermophoresis, and diffusiophoresis with linkage to DSMC studies, and thermal radiative transport. The library is based upon Cantera, a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. The method uses a discontinuous galerkinmore » formulation for the condensation and coagulation operator that conserves particles, elements, and enthalpy up to round-off error. Both O-D and 1-D time dependent applications have been developed with the library. Multiple species in the solid phase are handled as well. The O-D application, called Tdcads (Time Dependent CADS) is distributed with the library. Tdcads can address both constant volume and constant pressure adiabatic homogeneous problems. An extensive set of sample problems for Tdcads is also provided.« less
Experimental verification of dynamic simulation
NASA Technical Reports Server (NTRS)
Yae, K. Harold; Hwang, Howyoung; Chern, Su-Tai
1989-01-01
The dynamics model here is a backhoe, which is a four degree of freedom manipulator from the dynamics standpoint. Two types of experiment are chosen that can also be simulated by a multibody dynamics simulation program. In the experiment, recorded were the configuration and force histories; that is, velocity and position, and force output and differential pressure change from the hydraulic cylinder, in the time domain. When the experimental force history is used as driving force in the simulation model, the forward dynamics simulation produces a corresponding configuration history. Then, the experimental configuration history is used in the inverse dynamics analysis to generate a corresponding force history. Therefore, two sets of configuration and force histories--one set from experiment, and the other from the simulation that is driven forward and backward with the experimental data--are compared in the time domain. More comparisons are made in regard to the effects of initial conditions, friction, and viscous damping.
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.
Energy Science and Technology Software Center (ESTSC)
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.
Dynamic simulation of voltage collapses
Deuse, J.; Stubbe, M. )
1993-08-01
Most of the time the voltage collapse phenomena are studied by means of computer programs designed for the calculation of steady state conditions. But in the real world, the simultaneous occurrences of losses of synchronism, of AVR dynamics or of transformer tap changes call for a full dynamic simulation of voltage phenomena. The present paper shows some examples of dynamic simulations of voltage phenomena using a new general purpose stability program (EUROSTAG), covering in a continuous way the classical fields of transient, mid-term and long-term stability, and also the quasi steady state conditions of a power system.
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. PMID:24600690
Tree Modeling and Dynamics Simulation
NASA Astrophysics Data System (ADS)
Tian-shuang, Fu; Yi-bing, Li; Dong-xu, Shen
This paper introduces the theory about tree modeling and dynamic movements simulation in computer graphics. By comparing many methods we choose Geometry-based rendering as our method. The tree is decomposed into branches and leaves, under the rotation and quaternion methods we realize the tree animation and avoid the Gimbals Lock in Euler rotation. We take Orge 3D as render engine, which has good graphics programming ability. By the end we realize the tree modeling and dynamic movements simulation, achieve realistic visual quality with little computation cost.
Simulation visualization through dynamic instrumentation
Bisset, K.R.
1998-09-01
The goal of the instrument composition system is to allow a simulation user to dynamically create instruments as a simulation executes. Instruments can include graphical displays, data collectors, and debugging aides. Instruments are made up of small building blocks which can be easily combined into larger, more complex instruments. Through the sue of an Attribute Server (a distributed publication/subscription mechanism), the actors and instruments in a simulation can interact without direct knowledge of each other. Instead, each actor publishes the attributes which it has available. An instrument subscribes to the attributes in which it is interested, and is notified whenever the value of one of these attribute changes. An instrument can also publish attributes for use by other instruments. Since the Attribute Server is distributed, the publisher of an attribute need not execute on the same machine as the subscriber. This allows CPU intensive data visualization to execute on separate machines from the simulation, minimizing the impact on the simulation.
Dynamic Simulation Nuclear Power Plants
Energy Science and Technology Software Center (ESTSC)
1992-03-03
DSNP (Dynamic Simulator for Nuclear Power-Plants) is a system of programs and data files by which a nuclear power plant, or part thereof, can be simulated. The acronym DSNP is used interchangeably for the DSNP language, the DSNP libraries, the DSNP precompiler, and the DSNP document generator. The DSNP language is a special-purpose, block-oriented, digital-simulation language developed to facilitate the preparation of dynamic simulations of a large variety of nuclear power plants. It is amore » user-oriented language that permits the user to prepare simulation programs directly from power plant block diagrams and flow charts by recognizing the symbolic DSNP statements for the appropriate physical components and listing these statements in a logical sequence according to the flow of physical properties in the simulated power plant. Physical components of nuclear power plants are represented by functional blocks, or modules. Many of the more complex components are represented by several modules. The nuclear reactor, for example, has a kinetic module, a power distribution module, a feedback module, a thermodynamic module, a hydraulic module, and a radioactive heat decay module. These modules are stored in DSNP libraries in the form of a DSNP subroutine or function, a block of statements, a macro, or a combination of the above. Basic functional blocks such as integrators, pipes, function generators, connectors, and many auxiliary functions representing properties of materials used in nuclear power plants are also available. The DSNP precompiler analyzes the DSNP simulation program, performs the appropriate translations, inserts the requested modules from the library, links these modules together, searches necessary data files, and produces a simulation program in FORTRAN.« less
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.
Radiation in molecular dynamic simulations
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M
2008-10-13
Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.
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 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.
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.
Molecular Dynamics Simulations of Polymers
NASA Astrophysics Data System (ADS)
Han, Jie
1995-01-01
Molecular dynamics (MD) simulations have been undertaken in this work to explore structures and properties of polyethylene (PE), polyisobutylene (PIB), atactic polypropylene (aPP) and atactic polystyrene (aPS). This work has not only demonstrated the reliability of MD simulations by comparing results with available experiments, but more importantly has revealed structure-property relationships on a molecular level for these selected polymers. Structures of these amorphous polymers were characterized by radial distribution functions (RDFs) or scattering profiles, and properties of the polymers studied were pressure-volume -temperature (PVT) equation of state, enthalpy, cohesive energy, the diffusion coefficient of methane in the polymer, and glass transition temperature. Good agreement was found for these structures and properties between simulation and experiment. More importantly, the scientific understanding of structure-property relationships was established on a molecular level. In the order of aPP (PE), PIB and aPS, with the chain surface separation or free volume decreasing, the density increases and the diffusion coefficient decreases. Therefore, the effects of changes or modifications in the chemical structure of monomer molecules (substituting pendent hydrogen with methyl or phenyl) on polymeric materials performance were attributed to the effects of molecular chain structure on packing structure, which, in turn, affects the properties of these polymers. Local chain dynamics and relaxation have been studied for bulk PE and aPS. Cooperative transitions occur at second-neighbor bonds for PE, and first-neighbor bonds for aPS due to the role of side groups. The activation energy is a single torsional barrier for overall conformational transitions, and is single torsional barrier plus locally "trapped" barrier for relaxation. Temperature dependence is Arrhenius for transition time, and is WLF for relaxation time. The mean correlation times derived from
Simulation of Fault Zone Dynamics
NASA Astrophysics Data System (ADS)
Mora, P.; Abe, S.; Place, D.
2002-12-01
Particle models such as the discrete element model for granular assemblies and the lattice solid model provide a means to study the dynamics of fault zones. The lattice solid model was developed with the aim of progressively building up the capacity to simulate all relevent physical processes in fault zones. The present implementation of the model is able to simulate the dynamics of a granular lattice consisting of bonded or unbonded circular (2D) or spherical (3D) particles. Thermal effects (frictional hear generation, thermal expansion, heat flow) and pore fluid effects (heat induced pore pressure gradients and the consequent Darcian flow and impact on effective friction) can be modelled. Past work involving both circular particles and non-circular grains constructed as groups of bonded particles have demonstrated that grain shape has a fundamental impact on zero-th order behaviour. When circular particles are used, rolling is the most efficient means to accomodate slip of a simulated fault gouge layer leading to unrealistically low friction, typically around 0.2. This is consistent with laboratory results by Mair and Marone which have demonstrated that gouge consisting entirely of spherical beads shows a lower coefficient of friction than gouge containing irregular shaped particles. Recent work comparing quasi-2D laboratory results using pasta (Marone) with 2D numerical results (Morgan) have confirmed that numerical and laboratory results with circular ``particles'' are in agreement. When irregular grains are modelled at the lowest scale, the friction of simulated gouge layers matches with laboratory observations of rock friction (μ ~ 0.6) and is insentitive to the value used for interparticle friction (Mora et al, 2000). This indicates a self-regulation mechanism is occurring in which the group behaviour of the gouge layer remains constant at around 0.6 by balancing the amount of slip and rolling of grains within the gouge layer. A limitation of these studies
Demonstration of the Whole-Building Diagnostician in a Single-Building Operator Environment
Katipamula, Srinivas; Bauman, Nathan N.; Pratt, Robert G.; Brambley, Michael R.
2003-03-31
This report on documents the results of the single-building-operator, on-line, demonstration of the Whole-Building Diagnostician, conducted at the Symphony Towers building in San Diego, California. The on-line test was designed to evaluate the Outdoor-Air Economizer (OAE) diagnostic module’s capabilities to automatically and continually diagnose operational problems with air-handling units (AHUs). As part of this demonstration, all four AHUs at Symphony Towers were monitored. The measured data that were collected on a continuous basis included: 1) outdoor-air temperature, 2) return-air temperature, 3) mixed-air temperature, 4) supply-air temperature, 5) chilled-water valve position, 6) supply-fan status, 7) outdoor-air relative humidity, and 8) return-air relative humidity.
Dynamics of riboswitches: Molecular simulations.
Sanbonmatsu, Karissa Y
2014-10-01
Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail. Molecular dynamics simulations are useful for interpreting existing experimental data and producing predictions for new experiments. Here, a wide range of computational studies on riboswitches is reviewed. By elucidating the key principles of riboswitch operation, computation may aid in the effort to design more specific antibiotics with affinities greater than those of the native ligand. Such a detailed understanding may be required to improve efficacy and reduce side effects. These studies are laying the groundwork for understanding the action mechanism of new compounds that inhibit riboswitch activity. Future directions such as magnesium effects, large-scale conformational changes, expression platforms and co-transcriptional folding are also discussed. This article is part of a Special Issue entitled: Riboswitches. PMID:24953187
Molecular dynamics simulations of large macromolecular complexes
Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus
2015-01-01
Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770
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.
Brownian Dynamics Simulations of Dispersed Graphene Sheets
NASA Astrophysics Data System (ADS)
Xu, Yueyi; Green, Micah
2013-03-01
Past simulations of the dynamics of dispersed graphene sheets are limited to static fluids on small timescales, with little attention devoted to flow dynamics. To address this need, we investigated how flow fields affect graphene morphology dynamics using a coarse-grained model; this relatively untouched area is critical given the importance of graphene solution-processing of multifunctional devices and materials. In particular, we developed a Brownian Dynamics (BD) algorithm to study the morphology of sheetlike macromolecules in dilute, flowing solutions. We used a bead-rod lattice to represent the mesoscopic conformation of individual two dimensional sheets. We then analyzed the morphology dynamic modes (stretching, tumbling, crumpling) of these molecules as a function of sheet size, Weissenberg number, and bending stiffness. Our results indicate the model can successfully simulate a range of dynamic modes in a given flow field and yield fundamental insight into the flow processing of graphene sheets.
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)
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.
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.
Simulation of liquid dynamics onboard Sloshsat FLEVO
NASA Astrophysics Data System (ADS)
Vreeburg, J. P. B.
1999-01-01
The Sloshsat FLEVO project has an Investigators Working Group which prepared orbital experiments on the behavior of liquid in spacecraft. These are to be performed with a dedicated small satellite, of about 90 kg empty weight and about 34 kg of water in a 87 litre tank. The spacecraft dynamics are simulated by SMS, the Sloshsat Motion Simulator. SMS predictions and those generated by a CFD simulation are compared for an example.
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.
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.
Structure and dynamics of complex liquid water: Molecular dynamics simulation
NASA Astrophysics Data System (ADS)
S, Indrajith V.; Natesan, Baskaran
2015-06-01
We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.
DUVFEL PHOTOINJECTOR DYNAMICS: MEASUREMENT AND SIMULATION.
GRAVES, W.S.; DIMAURO, L.F.; HEESE, R.; JOHNSON, E.D.; ROSE, J.; RUDATI, J.; SHAFTAN, T.; SHEEHY, B.; YU, L.H.; DOWELL, D.H.
2001-06-18
The DUVFEL photoinjector consists of a 1.6 cell BNL gun IV with copper cathode, variable pulse length Ti:Sapp and solenoid magnet. The beam dynamics and the electromagnetic fields in the photoinjector have been characterized by producing a short electron beam with very low charge that is used as a field probe. Transverse beam size and divergence are measured as a function of initial RF phase and initial spot size and compared with simulations using the code HOMDYN. The electromagnetic fields used in the simulations are produced by SUPERFISH, and have been verified with RF measurements. The simulations and measurements of beam dynamics are presented.
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.
Dynamic system simulation of small satellite projects
NASA Astrophysics Data System (ADS)
Raif, Matthias; Walter, Ulrich; Bouwmeester, Jasper
2010-11-01
A prerequisite to accomplish a system simulation is to have a system model holding all necessary project information in a centralized repository that can be accessed and edited by all parties involved. At the Institute of Astronautics of the Technische Universitaet Muenchen a modular approach for modeling and dynamic simulation of satellite systems has been developed called dynamic system simulation (DySyS). DySyS is based on the platform independent description language SysML to model a small satellite project with respect to the system composition and dynamic behavior. A library of specific building blocks and possible relations between these blocks have been developed. From this library a system model of the satellite of interest can be created. A mapping into a C++ simulation allows the creation of an executable system model with which simulations are performed to observe the dynamic behavior of the satellite. In this paper DySyS is used to model and simulate the dynamic behavior of small satellites, because small satellite projects can act as a precursor to demonstrate the feasibility of a system model since they are less complex compared to a large scale satellite project.
Discrete dislocation dynamics simulations in a cylinder
NASA Astrophysics Data System (ADS)
Li, Maosheng; Gao, Chan; Xu, Jianing
2015-02-01
Mechanical properties of material are closely related to the motion of dislocations, and predicting the interactions and resulting collective motion of dislocations is a major task in understanding and modelling plastically deforming materials. A discrete dislocation dynamics model is used to describe the orientation substructure within the microstructure. Discrete dislocation dynamics simulations in three dimensions have been used to examine the role of dislocation multiplication and mobility on the plasticity in small samples under uniaxial compression. In this paper we describe the application of the dislocation dynamics simulations in a cylindrical geometry. The boundary conditions for the simulation were estimated from the distribution of the geometrically necessary dislocation density which was obtained from the orientation map. Numerical studies benchmark could validate the accuracy of the algorithms and the importance of handling the singularity correctly. The results of the simulation explain the formation of the experimentally observed substructure.
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.
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
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
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
Buckybomb: Reactive Molecular Dynamics Simulation.
Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V
2015-03-01
Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672
Crawley, D.B.; Briggs, R.S.; Jones, J.W.; Seaton, W.W.; Kaufman, J.E.; Deringer, J.J.; Kennett, E.W.
1987-04-01
This report describes background research for preparation of a plan for development of whole-building energy targets for new commercial buildings. The lead laboratory for this program is the Pacific Northwest Laboratory. A wide variety of expertise and resources from industry, academia, other government entities, and other DOE laboratories are used in planning, reviewing and conducting research activities. Cooperative and complementary research development, and technology transfer activities with other interested organizations are actively pursued.
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.
Computer simulation of microstructural dynamics
Grest, G.S.; Anderson, M.P.; Srolovitz, D.J.
1985-01-01
Since many of the physical properties of materials are determined by their microstructure, it is important to be able to predict and control microstructural development. A number of approaches have been taken to study this problem, but they assume that the grains can be described as spherical or hexagonal and that growth occurs in an average environment. We have developed a new technique to bridge the gap between the atomistic interactions and the macroscopic scale by discretizing the continuum system such that the microstructure retains its topological connectedness, yet is amenable to computer simulations. Using this technique, we have studied grain growth in polycrystalline aggregates. The temporal evolution and grain morphology of our model are in excellent agreement with experimental results for metals and ceramics.
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.
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.
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. PMID:24073784
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.
Fully dynamical simulation of central nuclear collisions.
van der Schee, Wilke; Romatschke, Paul; Pratt, Scott
2013-11-27
We present a fully dynamical simulation of central nuclear collisions around midrapidity at LHC energies. Unlike previous treatments, we simulate all phases of the collision, including the equilibration of the system. For the simulation, we use numerical relativity solutions to anti-de Sitter space/conformal field theory for the preequilibrium stage, viscous hydrodynamics for the plasma equilibrium stage, and kinetic theory for the low-density hadronic stage. Our preequilibrium stage provides initial conditions for hydrodynamics, resulting in sizable radial flow. The resulting light particle spectra reproduce the measurements from the ALICE experiment at all transverse momenta. PMID:24329444
Molecular dynamics simulation of ice XII
NASA Astrophysics Data System (ADS)
Borzsák, István; Cummings, Peter T.
1999-02-01
Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.
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.
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.
ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*
Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan
2014-01-01
Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670
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.
Simulation studies using multibody dynamics code DART
NASA Technical Reports Server (NTRS)
Keat, James E.
1989-01-01
DART is a multibody dynamics code developed by Photon Research Associates for the Air Force Astronautics Laboratory (AFAL). The code is intended primarily to simulate the dynamics of large space structures, particularly during the deployment phase of their missions. DART integrates nonlinear equations of motion numerically. The number of bodies in the system being simulated is arbitrary. The bodies' interconnection joints can have an arbitrary number of degrees of freedom between 0 and 6. Motions across the joints can be large. Provision for simulating on-board control systems is provided. Conservation of energy and momentum, when applicable, are used to evaluate DART's performance. After a brief description of DART, studies made to test the program prior to its delivery to AFAL are described. The first is a large angle reorientating of a flexible spacecraft consisting of a rigid central hub and four flexible booms. Reorientation was accomplished by a single-cycle sine wave shape torque input. In the second study, an appendage, mounted on a spacecraft, was slewed through a large angle. Four closed-loop control systems provided control of this appendage and of the spacecraft's attitude. The third study simulated the deployment of the rim of a bicycle wheel configuration large space structure. This system contained 18 bodies. An interesting and unexpected feature of the dynamics was a pulsing phenomena experienced by the stays whole playout was used to control the deployment. A short description of the current status of DART is given.
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.
Dynamic simulation of the mastication muscles
NASA Astrophysics Data System (ADS)
Weingaertner, Tim; Albrecht, Jochen
1998-05-01
The purpose of a simulated operation system in craniofacial surgery is to evaluate and visualize the results of operations on the overall facial shape of the patient and on the functionality of his jaw. This paper presents the analyzation of muscle movements in the mastication system by applying real jaw movements to the simulation. With this method an accurate modeling of the mastication muscles can be performed which is a prerequisite for a realistic simulation and precise intra- operative registration. According to this results a large- scale musculoskeletal model of the mastication system is generated including kinematic and dynamic parameters. By integrating distance sensors in the simulation of a segmented CT (computer tomograph) image of the maxilla and mandible the motions of the masticatory muscles during different kinds of jaw movements have been analyzed. The data for this motions have been recorded by a commercial system (CONDYLOCOMP LR3) on a test person and transformed to the graphical simulation system. This method for the first time allows to observe the dynamics of the mastication muscles and their different parameters like muscle length ratio and velocity. The integration of a kinematic model for the jaw movement makes it possible to analyze non traced movements.
Dynamic Simulation of a Helium Liquefier
Maekawa, R.; Ooba, K.; Mito, T.; Nobutoki, M.
2004-06-23
Dynamic behavior of a helium liquefier has been studied in detail with a Cryogenic Process REal-time SimulaTor (C-PREST) at the National Institute for Fusion Science (NIFS). The C-PREST is being developed to integrate large-scale helium cryogenic plant design, operation and maintenance for optimum process establishment. As a first step of simulations of cooldown to 4.5 K with the helium liquefier model is conducted, which provides a plant-process validation platform. The helium liquefier consists of seven heat exchangers, a liquid-nitrogen (LN2) precooler, two expansion turbines and a liquid-helium (LHe) reservoir. Process simulations are fulfilled with sequence programs, which were implemented with C-PREST based on an existing liquefier operation. The interactions of a JT valve, a JT-bypass valve and a reservoir-return valve have been dynamically simulated. The paper discusses various aspects of refrigeration process simulation, including its difficulties such as a balance between complexity of the adopted models and CPU time.
Thermostability of Enzymes from Molecular Dynamics Simulations.
Zeiske, Tim; Stafford, Kate A; Palmer, Arthur G
2016-06-14
Thermodynamic stability is a central requirement for protein function, and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitro thermostability of members of the bacterial ribonuclease HI (RNase H) family of endonucleases. The temperature dependence of the generalized order parameter, S, for four RNase H homologues, from psychrotrophic, mesophilic, and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. PMID:27123810
Nanoindentation of Zr by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.
2015-12-01
Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.
Numerical Simulations of Ion Cloud Dynamics
NASA Astrophysics Data System (ADS)
Sillitoe, Nicolas; Hilico, Laurent
We explain how to perform accurate numerical simulations of ion cloud dynamics by discussing the relevant orders of magnitude of the characteristic times and frequencies involved in the problem and the computer requirement with respect to the ion cloud size. We then discuss integration algorithms and Coulomb force parallelization. We finally explain how to take into account collisions, cooling laser interaction and chemical reactions in a Monte Carlo approach and discuss how to use random number generators to that end.
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.
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. PMID:25615220
Electronic continuum model for molecular dynamics simulations.
Leontyev, I V; Stuchebrukhov, A A
2009-02-28
A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627
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.
Molecular dynamics simulation of liquid sulfur dioxide.
Ribeiro, Mauro C C
2006-05-01
A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k). PMID:16640437
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. PMID:20365123
Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Byutner, Oleksiy; Smith, Grant
2001-03-01
In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.
Simulating coronal condensation dynamics in 3D
NASA Astrophysics Data System (ADS)
Moschou, S. P.; Keppens, R.; Xia, C.; Fang, X.
2015-12-01
We present numerical simulations in 3D settings where coronal rain phenomena take place in a magnetic configuration of a quadrupolar arcade system. Our simulation is a magnetohydrodynamic simulation including anisotropic thermal conduction, optically thin radiative losses, and parametrised heating as main thermodynamical features to construct a realistic arcade configuration from chromospheric to coronal heights. The plasma evaporation from chromospheric and transition region heights eventually causes localised runaway condensation events and we witness the formation of plasma blobs due to thermal instability, that evolve dynamically in the heated arcade part and move gradually downwards due to interchange type dynamics. Unlike earlier 2.5D simulations, in this case there is no large scale prominence formation observed, but a continuous coronal rain develops which shows clear indications of Rayleigh-Taylor or interchange instability, that causes the denser plasma located above the transition region to fall down, as the system moves towards a more stable state. Linear stability analysis is used in the non-linear regime for gaining insight and giving a prediction of the system's evolution. After the plasma blobs descend through interchange, they follow the magnetic field topology more closely in the lower coronal regions, where they are guided by the magnetic dips.
Molecular Dynamics Simulation of Shock Induced Detonation
NASA Astrophysics Data System (ADS)
Tomar, Vikas; Zhou, Min
2004-07-01
This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.
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.
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.
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.
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
Local Refinements in Classical Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Fackeldey, Konstantin; Weber, Marcus
2014-03-01
Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.
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.
Molecular Dynamics Simulations of Graphene Oxide Frameworks
Zhu, Pan; Sumpter, Bobby G; Meunier, V.; Nicolai, Adrien
2013-01-01
We use quantum mechanical calculations to develop a full set of force field parameters in order to perform molecular dynamics simulations to understand and optimize the molecular storage properties inside Graphene Oxide Frameworks (GOFs). A set of boron-related parameters for commonly used empirical force fields is determined to describe the non-bonded and bonded interactions between linear boronic acid linkers and graphene sheets of GOF materials. The transferability of the parameters is discussed and their validity is quantified by comparing quantum mechanical and molecular mechanical structural and vibrational properties. The application of the model to the dynamics of water inside the GOFs reveals significant variations in structural flexibility of GOF depending on the linker density, which is shown to be usable as a tuning parameter for desired diffusion properties.
Finite element simulation of pipe dynamic response
Slagis, G.C.; Litton, R.W.
1996-12-01
Nonlinear finite element dynamic analyses of the response of a pipe span to controlled-displacement, sinusoidal vibration have been performed. The objective of this preliminary study is to compare strain and acceleration response data to those generated by Beaney in the Berkeley Nuclear Laboratories experiments. Results for an unpressurized, 5 Hz, carbon steel pipe are in good agreement with the experiments. Hence, it appears that analytical simulation will be useful to assess seismic margins. Recommendations for additional studies are provided. The analyses confirm the test results--dynamic response is greatly attenuated by material plasticity. Analytical strains and accelerations are about 30% higher than test data. There are several possible explanations for the differences. To assess the effect of frequency on response, the length of the pipe span was increased. Analysis of the longer, 2 Hz, pipe span shows significantly greater cyclic strains than the 5 Hz span at the same input excitation levels.
Molecular dynamics simulations of weak detonations.
Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie
2011-12-01
Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055
Dynamic simulations of membranes with cytoskeletal interactions
NASA Astrophysics Data System (ADS)
Lin, Lawrence C.-L.; Brown, Frank L. H.
2005-07-01
We describe a simulation algorithm for the dynamics of elastic membrane sheets over long length and time scales. Our model includes implicit hydrodynamic coupling between membrane and surrounding solvent and allows for arbitrary external forces acting on the membrane surface. In particular, the methodology is well suited to studying membranes in interaction with cytoskeletal filaments. We present results for the thermal undulations of a lipid bilayer attached to a regular network of spectrin filaments as a model for the red blood cell membrane. The dynamic fluctuations of the bilayer over the spectrin network are quantified and used to predict the macroscopic diffusion constant of band 3 on the surface of the red blood cell. We find that thermal undulations likely play a role in the mobility of band 3 in the plane of the erythrocyte membrane.
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..
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}.
Dynamic Curving Simulation of Tilting Train
NASA Astrophysics Data System (ADS)
Zeng, Jing; Luo, Ren
The application of carbody tilting technology is the most efficient way to raise train speed during curve negotiations. This paper mainly deals with the dynamic performance simulation of the tilting train. Through the establishment of the nonlinear mathematical model for the titling train electromechanical coupled system, the carbody tilting control law, bogie radial steering mechanism, and titling train curving performance are investigated. The effect of time delay caused by the sensing and control system on the tilting performance of the train is analyzed, and the compensation methods for the time delay effect are studied.
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.
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.
Dynamic stiffness removal for direct numerical simulations
Lu, Tianfeng; Law, Chung K.; Yoo, Chun Sang; Chen, Jacqueline H.
2009-08-15
A systematic approach was developed to derive non-stiff reduced mechanisms for direct numerical simulations (DNS) with explicit integration solvers. The stiffness reduction was achieved through on-the-fly elimination of short time-scales induced by two features of fast chemical reactivity, namely quasi-steady-state (QSS) species and partial-equilibrium (PE) reactions. The sparse algebraic equations resulting from QSS and PE approximations were utilized such that the efficiency of the dynamic stiffness reduction is high compared with general methods of time-scale reduction based on Jacobian decomposition. Using the dimension reduction strategies developed in our previous work, a reduced mechanism with 52 species was first derived from a detailed mechanism with 561 species. The reduced mechanism was validated for ignition and extinction applications over the parameter range of equivalence ratio between 0.5 and 1.5, pressure between 10 and 50 atm, and initial temperature between 700 and 1600 K for ignition, and worst-case errors of approximately 30% were observed. The reduced mechanism with dynamic stiffness removal was then applied in homogeneous and 1-D ignition applications, as well as a 2-D direct numerical simulation of ignition with temperature inhomogeneities at constant volume with integration time-steps of 5-10 ns. The integration was numerically stable and good accuracy was achieved. (author)
Molecular dynamics simulation of amorphous indomethacin.
Xiang, Tian-Xiang; Anderson, Bradley D
2013-01-01
Molecular dynamics (MD) simulations have been conducted using an assembly consisting of 105 indomethacin (IMC) molecules and 12 water molecules to investigate the underlying dynamic (e.g., rotational and translational diffusivities and conformation relaxation rates) and structural properties (e.g., conformation, hydrogen-bonding distributions, and interactions of water with IMC) of amorphous IMC. These properties may be important in predicting physical stability of this metastable material. The IMC model was constructed using X-ray diffraction data with the force-field parameters mostly assigned by analogy with similar groups in Amber-ff03 and atomic charges calculated with the B3LYP/ccpVTZ30, IEFPCM, and RESP models. The assemblies were initially equilibrated in their molten state and cooled through the glass transition temperature to form amorphous solids. Constant temperature dynamic runs were then carried out above and below the T(g) (i.e., at 600 K (10 ns), 400 K (350 ns), and 298 K (240 ns)). The density (1.312 ± 0.003 g/cm(3)) of the simulated amorphous solid at 298 K was close to the experimental value (1.32 g/cm(3)) while the estimated T(g) (384 K) was ~64 degrees higher than the experimental value (320 K) due to the faster cooling rate. Due to the hindered rotation of its amide bond, IMC can exist in different diastereomeric states. Different IMC conformations were sufficiently sampled in the IMC melt or vapor, but transitions occurred rarely in the glass. The hydrogen-bonding patterns in amorphous IMC are more complex in the amorphous state than in the crystalline polymorphs. Carboxylic dimers that are dominant in α- and γ-crystals were found to occur at a much lower probability in the simulated IMC glasses while hydrogen-bonded IMC chains were more easily identified patterns in the simulated amorphous solids. To determine molecular diffusivity, a novel analytical method is proposed to deal with the non-Einsteinian behavior, in which the temporal
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. PMID:27544106
Atomistic molecular dynamic simulations of multiferroics.
Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L
2012-08-10
A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300
Atomistic Molecular Dynamic Simulations of Multiferroics
NASA Astrophysics Data System (ADS)
Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.
2012-08-01
A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.
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.
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.
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
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
Dynamics simulations for engineering macromolecular interactions
Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey
2013-01-01
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
A whole building demonstration of re-cover over an existing wet roof
Desjarlais, A.O.; Petrie, T.W.; Christian, J.E.; McLain, H.A.; Childs, P.W.
1995-12-31
Roof re-cover, the practice of installing a new roof over an existing failed roof, has become commonplace. The 1994 National Roofing Contractors Annual Roofing Survey reported that approximately 33% of current reroofing activity is re-cover. Market trends suggest that re-cover will become an increasingly more popular option. Moisture in the failed roof complicates the decision whether or not to re-cover and how to do the recover if that is the decision. If the root to be re-covered contains moisture that will not be removed during reroofing, this moisture must be able to escape from the roof system. Otherwise, moisture entrapped in the roofing system may eventually lead to the mechanical failure of fasteners and the roof deck, especially if it is metal. In 1991, the Oak Ridge National Laboratory (ORNL) surveyed its own roofing inventory and found that 164 buildings or 70% of the laboratory roof area needed reroofing. Because of the high cost of tear off and replacement, an alterative was sought. This paper describes the procedure employed to determine the suitability of a particular roof system on a laboratory building for re-covering. The procedure involves the use of field diagnostics, laboratory experiments and numerical simulations that demonstrate that the particular roof type can be re-covered. Furthermore, the building and roof system have been monitored for approximately 16 months after re-cover. The monitoring results are compared to the numerical simulations and demonstrate that the roof system is drying and that the reroofing strategy that they used is cost-effective.
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.
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
Schwabe, Tobias
2015-08-20
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273
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.
Molecular Dynamics Simulations of Water Evaporation
NASA Astrophysics Data System (ADS)
Wen, Chengyuan; Grest, Gary; Cheng, Shengfeng
2015-03-01
The evaporation of water from the liquid/vapor interface is studied via large-scale molecular dynamics simulations for systems of more than a million atoms at 550K and 600K. The TIP4P-2005 water model whose liquid/vapor surface tension is in excellent agreement with experiments is used. Evaporative cooling at the interface is observed from temperature profiles determined from both translational and rotational kinetic energy. During evaporation, the density of water is slightly enhanced near the liquid-vapor interface. The velocity distribution of water molecules in the vapor phase during evaporation at various distances relative to the interface fit a Maxwell-Boltzmann distribution. While our results indicate an imbalance between evaporating and condensing water molecules, local thermal equilibrium is found to hold in addition to mechanical equilibrium. Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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.
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
Numerical simulations of Modified Newtonian Dynamics
NASA Astrophysics Data System (ADS)
Candlish, G. N.; Smith, R.; Fellhauer, M.
2016-05-01
The ΛCDM standard cosmological model is strongly supported by multiple lines of evidence, particularly from observations at large scales such as the CMB and large scale structure. There are some indications, however, of problems at smaller scales. An alternative to the CDM approach is to modify the gravitational force, as exemplified by the MOdified Newtonian Dynamics (MOND) idea. While evidence suggests MOND cannot account for dynamics at all scales without dark matter, it has been successful at galactic scales. Due to the complexity of the theory, however, most tests of MOND have extended no further than using a simple scaling relation to determine rotation curves or velocity dispersions. Therefore, to test the concept more thoroughly we require numerical simulations. We discuss the development and testing of a new N-body solver, using two distinct formulations of MOND, that is incorporated into the RAMSES code. The theory of MOND as a modification of Newtonian gravity is briefly summarised. We then show how it is implemented in the code, providing an example of an idealised test case and future applications.
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.
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.
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...
Validation of vehicle dynamics simulation models - a review
NASA Astrophysics Data System (ADS)
Kutluay, Emir; Winner, Hermann
2014-02-01
In this work, a literature survey on the validation of vehicle dynamics simulation models is presented. Estimating the dynamic responses of existing or proposed vehicles has a wide array of applications in the development of vehicle technologies, e.g. active suspensions, controller design, driver assistance systems, etc. Although simulation environments, measurement tools and mathematical theories on vehicle dynamics are well established, the methodical link between the experimental test data and validity analysis of the simulation model is still lacking. This report presents different views on the definition of validation, and its usage in vehicle dynamics simulation models.
Studying Interactions by Molecular Dynamics Simulations at High Concentration
Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro
2012-01-01
Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085
Analysis & Simulation of Dynamics in Supercooled Liquids
NASA Astrophysics Data System (ADS)
Elmatad, Yael Sarah
2011-12-01
The nature of supercooled liquids and the glass transition has been debated by many scientists. Several theories have been put forth to describe the remarkable properties of this out-of-equilibrium material. Each of these theories makes specific predictions as to how the scaling of various transport properties in supercooled materials should behave. Given access to a large pool of high-quality supercooled liquid data we seek to compare these theories to one another. Moreover, we explore properties of a pair of models which are the basis for one particularly attractive theory---Chandler-Garrahan theory---and discuss the models' behavior in space-time and possible implications to the behavior of experimental supercooled liquids. Here we investigate the nature of dynamics in supercooled liquids using a two pronged approach. First we analyze the transport properties found in experiments and simulations of supercooled liquids. Then, we analyze simulation trajectories for lattice models which reproduce many of the interesting properties of supercooled liquids. In doing so, we illuminate several glass universalities, common properties of a wide variety of glass formers. By analyzing relaxation time and viscosity data for over 50 data sets and 1200 points, we find that relaxation time can be collapsed onto a single, parabolic curve. This collapse supports a theory of universal glass behavior based on facilitated models proposed by David Chandler and Juan Garrahan in 2003. We then show that the parabolic fit parameters for any particular liquid are a material property: they converge fast and are capable of predicting behavior in regions beyond the included data sets. We compare this property to other popular fitting schemes such as the Vogel-Fulcher, double exponential, and fractional exponential forms and conclude that these three forms result in parameters which are non predictive and therefore not material properties. Additionally, we examine the role of attractive
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.
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
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.
Molecular dynamics simulations of supramolecular polymer rheology
NASA Astrophysics Data System (ADS)
Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.
2010-11-01
Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.
Numerical simulation of magma chamber dynamics.
NASA Astrophysics Data System (ADS)
Longo, Antonella; Papale, Paolo; Montagna, Chiara Paola; Vassalli, Melissa; Giudice, Salvatore; Cassioli, Andrea
2010-05-01
Magma chambers are characterized by periodic arrivals of deep magma batches that give origin to complex patterns of magma convection and mixing, and modify the distribution of physical quantities inside the chamber. We simulate the transient, 2D, multi-component homogeneous dynamics in geometrically complex dyke+chamber systems, by means of GALES, a finite element parallel C++ code solving mass, momentum and energy equations for multi-component homogeneous gas-liquid (± crystals) mixtures in compressible-to-incompressible flow conditions. Code validation analysis includes several cases from the classical engineering literature, corresponding to a variety of subsonic to supersonic gas-liquid flow regimes (see http://www.pi.ingv.it/~longo/gales/gales.html). The model allows specification of the composition of the different magmas in the domain, in terms of ten major oxides plus the two volatile species H2O and CO2. Gas-liquid thermodynamics are modeled by using the compositional dependent, non-ideal model in Papale et al. (Chem.. Geol., 2006). Magma properties are defined in terms of local pressure, temperature, and composition including volatiles. Several applications are performed within domains characterized by the presence of one or more magma chambers and one or more dykes, with different geometries and characteristic size from hundreds of m to several km. In most simulations an initial compositional interface is placed at the top of a feeding dyke, or at larger depth, with the deeper magma having a lower density as a consequence of larger volatile content. The numerical results show complex patterns of magma refilling in the chamber, with alternating phases of magma ingression and magma sinking from the chamber into the feeding dyke. Intense mixing takes place in feeding dykes, so that the new magma entering the chamber is always a mixture of the deep and the initially resident magma. Buoyant plume rise occurs through the formation of complex convective
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
2011-07-01
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. PMID:21797586
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.
Staggered solution procedures for multibody dynamics simulation
NASA Technical Reports Server (NTRS)
Park, K. C.; Chiou, J. C.; Downer, J. D.
1990-01-01
The numerical solution procedure for multibody dynamics (MBD) systems is termed a staggered MBD solution procedure that solves the generalized coordinates in a separate module from that for the constraint force. This requires a reformulation of the constraint conditions so that the constraint forces can also be integrated in time. A major advantage of such a partitioned solution procedure is that additional analysis capabilities such as active controller and design optimization modules can be easily interfaced without embedding them into a monolithic program. After introducing the basic equations of motion for MBD system in the second section, Section 3 briefly reviews some constraint handling techniques and introduces the staggered stabilized technique for the solution of the constraint forces as independent variables. The numerical direct time integration of the equations of motion is described in Section 4. As accurate damping treatment is important for the dynamics of space structures, we have employed the central difference method and the mid-point form of the trapezoidal rule since they engender no numerical damping. This is in contrast to the current practice in dynamic simulations of ground vehicles by employing a set of backward difference formulas. First, the equations of motion are partitioned according to the translational and the rotational coordinates. This sets the stage for an efficient treatment of the rotational motions via the singularity-free Euler parameters. The resulting partitioned equations of motion are then integrated via a two-stage explicit stabilized algorithm for updating both the translational coordinates and angular velocities. Once the angular velocities are obtained, the angular orientations are updated via the mid-point implicit formula employing the Euler parameters. When the two algorithms, namely, the two-stage explicit algorithm for the generalized coordinates and the implicit staggered procedure for the constraint Lagrange
System dynamic simulation of precision segmented reflector
NASA Technical Reports Server (NTRS)
Shih, Choon-Foo; Lou, Michael C.
1991-01-01
A joint effort was undertaken on a Precision Segmented Reflector (PSR) Project. The missions in which the PSR is to be used will use large (up to 20 m in diameter) telescopes. The essential requirement for the telescopes is that the reflector surface of the primary mirror must be made extremely precise to allow no more than a few microns of errors and, additionally, this high surface precision must be maintained when the telescope is subjected to on-orbital mechanical and thermal disturbances. Based on the mass, size, and stability considerations, reflector surface formed by segmented, probably actively or passively controlled, composite panels are regarded as most suitable for future space based astronomical telescope applications. In addition to the design and fabrication of composite panels with a surface error of less than 3 microns RMS, PSR also develops related reflector structures, materials, control, and sensing technologies. As part of the planning effort for PSR Technology Demonstration, a system model which couples the reflector, consisting of panels, support truss and actuators, and the optical bench was assembled for dynamic simulations. Random vibration analyses using seismic data obtained from actual measurements at the test site designated for PSR Technology Demonstration are described.
Kinetic simulations of plasmoid chain dynamics
Markidis, S.; Henri, P.; Lapenta, G.; Divin, A.; Goldman, M.; Newman, D.; Laure, E.
2013-08-15
The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids.
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.
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.
Nanoscale deicing by molecular dynamics simulation.
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-08-14
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. PMID:27431975
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.
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.
NASA Astrophysics Data System (ADS)
Brennan, John K.; Lísal, Martin; Gubbins, Keith E.; Rice, Betsy M.
2004-12-01
A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2+3H2⇔2NH3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.
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 note on simulation and dynamical hierarchies
Rasmussen, S.; Barrett, C.L. |; Baas, N.A.; Olesen, M.W.
1996-02-22
This paper summarizes some of the problems associated with the generation of higher order emergent structures in formal dynamical systems as well as some of the formal properties of dynamical systems capable of generating higher order structures.
Research on hyperspectral dynamic infrared scene simulation technology
NASA Astrophysics Data System (ADS)
Wang, Jun; Hu, Yu; Ding, Na; Sun, Kefeng; Sun, Dandan; Xie, Junhu; Wu, Wenli; Gao, Jiaobo
2015-02-01
The paper presents a hardware in loop dynamic IR scene simulation technology for IR hyperspectral imaging system. Along with fleetly development of new type EO detecting, remote sensing and hyperspectral imaging technique, not only static parameters' calibration of hyperspectral IR imaging system but also dynamic parameters' testing and evaluation are required, thus hyperspectral dynamic IR simulation and evaluation become more and more important. Hyperspectral dynamic IR scene projector utilizes hyperspectral space and time domain features controlling spectrum and time synchronously to realize hardware in loop simulation. Hyperspectral IR target and background simulating image can be gained by the accomplishment of 3D model and IR characteristic romancing, hyperspectral dynamic IR scene is produced by image converting device. The main parameters of a developed hyperspectral dynamic IR scene projector: wave band range is 3~5μm, 8~12μm Field of View (FOV) is 8°; spatial resolution is 1024×768 spectrum resolution is 1%~2%. IR source and simulating scene features should be consistent with spectrum characters of target, and different spectrum channel's images can be gotten from calibration. A hyperspectral imaging system splits light with dispersing type grating, pushbrooms and collects the output signal of dynamic IR scene projector. With hyperspectral scene spectrum modeling, IR features romancing, atmosphere transmission feature modeling and IR scene projecting, target and scene in outfield can be simulated ideally, simulation and evaluation of IR hyperspectral imaging system's dynamic features are accomplished in laboratory.
Simulating system dynamics with arbitrary time step
NASA Astrophysics Data System (ADS)
Kantorovich, L.
2007-02-01
We suggest a dynamic simulation method that allows efficient and realistic modeling of kinetic processes, such as atomic diffusion, in which time has its actual meaning. Our method is similar in spirit to widely used kinetic Monte Carlo (KMC) techniques; however, in our approach, the time step can be chosen arbitrarily. This has an advantage in some cases, e.g., when the transition rates change with time sufficiently fast over the period of the KMC time step (e.g., due to time dependence of some external factors influencing kinetics such as moving scanning probe microscopy tip or external time-dependent field) or when the clock time is set by some external conditions, and it is convenient to use equal time steps instead of the random choice of the KMC algorithm in order to build up probability distribution functions. We show that an arbitrary choice of the time step can be afforded by building up the complete list of events including the “residence site” and multihop transitions. The idea of the method is illustrated in a simple “toy” model of a finite one-dimensional lattice of potential wells with unequal jump rates to either side, which can be studied analytically. We show that for any choice of the time step, our general kinetics method reproduces exactly the solution of the corresponding master equations for any choice of the time steps. The final kinetics also matches the standard KMC, and this allows better understanding of this algorithm, in which the time step is chosen in a certain way and the system always advances by a single hop.
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…
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.
Dynamical simulations of strongly correlated electron materials
NASA Astrophysics Data System (ADS)
Kress, Joel; Barros, Kipton; Batista, Cristian; Chern, Gia-Wei; Kotliar, Gabriel
We present a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. We use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms.
An electro-fluid-dynamic simulator for the cardiovascular system.
Felipini, Celso Luiz; de Andrade, Aron José Pazin; Lucchi, Júlio César; da Fonseca, Jeison Willian Gomes; Nicolosi, Denys
2008-04-01
This work presents the initial studies and the proposal for a cardiovascular system electro-fluid-dynamic simulator to be applied in the development of left ventricular assist devices (LVADs). The simulator, which is being developed at University Sao Judas Tadeu and at Institute Dante Pazzanese of Cardiology, is composed of three modules: (i) an electrical analog model of the cardiovascular system operating in the PSpice electrical simulator environment; (ii) an electronic controller, based on laboratory virtual instrumentation engineering workbench (LabVIEW) acquisition and control tool, which will act over the physical simulator; and (iii) the physical simulator: a fluid-dynamic equipment composed of pneumatic actuators and compliance tubes for the simulation of active cardiac chambers and big vessels. The physical simulator (iii) is based on results obtained from the electrical analog model (i) and physiological parameters. PMID:18370952
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.
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.
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.
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.
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.
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.
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. PMID:26874473
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
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.
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
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.
Simulation of dynamic interface fracture using spectral boundary integral method
NASA Astrophysics Data System (ADS)
Harish, Ajay Bangalore
Simulation of three-dimensional dynamic fracture events constitutes one of the most challenging topics in the field of computational mechanics. Spontaneous dynamic fracture along the interface of two elastic solids is of great importance and interest to a number of disciplines in engineering and science. Applications include dynamic fractures in aircraft structures, earthquakes, thermal shocks in nuclear containment vessels and delamination in layered composite materials.
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.
Dynamics of a compound vesicle: numerical simulations
NASA Astrophysics Data System (ADS)
Veerapaneni, Shravan; Young, Yuan-Nan; Vlahovska, Petia; Blawzdziewicz, Jerzy
2010-11-01
Vesicles (self-enclosing lipid membranes) in simple linear flows are known to exhibit rich dynamics such as tank-treading, tumbling, trembling (swinging), and vacillating breathing. Recently, vesicles have been used as a multi-functional platform for drug-delivery. In this work, the dynamics of simplified models for such compound vesicles is investigated numerically using a state-of-the-art boundary-integral code that has been validated with high accuracy and efficiency. Results show that for a vesicle enclosing a rigid particle in a simple shear flow, transition from tank-treading to tumbling is possible even in the absence of viscosity mismatch in the interior and exterior fluids. We will discuss the shape transformations, multiple particle interactions and the flow properties. Comparison with results from analytical modeling gives insights to the underlying physics for such novel dynamics.
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.
Particle dynamics simulations of Turing patterns
NASA Astrophysics Data System (ADS)
Dziekan, P.; Lemarchand, A.; Nowakowski, B.
2012-08-01
The direct simulation Monte Carlo method is used to reproduce Turing patterns at the microscopic level in reaction-diffusion systems. In order to satisfy the basic condition for the development of such a spatial structure, we propose a model involving a solvent, which allows for disparate diffusivities of individual reactive species. One-dimensional structures are simulated in systems of various lengths. Simulation results agree with the macroscopic predictions obtained by integration of the reaction-diffusion equations. Additional effects due to internal fluctuations are observed, such as temporal transitions between structures of different wavelengths in a confined system. For a structure developing behind a propagating wave front, the fluctuations suppress the induction period and accelerate the formation of the Turing pattern. These results support the ability of reaction-diffusion models to robustly reproduce axial segmentation including the formation of early vertebrae or somites in noisy biological environments.
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.
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).
Brownian dynamics simulation for modeling ion permeation across bionanotubes.
Krishnamurthy, Vikram; Chung, Shin-Ho
2005-03-01
The principles underlying Brownian dynamics (BD), its statistical consistency, and algorithms for practical implementation are outlined here. The ability to compute current flow across ion channels confers a distinct advantage to BD simulations compared to other simulation techniques. Thus, two obvious applications of BD ion channels are in calculation of the current-voltage and current-concentration curves, which can be directly compared to the physiological measurements to assess the reliability of the model and predictive power of the method. We illustrate how BD simulations are used to unravel the permeation dynamics in two biological ion channels-the KcsA K+ channel and CIC Cl- channel. PMID:15816176
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.
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. PMID:21119749
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.
Programmable quantum simulation by dynamic Hamiltonian engineering
NASA Astrophysics Data System (ADS)
Hayes, David; Flammia, Steven T.; Biercuk, Michael J.
2014-08-01
Quantum simulation is a promising near term application for quantum information processors with the potential to solve computationally intractable problems using just a few dozen interacting qubits. A range of experimental platforms have recently demonstrated the basic functionality of quantum simulation applied to quantum magnetism, quantum phase transitions and relativistic quantum mechanics. However, in all cases, the physics of the underlying hardware restricts the achievable inter-particle interactions and forms a serious constraint on the versatility of the simulators. To broaden the scope of these analog devices, we develop a suite of pulse sequences that permit a user to efficiently realize average Hamiltonians that are beyond the native interactions of the system. Specifically, this approach permits the generation of all symmetrically coupled translation-invariant two-body Hamiltonians with homogeneous on-site terms, a class which includes all spin-1/2 XYZ chains, but generalized to include long-range couplings. Our work builds on previous work proving that universal simulation is possible using both entangling gates and single-qubit unitaries. We show that determining the appropriate ‘program’ of unitary pulse sequences which implements an arbitrary Hamiltonian transformation can be formulated as a linear program over functions defined by those pulse sequences, running in polynomial time and scaling efficiently in hardware resources. Our analysis extends from circuit model quantum information to adiabatic quantum evolutions, representing an important and broad-based success in applying functional analysis to the field of quantum information.
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...
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…
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
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.
Multi-petaflop/s quantum and reactive molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Nakano, Aiichiro
We have developed a divide-conquer-recombine algorithmic framework for large quantum molecular dynamics (QMD) and reactive molecular dynamics (RMD) simulations. The algorithms have achieved parallel efficiency over 0.98 on 786,432 IBM Blue Gene/Q processors for 39.8 trillion electronic degrees-of-freedom QMD in the framework of density functional theory and 67.6 billion-atom RMD. We will discuss several applications including (1) 16,616-atom QMD simulation of rapid hydrogen production from water using metallic alloy nanoparticles, (2) 6,400-atom nonadiabatic QMD simulation of exciton dynamics for efficient solar cells, and (3) 112 million-atom RMD simulation of nanocarbon synthesis by high temperature oxidation of SiC nanoparticles.
Dynamic simulation of chemical industry wastewater treatment plants.
Bury, S J; Groot, C K; Huth, C; Hardt, N
2002-01-01
High variability, stringent effluent permits, and often extreme operating conditions define the practice of wastewater treatment in the chemical industry. This paper reviews the benefits and challenges of applying dynamic simulation to chemical-industry wastewater treatment plants by describing case studies at full-scale wastewater treatment plants (WWTP). The applications range from process troubleshooting to optimization and control. The applications have been valuable and useful in developing a deeper understanding of the plants as integrated systems. However there still remains substantial work to implement the dynamic simulations for daily real-time use by plant engineers and operators. This opportunity to improve plant operations is still largely untapped and will remain so until dynamic state estimation and data reconciliation are incorporated into simulation packages for use in developing the on-line simulations. PMID:11936653
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.
Quantum dynamics simulation with classical oscillators
NASA Astrophysics Data System (ADS)
Briggs, John S.; Eisfeld, Alexander
2013-12-01
In a previous paper [J. S. Briggs and A. Eisfeld, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.052111 85, 052111 (2012)] we showed that the time development of the complex amplitudes of N coupled quantum states can be mapped by the time development of positions and velocities of N coupled classical oscillators. Here we examine to what extent this mapping can be realized to simulate the “quantum,” properties of entanglement and qubit manipulation. By working through specific examples, e.g., of quantum gate operation, we seek to illuminate quantum and classical differences which hitherto have been treated more mathematically. In addition, we show that important quantum coupled phenomena, such as the Landau-Zener transition and the occurrence of Fano resonances can be simulated by classical oscillators.
Chain networking revealed by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing
Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)
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.
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.
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.
Simulating Dynamics Of The Gamma-Ray Observatory Satellite
NASA Technical Reports Server (NTRS)
Stark, M.
1991-01-01
GRODY developed alongside GROSS computer program (GSC-13147), a FORTRAN dynamics-simulator program performing same functions. GRODY conceived for use in case study to assess feasibility and effectiveness of Ada programming language for development of flight-dynamics software. Designed for those familiar with analysis of attitudes of spacecraft. Supports planning of maneuvers as well as analytical testing and evaluation of attitude-determination and -control system used on board Gamma-Ray Observatory (GRO) satellite. Simulates computer and control processor electronics aboard GRO satellite. Enables analyst to check and update commands sent from ground and values of parameters, obtain displays of status of simulation, interrupt simulation, analyze previous runs, and obtain printed output of simulation runs. Written mainly in Ada (99 percent) with remainder in FORTRAN.
A reduced basis method for molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Vincent-Finley, Rachel Elisabeth
In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D. Kühn, Oliver
2015-06-28
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.
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
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
Solar simulator for solar dynamic space power system testing
NASA Technical Reports Server (NTRS)
Jefferies, Kent S.
1993-01-01
Planned vacuum tank testing of a solar dynamic space power system requires a solar simulator. Several solar simulators were previously built and used for vacuum tank testing of various space systems. However, the apparent solar subtense angle, i.e., the angular size of the apparent sun as viewed from the experiment, of these solar simulators is too large to enable testing of solar dynamic systems. A new design was developed to satisfy the requirements of the solar dynamic testing. This design provides 1.8 kW/m(sup 2) onto a 4.5M diameter test area from a source that subtends only 1 deg, full cone angle. Key features that enable this improved performance are (1) elimination of the collimating mirror commonly used in solar simulators to transform the diverging beam into a parallel beam; (2) a redesigned lamp module that has increased efficiency; and (3) the use of a segmented reflective surface to combine beams from several individual lamp modules at the pseudosun. Each segment of this reflective surface has complex curvature to control the distribution of light. By developing a new solar simulator design for testing of the solar dynamic system instead of modifying current designs, the initial cost was cut in half, the efficiency was increased by 50 percent reducing the operating costs by one-third, and the volume occupied by the solar simulator was reduced by a factor of 10.
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
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.
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.
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. PMID:24832301
Distortion and flow of nematics simulated by dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Zhao, Tongyang; Wang, Xiaogong
2014-05-01
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.
Development of semiclassical molecular dynamics simulation method.
Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi
2016-04-28
Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383
Simulation of plume dynamics using particle graphics
NASA Astrophysics Data System (ADS)
Tourtellott, John; Coker, Charles F.; Crow, Dennis R.
2000-07-01
To enhance the fidelity of numerical flow field (plume) imagery in hardware-in-the-loop (HIL) systems, new methods using particle system graphics have been developed. To render infrared (IR) images that are consistent with the underlying physical phenomenology, techniques for particle placement, pixel rasterization and drawing were developed and implemented in computer software. The software was integrated into an existing HIL scene generator and used to demonstrate several new capabilities. Moving particle systems were used to depict the internal flow and turbulence common to plumes. Persistent particle systems were used to depict the trail of hot gas and particulates left behind typical plumes. The addition of plume dynamic behaviors such as these can potentially improve HIL systems and, as a result, improve the testing of seekers and other weapon systems.
Dynamic Discharge Arc Driver. [computerized simulation
NASA Technical Reports Server (NTRS)
Dannenberg, R. E.; Slapnicar, P. I.
1975-01-01
A computer program using nonlinear RLC circuit analysis was developed to accurately model the electrical discharge performance of the Ames 1-MJ energy storage and arc-driver system. Solutions of circuit parameters are compared with experimental circuit data and related to shock speed measurements. Computer analysis led to the concept of a Dynamic Discharge Arc Driver (DDAD) capable of increasing the range of operation of shock-driven facilities. Utilization of mass addition of the driver gas offers a unique means of improving driver performance. Mass addition acts to increase the arc resistance, which results in better electrical circuit damping with more efficient Joule heating, producing stronger shock waves. Preliminary tests resulted in an increase in shock Mach number from 34 to 39 in air at an initial pressure of 2.5 torr.
Expansion techniques for collisionless stellar dynamical simulations
NASA Astrophysics Data System (ADS)
Meiron, Yohai
2016-02-01
We present ETICS, a collisionless N-body code based on two kinds of series expansions of the Poisson equation, implemented for graphics processing units (GPUs). The code is publicly available and can be used as a standalone program or as a library (an AMUSE plugin is included). One of the two expansion methods available is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other 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.
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.
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 simulations of heme reorientational motions in myoglobin.
Henry, E R
1993-01-01
Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes
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.
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.
Dynamic Multiscale Quantum Mechanics/Electromagnetics Simulation Method.
Meng, Lingyi; Yam, ChiYung; Koo, SiuKong; Chen, Quan; Wong, Ngai; Chen, GuanHua
2012-04-10
A newly developed hybrid quantum mechanics and electromagnetics (QM/EM) method [Yam et al. Phys. Chem. Chem. Phys.2011, 13, 14365] is generalized to simulate the real time dynamics. Instead of the electric and magnetic fields, the scalar and vector potentials are used to integrate Maxwell's equations in the time domain. The TDDFT-NEGF-EOM method [Zheng et al. Phys. Rev. B2007, 75, 195127] is employed to simulate the electronic dynamics in the quantum mechanical region. By allowing the penetration of a classical electromagnetic wave into the quantum mechanical region, the electromagnetic wave for the entire simulating region can be determined consistently by solving Maxwell's equations. The transient potential distributions and current density at the interface between quantum mechanical and classical regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. Charge distribution, current density, and potentials at different temporal steps and spatial scales are integrated seamlessly within a unified computational framework. PMID:26596737
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
Vashishta, Priya; Kalia, Rajiv
2005-02-24
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report.
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
Study of simulating dynamic polarization laser echo signal
NASA Astrophysics Data System (ADS)
Yang, Di; Liu, Qing; Zhan, Yong-hong; Zeng, Chang-e.
2014-12-01
In the test for the laser seeker in the hardware-in-loop simulation, acquiring the effect of polarization laser echo wave to optical stress polarization of the seeker and to the polarization guidance performance was not considered. A new method to generating the dynamic polarization laser echo signal was provided based on the scene model; furthermore, the method to adding the polarization characters to the energy scene was introduced. At last, the insufficient of the method to generating and simulating the dynamic polarization signal was analyzed.
Simulation: A tool for steam plant dynamic analysis
NASA Astrophysics Data System (ADS)
Anneveld, H.
Stringent requirements of combined cycles makes design and operation of process plants increasingly complex. The behavior of the complete controlled process is studied by way of simulation. By utilizing this method, process conditions can be optimized with reduced risk. This will lead to greater financial benefits. There is a large range of simulation programs which make it possible to study realistically the dynamic behavior of a wide range of complex process conditions and problematic interactions. The steam generation and distribution, the pressure limitation controls, and the dynamic behavior of a steam plant are discussed.
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.
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.
Turbulent Simulation of the Dynamics of the Magnetotail
NASA Technical Reports Server (NTRS)
Wu, Cheng-Chin
2003-01-01
In situ observations indicate that the dynamical processes in the geoplasma environment generally entail localized intermittent processes and anomalous global transports. It was suggested by T. Chang that instead of considering the turbulence as a mixture of interacting waves, such type of patchy intermittency could be more easily understood in terms of the development, interaction, merging, preferential acceleration and evolution of coherent magnetic structures. In this three-year project, we have used direct numerical MHD simulations to study some aspects of the MHD dynamics in Chang's model. Our large-scale numerical calculations and simulations have been supplemented by and coordinated with theoretical studies conducted by Chang and his colleagues.
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.
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.
Improving the performance of molecular dynamics simulations on parallel clusters.
Borstnik, Urban; Hodoscek, Milan; Janezic, Dusanka
2004-01-01
In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds. PMID:15032512
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.
Error and efficiency of replica exchange molecular dynamics simulations
Rosta, Edina; Hummer, Gerhard
2009-01-01
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977
Error and efficiency of replica exchange molecular dynamics simulations.
Rosta, Edina; Hummer, Gerhard
2009-10-28
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977
Simulating spin dynamics in organic solids under heteronuclear decoupling.
Frantsuzov, Ilya; Ernst, Matthias; Brown, Steven P; Hodgkinson, Paul
2015-09-01
Although considerable progress has been made in simulating the dynamics of multiple coupled nuclear spins, predicting the evolution of nuclear magnetisation in the presence of radio-frequency decoupling remains challenging. We use exact numerical simulations of the spin dynamics under simultaneous magic-angle spinning and RF decoupling to determine the extent to which numerical simulations can be used to predict the experimental performance of heteronuclear decoupling for the CW, TPPM and XiX sequences, using the methylene group of glycine as a model system. The signal decay times are shown to be strongly dependent on the largest spin order simulated. Unexpectedly large differences are observed between the dynamics with and without spin echoes. Qualitative trends are well reproduced by modestly sized spin system simulations, and the effects of finite spin-system size can, in favourable cases, be mitigated by extrapolation. Quantitative prediction of the behaviour in complex parameter spaces is found, however, to be very challenging, suggesting that there are significant limits to the role of numerical simulations in RF decoupling problems, even when specialist techniques, such as state-space restriction, are used. PMID:26073419
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
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
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.
Dynamic risk simulation to assess risk along roads
NASA Astrophysics Data System (ADS)
Voumard, Jérémie; Caspar, Olivier; Derron, Marc-Henri; Jaboyedoff, Michel
2013-04-01
Risk generated through natural hazards on roads is usually calculated with an equation which integrates various parameters of hazard and traffic. These are static variables as hazard frequency and number of vehicles crossing the dangerous section. This traditional methodology cannot take into account the dynamic variations of traffic and interactions between vehicles such as speeds modifications due to the section sinuosity, slowdowns resulting saturated traffic or creation of vehicles columns in front of traffic lights. The influence of traffic dynamics on the risk estimation is not addressed with the standard methodologies. Here we show, with the help of a dynamic traffic simulator specially developed for this project, that the variations of traffic greatly influence the risk results. Several sections of an alpine road in Switzerland were analyzed with the method of dynamic risk and compared with the results of the conventional method of risk calculation. It was possible to demonstrate that risk significantly increases on sinuous sections with the decreasing of vehicles speed. It has been highlighted that well positioned traffic lights, outside the risk area, can prevent a risk increase during a construction site, while a column of vehicles located within the danger zone greatly increases the risk. These results demonstrate the importance to consider the traffic in a dynamic way to assess risk to the closest field reality. Thus, recommendations to reduce risk on the roads can be given using a dynamic traffic simulator, modeling interactions between vehicles. Eventually, dynamic risk assessment can also be integrated into existing methodologies that consider only static parameters.
Validating clustering of molecular dynamics simulations using polymer models
2011-01-01
Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the
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.
Simulation of Pedestrian Dynamic Using a Vector Floor Field Model
NASA Astrophysics Data System (ADS)
Yang, Jun; Hou, Zhongsheng; Zhan, Minghui
2013-04-01
Simulation of complex scenarios and multi-direction pedestrian flow is a main challenge to microscopic model of pedestrian movement. It is an issue to simulate real pedestrian traffic with great fidelity while keeping its computational cost at an acceptable level. This paper reports on an improved floor field model called vector floor field model to simulate pedestrian flows in some basic scenarios. In this model, vectorization of static floor field and dynamic floor field are used to indicate preference directions and the pedestrian flow tendency, respectively. Pedestrian transition depends on both their preference directions and tendency. The simulations in some basic scenarios are conducted, quantitative comparison to the record of practical experiments and standard floor field model is given as well, and the results indicate the effectivity of this model. An adjusted static vector floor field is also proposed to simulate pedestrian flow in turning scenario. The vector floor field model is also sufficient to simulate some essential features in pedestrian dynamic, such as lane formation. This model can be widely used in the simulation of multi-direction pedestrian at turning, crossing and other junctions.
Dynamic materials response at multiscales: Experiments and simulations
NASA Astrophysics Data System (ADS)
Luo, Sheng-Nian
One of the grand challenges in materials physics is dynamic responses to impulsive loading, including shock waves, radiation, and pulsed fields, due to their highly transient nature and extremely complex microstructure effects. Dynamic responses, such as plasticity, damage, cavitation, phase changes, and chemical reactions, are inherently multiscale and heavily dependent on microstructure. One has to resort to a suite of tools, including experiments, modeling and simulations, and theory. However, the gaps in spatial or temporal scales between experiments and simulations are still wide, while cross-scale theories are still in early development. To this end, we exploit large-scale molecular dynamics simulations, electron microscopy, and ultrafast synchrotron X-ray imaging and scattering, to probe materials response at length scales ranging from lattice to micron, and time scales, from picosecond to second. For examples, simultaneous, high-speed, X-ray imaging (mesoscale strain-field mapping) and diffraction measurements along with macroscopic measurements have been achieved. Based on classical nucleation theory and large-scale molecular dynamics simulations, we demonstrate the equivalence between length and time scales for nucleation events, which provides a framework to bridge different scales. Certainly, advancing multiscale science requires sustained, concerted, experimental, modeling and theoretical efforts. We have benefited from the colleagues at the Advanced Photon Source, and the Peac Institute of Multiscales Sciences.
Simulating field-scale soil organic carbon dynamics using EPIC
Technology Transfer Automated Retrieval System (TEKTRAN)
Simulation models integrate our understanding 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 e...
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.
Diffusion of Particle in Hyaluronan Solution, a Brownian Dynamics Simulation
NASA Astrophysics Data System (ADS)
Takasu, Masako; Tomita, Jungo
2004-04-01
Diffusion of a particle in hyaluronan solution is investigated using Brownian dynamics simulation. The slowing down of diffusion is observed, in accordance with the experimental results. The temperature dependence of the diffusion is calculated, and a turnover is obtained when the temperature is increased.
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…
Generating dynamic simulations of movement using computed muscle control.
Thelen, Darryl G; Anderson, Frank C; Delp, Scott L
2003-03-01
Computation of muscle excitation patterns that produce coordinated movements of muscle-actuated dynamic models is an important and challenging problem. Using dynamic optimization to compute excitation patterns comes at a large computational cost, which has limited the use of muscle-actuated simulations. This paper introduces a new algorithm, which we call computed muscle control, that uses static optimization along with feedforward and feedback controls to drive the kinematic trajectory of a musculoskeletal model toward a set of desired kinematics. We illustrate the algorithm by computing a set of muscle excitations that drive a 30-muscle, 3-degree-of-freedom model of pedaling to track measured pedaling kinematics and forces. Only 10 min of computer time were required to compute muscle excitations that reproduced the measured pedaling dynamics, which is over two orders of magnitude faster than conventional dynamic optimization techniques. Simulated kinematics were within 1 degrees of experimental values, simulated pedal forces were within one standard deviation of measured pedal forces for nearly all of the crank cycle, and computed muscle excitations were similar in timing to measured electromyographic patterns. The speed and accuracy of this new algorithm improves the feasibility of using detailed musculoskeletal models to simulate and analyze movement. PMID:12594980
Modeling and Dynamic Simulation of a Large Scale Helium Refrigerator
NASA Astrophysics Data System (ADS)
Lv, C.; Qiu, T. N.; Wu, J. H.; Xie, X. J.; Li, Q.
In order to simulate the transient behaviors of a newly developed 2 kW helium refrigerator, a numerical model of the critical equipment including a screw compressor with variable-frequency drive, plate-fin heat exchangers, a turbine expander, and pneumatic valves wasdeveloped. In the simulation,the calculation of the helium thermodynamic properties arebased on 32-parameter modified Benedict-Webb-Rubin (MBWR) state equation.The start-up process of the warm compressor station with gas management subsystem, and the cool-down process of cold box in an actual operation, were dynamically simulated. The developed model was verified by comparing the simulated results with the experimental data.Besides, system responses of increasing heat load were simulated. This model can also be used to design and optimize other large scale helium refrigerators.
Evaluating the Accuracy of Hessian Approximations for Direct Dynamics Simulations.
Zhuang, Yu; Siebert, Matthew R; Hase, William L; Kay, Kenneth G; Ceotto, Michele
2013-01-01
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. PMID:26589009
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.
Large Dynamic Range Simulations of Galaxies Hosting Supermassive Black Holes
NASA Astrophysics Data System (ADS)
Levine, Robyn
2011-08-01
The co-evolution of supermassive black holes (SMBHs) and their host galaxies is a rich problem, spanning a large-dynamic range and depending on many physical processes. Simulating the transport of gas and angular momentum from super-galactic scales all the way down to the outer edge of the black hole's accretion disk requires sophisticated numerical techniques with extensive treatment of baryonic physics. We use a hydrodynamic adaptive mesh refinement simulation to follow the growth and evolution of a typical disk galaxy hosting an SMBH, in a cosmological context (covering a dynamical range of 10 million!). We have adopted a piecemeal approach, focusing our attention on the gas dynamics in the central few hundred parsecs of the simulated galaxy (with boundary conditions provided by the larger cosmological simulation), and beginning with a simplified picture (no mergers or feedback). In this scenario, we find that the circumnuclear disk remains marginally stable against catastrophic fragmentation, allowing stochastic fueling of gas into the vicinity of the SMBH. I will discuss the successes and the limitations of these simulations, and their future direction.
Reactive Molecular Dynamics Simulations at the Petascale (Invited)
NASA Astrophysics Data System (ADS)
Nakano, A.
2013-12-01
We are developing a divide-conquer-recombine algorithmic framework into a metascalable (or 'design once, scale on new architectures') parallelization scheme to perform large spatiotemporal-scale reactive molecular dynamics simulations. The scheme has achieved parallel efficiency well over 0.9 on 786,432 IBM BlueGene/Q processors for 8.5 trillion-atom molecular dynamics and 1.9 trillion electronic degrees-of-freedom quantum molecular dynamics in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic alloy nanoparticles; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; and (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets.
Dynamics simulation and controller interfacing for legged robots
Reichler, J.A.; Delcomyn, F.
2000-01-01
Dynamics simulation can play a critical role in the engineering of robotic control code, and there exist a variety of strategies both for building physical models and for interacting with these models. This paper presents an approach to dynamics simulation and controller interfacing for legged robots, and contrasts it to existing approaches. The authors describe dynamics algorithms and contact-resolution strategies for multibody articulated mobile robots based on the decoupled tree-structure approach, and present a novel scripting language that provides a unified framework for control-code interfacing, user-interface design, and data analysis. Special emphasis is placed on facilitating the rapid integration of control algorithms written in a standard object-oriented language (C++), the production of modular, distributed, reusable controllers, and the use of parameterized signal-transmission properties such as delay, sampling rate, and noise.
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).
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.
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.
Simulation of the dynamic inefficiency of the CMS pixel detector
NASA Astrophysics Data System (ADS)
Bartók, M.
2015-05-01
The Pixel Detector is the innermost part of the CMS Tracker. It therefore has to prevail in the harshest environment in terms of particle fluence and radiation. There are several mechanisms that may decrease the efficiency of the detector. These are mainly caused by data acquisition (DAQ) problems and/or Single Event Upsets (SEU). Any remaining efficiency loss is referred to as the dynamic inefficiency. It is caused by various mechanisms inside the Readout Chip (ROC) and depends strongly on the data occupancy. In the 2012 data, at high values of instantaneous luminosity the inefficiency reached 2% (in the region closest to the interaction point) which is not negligible. In the 2015 run higher instantaneous luminosity is expected, which will result in lower efficiencies; therefore this effect needs to be understood and simulated. A data-driven method has been developed to simulate dynamic inefficiency, which has been shown to successfully simulate the effects.
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 simulations of a lithium/sodium carbonate mixture.
Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo
2016-03-01
The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates. PMID:26897519
Molecular dynamics simulations of detonation on the roadrunner supercomputer
NASA Astrophysics Data System (ADS)
Mniszewski, Susan; Cawkwell, Marc; Germann, Timothy C.
2012-03-01
The temporal and spatial scales intrinsic to a real detonating explosive are extremely difficult to capture using molecular dynamics (MD) simulations. Nevertheless, MD remains very attractive since it allows for the resolution of dynamic phenomena at the atomic scale. Large-scale reactive MD simulations in three dimensions require immense computational resources even when simple reactive force fields are employed. We focus on the REBO force field for 'AB' since it has been shown to support a detonation while being simple, analytic, and short-ranged. The transition from two-to three- dimensional simulations is being facilitated by the port of the REBO force field in the parallel MD code SPaSM to LANL's petaflop supercomputer 'Roadrunner'. We provide a detailed discussion of the challenges associated with computing interatomic forces on a hybrid Opteron/Cell BE computational architecture.
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.
Quantum simulation of the dynamical Casimir effect with trapped ions
NASA Astrophysics Data System (ADS)
Trautmann, N.; Hauke, P.
2016-04-01
Quantum vacuum fluctuations are a direct manifestation of Heisenberg’s uncertainty principle. The dynamical Casimir effect (DCE) allows for the observation of these vacuum fluctuations by turning them into real, observable photons. However, the observation of this effect in a cavity QED experiment would require the rapid variation of the length of a cavity with relativistic velocities, a daunting challenge. Here, we propose a quantum simulation of the DCE using an ion chain confined in a segmented ion trap. We derive a discrete model that enables us to map the dynamics of the multimode radiation field inside a variable-length cavity to radial phonons of the ion crystal. We perform a numerical study comparing the ion-chain quantum simulation under realistic experimental parameters to an ideal Fabry–Perot cavity, demonstrating the viability of the mapping. The proposed quantum simulator, therefore, allows for probing the photon (respectively phonon) production caused by the DCE on the single photon level.
Molecular Dynamics Simulation of Electrophoresis of a Telehelic Polymer Chain
NASA Astrophysics Data System (ADS)
Bhattacharya, Aniket
2002-08-01
We report the conformational and the dynamical properties of an end-labeled polymer chain embedded in a porous medium made of randomly distributed immobile spherical obstacles using a stochastic Molecular Dynamic(MD) simulation method for several obstacle densities and for various bias strenghts applied only to one end of the chain. First, various properties of the chain are studied when the external bias is set to zero. We then extend the stochastic MD simulation to study the electrophresis of a polymer chain driven by (i) a steady and (ii) a time dependent electric field. These studies are relevant for various time dependent gel electrophoresis methods widely used to separate DNA molecules. The qualitative features are compared with experiments, analytic theories, and recent Monte Carlo Simulation results.
McGroddy, K A; Brady, J W; Oswald, R E
1994-01-01
Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED. Images FIGURE 1 FIGURE 2 PMID:8161685
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. PMID:26013419
Dynamic simulations for the Terrestrial Planet Finder interferometer
NASA Astrophysics Data System (ADS)
Li, Ying-Yong; Hamlin, Louise A.; Wirz, Richie; Adams, Douglas; Moore, Greg; Coppolino, Robert; Peng, Chia-Yen; Levine, Marie
2005-08-01
The Terrestrial Planet Finder Interferometer (TPF-I) mission requires a set of formation-flying collector telescopes that direct the incoming light to a beam combiner where the beams are combined and detected to identify habitable planets. A baseline TPF collector design, using a primary mirror of 4.2 meters in diameter, is used here to conduct a dynamic study. The objective is to investigate the effects of dynamic response of the spacecraft on the system optical performance at the presence of disturbances that arise from the reaction wheel assembly and thruster loading, respectively. Frequency responses where the frequency is associated with the flywheel speed are presented in the paper. The results focus on the surface oscillation of the primary mirror and the point at which the secondary mirror is located. Transient response simulations under the baseline four thruster-assembly configuration were conducted using various duty cycles and thrust levels determined by the TPF formation rotation requirements. This paper will also describe an investigation conducted using new IMOS (Integrated Modeling of Optical Systems), which is an open, multi-disciplinary, and Matlab-based dynamic/optical system simulation code. A pre-processor that is able to generate the sub-structure modal models required by ISYSD (Integrated System Dynamics) was developed in new IMOS. ISYSD is used to develop a high-fidelity system dynamic model by integrating the sub-structure modal models. Finally, the paper will summarize current and future work in order to meet the TPF dynamic requirements.
Dynamic risk simulation to assess risk along roads
NASA Astrophysics Data System (ADS)
Voumard, J.; Caspar, O.; Derron, M.-H.; Jaboyedoff, M.
2013-04-01
Risk generated by natural hazards on roads is usually calculated with equations integrating various parameters related to hazard and traffic. These are static variables, like a rockfall hazard estimation for a road section or the average number of vehicles crossing this section every day. This methodology cannot take into account dynamic variations of traffic and interactions between vehicles such as speed modifications due to the sinuosity, slowdowns resulting of saturated traffic or vehicles columns forming in front of traffic lights. The influence of traffic dynamics on the risk estimation is not assessed with standard methodologies. Here we show, by mean of a dynamic traffic simulator, that the traffic variations may greatly influence the risk estimation over time. The risk is analysed on several alpine road sections in Switzerland using a dynamic vehicles approach and compared with the results of the static methodology. It demonstrates that risk significantly increases on sinuous sections because of the decreasing of vehicles speed. A more realistic risk can be obtained from a dynamic approach especially on mountain roads. A dynamic traffic simulator, modelling interactions between vehicles is a helpful tool to support decision making to reduce risk on roads.
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. PMID:16384158
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.
Multiscale Simulations of the Structure and Dynamics of the Magnetopause
NASA Astrophysics Data System (ADS)
Berchem, Jean; Lapenta, Giovanni; Ashour-Abdalla, Maha
2016-04-01
Ongoing observations by the spacecraft of NASA's Magnetospheric Multiscale Mission are revealing a very complex structure and dynamics of the low-latitude magnetopause. One of the main difficulties to comprehend physical processes occurring at the magnetopause is that it requires following both the evolution of the large-scale interaction of the solar wind with the dayside magnetosphere, and the details of the kinetic processes that enable transport of energy and mass in localized regions of the magnetospheric boundary. To address this multiscale problem, we have carried out particle-in-cell (PIC) simulations of the dayside magnetopause. These simulations employ domains that are large enough to include large-scale features of the solar wind interaction with the geomagnetic field (e.g., field curvature and plasma asymmetries). The numerical challenge is dealt with by using the implicit iPic3d simulation code together with the results of global magnetohydrodynamic (MHD) simulations. We discuss the results of the PIC simulations in the context of the global MHD states that provide initial and boundary conditions, and local spacecraft observations at the magnetopause. In particular, we analyze the evolution of electromagnetic fields and particle distributions in different regions of the simulations to determine how reconnection processes affect the structure and dynamics of the magnetospheric boundary.
The molecular dynamics simulation of ion-induced ripple growth
Suele, P.; Heinig, K.-H.
2009-11-28
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 ({lambda}) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths ({lambda}<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 {lambda}>35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in {lambda} long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for {lambda}>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.
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.
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics
2016-01-01
Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886
Synthesis of recurrent neural networks for dynamical system simulation.
Trischler, Adam P; D'Eleuterio, Gabriele M T
2016-08-01
We review several of the most widely used techniques for training recurrent neural networks to approximate dynamical systems, then describe a novel algorithm for this task. The algorithm is based on an earlier theoretical result that guarantees the quality of the network approximation. We show that a feedforward neural network can be trained on the vector-field representation of a given dynamical system using backpropagation, then recast it as a recurrent network that replicates the original system's dynamics. After detailing this algorithm and its relation to earlier approaches, we present numerical examples that demonstrate its capabilities. One of the distinguishing features of our approach is that both the original dynamical systems and the recurrent networks that simulate them operate in continuous time. PMID:27182811
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
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.
Dynamical Effects and Product Distributions in Simulated CN + Methane Reactions.
Preston, Thomas J; Hornung, Balázs; Pandit, Shubhrangshu; Harvey, Jeremy N; Orr-Ewing, Andrew J
2016-07-14
Dynamics of collisions between structured molecular species quickly become complex as molecules become large. Reactions of methane with halogen and oxygen atoms serve as model systems for polyatomic molecule chemical dynamics, and replacing the atomic reagent with a diatomic radical affords further insights. A new, full-dimensional potential energy surface for collisions between CN + CH4 to form HCN + CH3 is developed and then used to perform quasi-classical simulations of the reaction. Coupled-cluster energies serve as input to an empirical valence bonding (EVB) model, which provides an analytical function for the surface. Efficient sampling permits simulation of velocity-map ion images and exploration of dynamics over a range of collision energies. Reaction populates HCN vibration, and energy partitioning changes with collision energy. The reaction cross-section depends on the orientation of the diatomic CN radical. A two-dimensional extension of the cone of acceptance for an atom in the line-of-centers model appropriately describes its reactivity. The simulation results foster future experiments and diatomic extensions to existing atomic models of chemical collisions and reaction dynamics. PMID:26812395
Frank, Martin; Gutbrod, Peter; Hassayoun, Chokri; von Der Lieth, Claus-W
2003-10-01
Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions at an atomic level. The "Dynamic Molecules" approach is the first internet portal that provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The aim is to open molecular dynamics techniques to a broader range of users including undergraduate students, teachers and scientists outside the bioinformatics field. The time-limiting factors are the availability of free capacity on the computing server to run the simulations and the time required to transport the history file through the internet for the animation mode. The interactive access mode of the portal is acceptable for animations of molecules having up to about 500 atoms. PMID:12908101
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.
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.
2000-10-10
Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.
A dynamic traffic simulator for roads affected by natural hasards
NASA Astrophysics Data System (ADS)
Voumard, J.; Jaboyedoff, M.; Derron, M.-H.
2012-04-01
This work focuses on the issue of natural hazards threatening roads. Nowadays, risk estimations of rock falls or landslides affecting whole sections of road are generally quite accurate and under relatively good control. Mitigation measures provide intervention means to reduce the hazards along roads. However, as classical models of risk calculation on communication routes do not take into account the dynamic traffic parameters, little is known on the way of reducing the risk at road level. It is not known precisely what really happens on the road when an event occurs and how vehicles interact. A dynamic traffic simulator in development provides information on factors having an impact on the risk level related to the road. Variables such as visibility, curvature radius of turns or vehicle type were included in the model. Varying these variables within dynamic traffic simulations can suggest solutions to minimize the risks for road users. These simulations can provide answers to various questions, such as: does speed have a significant impact on the risk incurred by drivers? Is it possible to significantly reduce the risk with appropriate speeds? The simulation is performed with the MATLAB © software. The model is yet to be calibrated and validated through in situ tests.
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. PMID:26879667
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.
A dynamic simulation tool for hydrogen fuel cell vehicles
NASA Astrophysics Data System (ADS)
Moore, R. M.; Hauer, K. H.; Friedman, D.; Cunningham, J.; Badrinarayanan, P.; Ramaswamy, S.; Eggert, A.
This paper describes a dynamic fuel cell vehicle simulation (FCVSim) tool for the load-following direct-hydrogen (DH) fuel cell vehicle. The emphasis is on simulation of the direct-hydrogen fuel cell system (FC System) within the vehicle simulation tool. This paper is focused on the subsystems that are specific to the load-following direct-hydrogen model. The four major subsystems discussed are the fuel cell stack, the air supply, the water and thermal management (WTM), and the hydrogen supply. The discussion provides the details of these subsystem simulations. The basic vehicle configuration has been previously outlined by Hauer [An Analysis Tool For Fuel Cell Vehicle Hardware and Software (Controls) with an Application to Fuel Economy Comparisons of Alternative System Designs, Dissertation, UC California, Davis, USA, 2001] and Hauer and Moore [Fuel Cells for Automotive Applications, Professional Engineering Publishing, 2003, pp. 157-177, ISBN 1860584233] and is only briefly reviewed in this paper.
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.
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.
Novel procedure for thermal equilibration in molecular dynamics simulation.
Gallo, Marco T; Grant, Barry J; Teodoro, Miguel L; Melton, Julia; Cieplak, Piotr; Phillips, George N; Stec, Boguslaw
2009-04-01
We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797
Novel procedure for thermal equilibration in molecular dynamics simulation
Gallo, Marco T.; Grant, Barry J.; Teodoro, Miguel L.; Melton, Julia; Cieplak, Piotr; Phillips, George N.; Stec, Boguslaw
2014-01-01
We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797
Spotting the difference in molecular dynamics simulations of biomolecules.
Sakuraba, Shun; Kono, Hidetoshi
2016-08-21
Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (LDA-ITER) to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the "difference" between two trajectories. PMID:27544096
Insights into Buforin II Membrane Translocation from Molecular Dynamics Simulations
Elmore, Donald E.
2012-01-01
Buforin II is a histone-derived antimicrobial peptide that readily translocates across lipid membranes without causing significant membrane permeabilization. Previous studies showed that mutating the sole proline of buforin II dramatically decreases its translocation. As well, researchers have proposed that the peptide crosses membranes in a cooperative manner through forming transient toroidal pores. This paper reports molecular dynamics simulations designed to investigate the structure of buforin II upon membrane entry and evaluate whether the peptide is able to form toroidal pore structures. These simulations showed a relationship between protein-lipid interactions and increased structural deformations of the buforin N-terminal region promoted by proline. Moreover, simulations with multiple peptides show how buforin II can embed deeply into membranes and potentially form toroidal pores. Together, these simulations provide structural insight into the translocation process for buforin II in addition to providing more general insight into the role proline can play in antimicrobial peptides. PMID:23022591
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.
Computational Fluid Dynamics (CFD) simulation of the Madison Dynamo Experiment.
NASA Astrophysics Data System (ADS)
Haehn, N. S.; Forest, C. B.; Weber, C. R.; Kendrick, R. D.; Taylor, N. Z.; Oakley, J. G.; Bonazza, R.; Spence, Erik
2007-11-01
The Madison Dynamo Experiment is designed to study a self-generated magnetic field called a dynamo. The flow characteristics of a water experiment that is dimensionally similar to the liquid sodium experiment has been modeled using the Computational Fluid Dynamics (CFD) software Fluent. Results from the CFD simulations are used to confirm flow characteristics measured experimentally by both Laser Doppler Velocimetry (LDV) and Particle Imaging Velocimetry (PIV). Simulations can also give insight into the flow characteristics in regions of the experiment which are not accessible via the LDV and PIV systems. The results from the simulations are also used as input for a MHD code to predict the threshold for Dynamo onset. The CFD simulations -- in conjunction with the MHD dynamo prediction code -- can be used to design modifications to the experiment to minimize costly changes. The CFD code has shown that the addition of an equatorial baffle along with several poloidal baffles can lower the threshold for Dynamo onset.
Analysis of utilization of desert habitats with dynamic simulation
Williams, B.K.
1986-01-01
The effects of climate and herbivores on cool desert shrubs in north-western Utah were investigated with a dynamic simulation model. Cool desert shrublands are extensively managed as grazing lands, and are defoliated annually by domestic livestock. A primary production model was used to simulate harvest yields and shrub responses under a variety of climatic regimes and defoliation patterns. The model consists of six plant components, and it is based on equations of growth analysis. Plant responses were simulated under various combinations of 20 annual weather patterns and 14 defoliation strategies. Results of the simulations exhibit some unexpected linearities in model behavior, and emphasize the importance of both the pattern of climate and the level of plant vigor in determining optimal harvest strategies. Model behaviors are interpreted in terms of shrub morphology, physiology and ecology.
Shafique, Neha; Kennedy, Kiley E; Douglas, Jack F; Starr, Francis W
2016-06-16
Heterogeneity of dynamics plays a vital role in membrane function, but the methods for quantifying this heterogeneity are still being developed. Here we examine membrane dynamical heterogeneity via molecular simulations of a single-component dipalmitoylphosphatidylcholine (DPPC) lipid bilayer using the MARTINI force field. We draw upon well-established analysis methods developed in the study of glass-forming fluids and find significant changes in lipid dynamics between the fluid (Lα), and gel (Lβ) phases. In particular, we distinguish two mobility groups in the more ordered Lβ phase: (i) lipids that are transiently trapped by their neighbors and (ii) lipids with displacements on the scale of the intermolecular spacing. These distinct mobility groups spatially segregate, forming dynamic clusters that have characteristic time (1-2 μs) and length (1-10 nm) scales comparable to those of proteins and other biomolecules. We suggest that these dynamic clusters could couple to biomolecules within the membrane and thus may play a role in many membrane functions. In the equilibrium membrane, lipid molecules dynamically exchange between the mobility groups, and the resulting clusters are not associated with a thermodynamic phase separation. Dynamical clusters having similar characteristics arise in many other condensed phase materials, placing membranes in a broad class of materials with strong intermolecular interactions. PMID:27223339
Molecular dynamics simulations of solvated yeast tRNA(Asp).
Auffinger, P; Louise-May, S; Westhof, E
1999-01-01
Transfer RNA molecules are involved in a variety of biological processes, implying complex recognition events with proteins and other RNAs. From a structural point of view, tRNAs constitute a reference system for studying RNA folding and architecture. A deeper understanding of their structural and functional properties will derive from our ability to model accurately their dynamical behavior. We present the first dynamical model of a fully neutralized and solvated tRNA molecule over a 500-ps time scale. Starting from the crystallographic structure of yeast tRNA(Asp), the 75-nucleotide molecule was modeled with 8055 water molecules and 74 NH4+ counterions, using the AMBER4.1 program and the particle mesh Ewald (PME) method for the treatment of long-range electrostatic interactions. The calculations led to a dynamically stable model of the tRNA molecule. During the simulation, all secondary and tertiary base pairs are maintained while a certain lability of base triples in the tRNA core is observed. This lability was interpreted as resulting from intrinsic factors associated with the "weaker" hydrogen bonding patterns seen in these base triples and from an altered ionic environment of the tRNA molecule. Calculated thermal factors are used to compare the dynamics of the tRNA in solution and in the crystal. The present molecular dynamics simulation of a complex and highly charged nucleic acid molecule attests to the fact that simulation methods are now able to investigate not only the dynamics of proteins, but also that of large RNA molecules. Thus they also provide a basis for further investigations on the structural and functional effects of chemical and posttranscriptionally modified nucleotides as well as on ionic environmental effects. PMID:9876122
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
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.
Identifying the mechanisms of polymer friction through molecular dynamics simulation.
Dai, Ling; Minn, M; Satyanarayana, N; Sinha, Sujeet K; Tan, V B C
2011-12-20
Mechanisms governing the tribological behavior of polymer-on-polymer sliding were investigated by molecular dynamics simulations. Three main mechanisms governing frictional behavior were identified. Interfacial "brushing" of molecular chain ends over one another was observed as the key contribution to frictional forces. With an increase of the sliding speed, fluctuations in frictional forces reduced in both magnitude and periodicity, leading to dynamic frictional behavior. While "brushing" remained prevalent, two additional irreversible mechanisms, "combing" and "chain scission", of molecular chains were observed when the interfaces were significantly diffused. PMID:22044344
Beam Dynamics Design and Simulation in Ion Linear Accelerators (
Energy Science and Technology Software Center (ESTSC)
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 modernmore » ion linear accelerators and beam transport systems.« less
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.
Analysis of motion features for molecular dynamics simulation of proteins
NASA Astrophysics Data System (ADS)
Kamada, Mayumi; Toda, Mikito; Sekijima, Masakazu; Takata, Masami; Joe, Kazuki
2011-01-01
Recently, a new method for time series analysis using the wavelet transformation has been proposed by Sakurai et al. We apply it to molecular dynamics simulation of Thermomyces lanuginosa lipase (TLL). Introducing indexes to characterize collective motion of the protein, we have obtained the following two results. First, time evolution of the collective motion involves not only the dynamics within a single potential well but also takes place wandering around multiple conformations. Second, correlation of the collective motion between secondary structures shows that collective motion exists involving multiple secondary structures. We discuss future prospects of our study involving 'disordered proteins'.
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.
Simulation of Ionic Aggregation and Ion Dynamics in Model Ionomers
NASA Astrophysics Data System (ADS)
Frischknecht, Amalie L.
2012-02-01
Ionomers, polymers containing a small fraction of covalently bound ionic groups, are of interest as possible electrolytes in batteries. A single-ion conducting polymer electrolyte would be safer and have higher efficiency than the currently-used liquid electrolytes. However, to date ionomeric materials do not have sufficiently high conductivities for practical application. This is most likely because the ions tend to form aggregates, leading to slow ion transport. A key question is therefore how molecular structure affects the ionic aggregation and ion dynamics. To probe these structure-property relationships, we have performed molecular simulations of a set of recently synthesized poly(ethylene-co-acrylic acid) copolymers and ionomers, with a focus on the morphology of the ionic aggregates. The ionomers have a precise, constant spacing of charged groups, making them ideal for direct comparisons with simulations. Ab initio calculations give insight into the expected coordination of cations with fragments of the ionomers. All-atom molecular dynamics (MD) simulations of the ionomer melt show aggregation of the ionic groups into extended string-like clusters. An extensive set of coarse-grained molecular dynamics simulations extend the results to longer times and larger length scales. The structure factors calculated from the MD simulations compare favorably with x-ray scattering data. Furthermore, the simulations give a detailed picture of the sizes, shapes, and composition of the ionic aggregates, and how they depend on polymer architecture. Implications for ion transport will be discussed. [Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
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.
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)
Setting up and running molecular dynamics simulations of membrane proteins.
Kandt, Christian; Ash, Walter L; Tieleman, D Peter
2007-04-01
Molecular dynamics simulations have become a popular and powerful technique to study lipids and membrane proteins. We present some general questions and issues that should be considered prior to embarking on molecular dynamics simulation studies of membrane proteins and review common simulation methods. We suggest a practical approach to setting up and running simulations of membrane proteins, and introduce two new (related) methods to embed a protein in a lipid bilayer. Both methods rely on placing lipids and the protein(s) on a widely spaced grid and then 'shrinking' the grid until the bilayer with the protein has the desired density, with lipids neatly packed around the protein. When starting from a grid based on a single lipid structure, or several potentially different lipid structures (method 1), the bilayer will start well-packed but requires more equilibration. When starting from a pre-equilibrated bilayer, either pure or mixed, most of the structure of the bilayer stays intact, reducing equilibration time (method 2). The main advantages of these methods are that they minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins. PMID:17367719
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2015-01-01
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.
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.
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.
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.
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.
Simulating the Dynamic Coupling of Market and Physical System Operations
Widergren, Steven E.; Roop, Joseph M.; Guttromson, Ross T.; Huang, Zhenyu
2004-06-01
Abstract-As energy trading products cover shorter time periods and demand response programs move toward real-time pricing, financial market-based activity impacts ever more directly the physical operation of the system. To begin to understand the complex interactions between the market-driven operation signals, the engineered controlled schemes, and the laws of physics, new system modeling and simulation techniques must be explored. This discussion describes requirements for new simulation tools to address such market transaction control interactions and an approach to capture the dynamic coupling between energy markets and the physical operation of the power system appropriate for dispatcher reaction time frames.
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.
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.
Simulating Hamiltonian dynamics with a truncated Taylor series.
Berry, Dominic W; Childs, Andrew M; Cleve, Richard; Kothari, Robin; Somma, Rolando D
2015-03-01
We describe a simple, efficient method for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. Our method can simulate the time evolution of a wide variety of physical systems. As in another recent algorithm, the cost of our method depends only logarithmically on the inverse of the desired precision, which is optimal. However, we simplify the algorithm and its analysis by using a method for implementing linear combinations of unitary operations together with a robust form of oblivious amplitude amplification. PMID:25793789
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.
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.
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. PMID:17025782
Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks
NASA Astrophysics Data System (ADS)
Fahrenthold, Eric; Bass, Joseph
2015-06-01
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 these 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 noholonomic 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 model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.
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%.
Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics
NASA Astrophysics Data System (ADS)
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.
Annihilation of craters: Molecular dynamic simulations on a silver surface
Henriksson, K. O. E.; Nordlund, K.; Keinonen, J.
2007-12-15
The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.
Molecular Dynamics Simulations of Phospholipid Bilayers with Cholesterol
Hofsäß, Christofer; Lindahl, Erik; Edholm, Olle
2003-01-01
To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0–40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations—corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols. PMID:12668428
Dynamic simulation of shell-and-tube heat exchangers
Correa, D.J.; Marchetti, J.L.
1987-01-01
The transient operation of a multipass shell-and-tube heat exchanger with baffles is described by a multicell dynamic model where every cell represents a specific part of the exchanger. The proposed modeling technique can be used in a digital computer for the dynamic simulation of almost any type of shell-and-tube heat exchanger. The model includes time-dependent inlet conditions for both the cold and the hot streams. Hence, a number of start-up cases can be simulated and, once the system reaches a stationary operating point, a disturbance can be introduced in the inlet temperatures or the flow rates. This particular feature makes the model very useful not only for design purposes but also for transient analysis and control system design.
Reduced order component models for flexible multibody dynamics simulations
NASA Technical Reports Server (NTRS)
Tsuha, Walter S.; Spanos, John T.
1990-01-01
Many flexible multibody dynamics simulation codes require some form of component description that properly characterizes the dynamic behavior of the system. A model reduction procedure for producing low order component models for flexible multibody simulation is described. Referred to as projection and assembly, the method is a Rayleigh-Ritz approach that uses partitions of the system modal matrix as component Ritz transformation matrices. It is shown that the projection and assembly method yields a reduced system model that preserves a specified set of the full order system modes. Unlike classical component mode synthesis methods, the exactness of the method described is obtained at the expense of having to compute the full order system modes. The paper provides a comprehensive description of the method, a proof of exactness, and numerical results demonstrating the method's effectiveness.
Molecular dynamics simulations of dislocation instability in a stress gradient
NASA Astrophysics Data System (ADS)
Li, Ming; Selinger, Robin L.
2003-04-01
We present simulation studies of a morphological instability arising in dislocation dynamics. When an initially straight dislocation line is driven by a stress whose magnitude grows along the direction of dislocation motion, vibrational modes of the dislocation line with wavelength above a threshold value become linearly unstable. Molecular dynamics simulation studies of screw dislocations in Al demonstrate the onset of the instability during dislocation pair annihilation and annihilation at a crack tip. The wavelength of the unstable vibrational mode observed in each case agrees with the predictions of theoretical analysis. We discuss the role of temperature in nucleating the instability and speculate about how instabilities in dislocation motion could affect the density of threading dislocations during growth of heteroepitaxial thin films.
Time series analysis of molecular dynamics simulation using wavelet
NASA Astrophysics Data System (ADS)
Toda, Mikito
2012-08-01
A new method is presented to extract nonstationary features of slow collective motion toward time series data of molecular dynamics simulation for proteins. The method consists of the following two steps: (1) the wavelet transformation and (2) the singular value decomposition (SVD). The wavelet transformation enables us to characterize time varying features of oscillatory motions and SVD enables us to reduce the degrees of freedom of the movement. We apply the method to molecular dynamics simulation of various proteins such as Adenylate Kinase from Escherichia coli (AKE) and Thermomyces lanuginosa lipase (TLL). Moreover, we introduce indexes to characterize collective motion of proteins. These indexes provide us with information of nonstationary deformation of protein structures. We discuss future prospects of our study involving "intrinsically disordered proteins".
Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics.
Petsev, Nikolai D; Leal, L Gary; Shell, M Scott
2016-02-28
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. PMID:26931689
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.
The role of dynamic simulation in pipeline field applications
Chiu, K.C.; Kakka, R.S.
1998-12-31
In gas transmission pipeline and oil/gas field applications, gas compression is a key operation. Knowledge of the behavior of a gas compression system during upset conditions is required to evaluate the proposed compressor anti-surge control system, gas relief safety system and any future expansion and modifications. Dynamic simulation is a good engineering tool for such analyses. In this paper, a gas compression system is modeled which consists of eight identical parallel export compressors cascaded to four identical parallel reinjection compressors. The results of dynamic simulation for various what if scenarios are presented., The peak pressure of each header and amount of relieved gas were evaluated for the gas relief safety system. The surge margin of each compressor and other pertinent variables were analyzed for the compressor anti-surge control system.
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. PMID:19449821
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.
Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining
NASA Astrophysics Data System (ADS)
Khasin, M.; Kosloff, R.
2010-04-01
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 n3/2(lnn)-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 2×104 and 2×106 cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.
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
Flexing computational muscle: modeling and simulation of musculotendon dynamics.
Millard, Matthew; Uchida, Thomas; Seth, Ajay; Delp, Scott L
2013-02-01
Muscle-driven simulations of human and animal motion are widely used to complement physical experiments for studying movement dynamics. Musculotendon models are an essential component of muscle-driven simulations, yet neither the computational speed nor the biological accuracy of the simulated forces has been adequately evaluated. Here we compare the speed and accuracy of three musculotendon models: two with an elastic tendon (an equilibrium model and a damped equilibrium model) and one with a rigid tendon. Our simulation benchmarks demonstrate that the equilibrium and damped equilibrium models produce similar force profiles but have different computational speeds. At low activation, the damped equilibrium model is 29 times faster than the equilibrium model when using an explicit integrator and 3 times faster when using an implicit integrator; at high activation, the two models have similar simulation speeds. In the special case of simulating a muscle with a short tendon, the rigid-tendon model produces forces that match those generated by the elastic-tendon models, but simulates 2-54 times faster when an explicit integrator is used and 6-31 times faster when an implicit integrator is used. The equilibrium, damped equilibrium, and rigid-tendon models reproduce forces generated by maximally-activated biological muscle with mean absolute errors less than 8.9%, 8.9%, and 20.9% of the maximum isometric muscle force, respectively. When compared to forces generated by submaximally-activated biological muscle, the forces produced by the equilibrium, damped equilibrium, and rigid-tendon models have mean absolute errors less than 16.2%, 16.4%, and 18.5%, respectively. To encourage further development of musculotendon models, we provide implementations of each of these models in OpenSim version 3.1 and benchmark data online, enabling others to reproduce our results and test their models of musculotendon dynamics. PMID:23445050
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.
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. PMID:19518394
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.
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. PMID:26358333
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.
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.
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). PMID:14761255
Long-time dynamics of Met-enkephalin: comparison of theory with Brownian dynamics simulations.
Kostov, K S; Freed, K F
1999-01-01
A recent theory for the long time dynamics of flexible chain molecules is applied for the first time to a peptide of biological importance, the neurotransmitter met-enkephalin. The dynamics of met-enkephalin is considerably more complicated than that of the previously studied glycine oligomers; met-enkephalin contains the interesting motions of phenyl groups and of side chains relative to the backbone, motions that are present in general flexible peptides. The theory extends the generalized Rouse (GR) model used to study the dynamics of polymers by providing a systematic procedure for including the contributions from the memory function matrices neglected in the GR theory. The new method describes the dynamics by time correlation functions instead of individual trajectories. These correlation functions are analytically expressed in terms of a set of equilibrium averages and the eigenvalues and eigenfunctions of the diffusion operator. The predictions of the theory are compared with Brownian dynamics (BD) simulations, so that both theory and simulation use identical potential functions and solvent models. The theory thus contains no adjustable parameters. Inclusion of the memory function contributions profoundly affects the dynamics. The theory produces very good agreement with the BD simulations for the global motions of met-enkephalin. It also correctly predicts the long-time relaxation rate for local motions. PMID:9876130
NASA Astrophysics Data System (ADS)
Dillon, James E.; Schildkraut, Elliot Robert; Silk, J. K.; Kitajewski, L.; Martin, Robert A.; Woolhouse, Geoffrey R.
1990-09-01
This paper addresses the development of an Infrared Scene Simulator for Hardware-in-the-loop simulation of tactical IR air-to-air missile seekers. The simulator uses infrared target and background images produced by several technologies which are optically combined, collimated, and presented to the seeker under test. The system is configured for use on an optical bench but could also be hardened for flight simulator mounting. The high radiance target images of the air-to-air engagement scenarios are generated using high temperature blackbody sources and iris targets in the form of geometric figures with the size under servo control. The targets use an X-Y translation slide and dynamic attenuator to simulate movement within the field of view, range closure and the attenuation effects of the atmosphere. These targets are used to generate the aircraft tailpipe and flare decoy images required by the simulation. The high radiance targets are combined with the image from a Multiple Dynamic Simulator-Infrared Emitter Array which produces the engine plume, aircraft fuselage and background image. The three targets are combined using two beamsplitters and the composite image is collimated and relayed to the seeker under test. A workstation-based computational system generates the array image for display in real time.
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.
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.
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.
Surface Diffusion of Single Polymer Chain Using Molecular Dynamics SIMULATION*
NASA Astrophysics Data System (ADS)
Desai, Tapan; Keblinski, Pawel; Kumar, Sanat; Granick, Steve
2004-05-01
Results of recent experiments on polymer chains adsorbed from dilute solution at solid-liquid interface show the power scaling law dependence of the chain diffusivity, D, as a function of the degree of polymerization, N, D ˜ N^3/2. By contrast, DNA molecules bound to fluid cationic lipid bilayers follows Rouse dynamics with D ˜ N^1. We used molecular dynamics simulations to gain an understanding of these dissimilar scaling behaviors. Our model systems contain chains comprised of N monomers connected by anharmonic springs described by the finite extendible nonlinear elastic, FENE potential, embedded into a solvent of N=1 monomers. Two types of simulations we performed: (i) the chain is confined to two dimensions, (ii) the three dimensional chain in the solvent is confined between two solids plates. With randomly placed impenetrable obstacles on the surface, the diffusion of 2D chains exhibits, D ˜ N^3/2 behavior, when the chain radius of gyration, Rg, is larger than half the distance between obstacles, and D ˜ N^1 for shorter chains. In the presence of an athermal solvent, the scaling exponent is 0.75 due to hydrodynamic forces, for the two-dimensional system. We will also discuss the nature of dynamic adsorption transition and effects of hydrodynamics forces on chain diffusion for the three-dimensional simulations.
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
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).
Dynamic mixing in magma bodies - Theory, simulations, and implications
NASA Technical Reports Server (NTRS)
Oldenburg, Curtis M.; Spera, Frank J.; Yuen, David A.; Sewell, Granville
1989-01-01
The magma-mixing process is different from the mantle mixing process in that the mixing components of magma are dynamically active, with the melt density depending strongly on composition. This paper describes simulations of time-dependent variable-viscosity double-diffusive convection which were carried out to investigate quantitatively the mixing dynamics of magma in melt-dominated magma bodies. Results show that the dynamics of double-diffusive convection can impart complex patterns of composition, through time and space. The mixing time depends nonlinearly on many factors, including heat flux driving convection, the rate of diffusion of chemical species, the relative importance of thermal and chemical buoyancy, the viscosities of the mixing components, and the shape of the magma body.
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.
Detailed Multidimensional Simulations of the Structure and Dynamics of Flames
NASA Technical Reports Server (NTRS)
Patnaik, G.; Kailasanath, K.
1999-01-01
Numerical simulations in which the various physical and chemical processes can be independently controlled can significantly advance our understanding of the structure, stability, dynamics and extinction of flames. Therefore, our approach has been to use detailed time-dependent, multidimensional, multispecies numerical models to perform carefully designed computational experiments of flames on Earth and in microgravity environments. Some of these computational experiments are complementary to physical experiments performed under the Microgravity Program while others provide a fundamental understanding that cannot be obtained from physical experiments alone. In this report, we provide a brief summary of our recent research highlighting the contributions since the previous microgravity combustion workshop. There are a number of mechanisms that can cause flame instabilities and result in the formation of dynamic multidimensional structures. In the past, we have used numerical simulations to show that it is the thermo-diffusive instability rather than an instability due to preferential diffusion that is the dominant mechanism for the formation of cellular flames in lean hydrogen-air mixtures. Other studies have explored the role of gravity on flame dynamics and extinguishment, multi-step kinetics and radiative losses on flame instabilities in rich hydrogen-air flames, and heat losses on burner-stabilized flames in microgravity. The recent emphasis of our work has been on exploring flame-vortex interactions and further investigating the structure and dynamics of lean hydrogen-air flames in microgravity. These topics are briefly discussed after a brief discussion of our computational approach for solving these problems.
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.
Dynamic risk simulation to assess natural hazards risk along roads
NASA Astrophysics Data System (ADS)
Voumard, J.; Caspar, O.; Derron, M.-H.; Jaboyedoff, M.
2013-11-01
Risk generated by natural hazards on roads is usually calculated with equations integrating various parameters related to hazard and traffic. These are static variables, like an average number of vehicles crossing this section every day and an average vehicle speed. This methodology cannot take into account dynamic variations of traffic and interactions between vehicles such as speed modifications due to windy roads, slowdowns resulting from saturated traffic or vehicle tailbacks forming in front of traffic lights. Here we show, by means of a dynamic traffic simulator, that traffic variations may greatly influence the risk estimation over time. The risk is analysed on several sections of an Alpine road in Switzerland using a dynamic vehicles approach, and compared with the results of the static methodology. It demonstrates that risk can significantly increase on sinuous sections because of decreasing vehicle speed. For example, along an 800 m-long section of road containing two hairpin bends, the dynamic risk is about 50% higher than the static one. Badly placed signalization, slowing down, or stopping the vehicles in a hazardous area may increase the risk by about 150% (i.e. 2.5 times higher) along a straight road section where vehicles speed is high. A more realistic risk can thus be obtained from a dynamic approach, especially on mountain roads. The dynamic traffic simulator developed for this work appears to be a helpful tool to support decision-making in reducing risk on mountain roads and it shows the importance of keeping the traffic moving as freely as possible.
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. PMID:24525420
Simulation laboratory for evaluating dynamic traffic management systems
Ban-Akiva, M.E.; Mishalani, R.G.; Yang, Q.; Koutsopoulos, H.N.
1997-08-01
This paper presents a simulation laboratory for performance evaluation and design refinement of dynamic traffic management systems. The laboratory consists of four integrated components: (1) a traffic management simulator, which mimics the generation of route guidance and operations of traffic signals and signs; (2) a traffic flow simulator, which models individual vehicle movements and drivers` route choice decisions in the presence of real-time traffic information; (3) a surveillance system module, which collects real-time traffic data from sensors and probe vehicles in the simulated network; and (4) a control device module, which implements control strategies and route guidance generated by the traffic management system under evaluation. The simulation laboratory has been implemented in C++ using object-oriented programming and a distributed environment. It features a graphical user interface that allows users to visualize the simulation process, including animation of vehicle movements, state of surveillance sensors, traffic signals, signs, and so on. This modeling system provides a unique tool for evaluating integrated ATIS and ATMS applications in a computer-based laboratory environment.
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. PMID:27248512
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.
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
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.
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.
Real-time simulation of dynamic fluoroscopy of ERCP
NASA Astrophysics Data System (ADS)
Jung, Hoeryong; Lee, Doo Yong
2010-02-01
This paper discusses the methods for real-time rendering of time-varying dynamic fluoroscope images including fluid flow for the ERCP (Endoscopic Retrograde Cholangiopancreatography) simulation. A volume rendering technique is used to generate virtual fluoroscopy images. This paper develops an image-overlaying method which overlaps the timevarying images onto the constant background image. The full size fluoroscopy image is computed from the initial volume data set during the pre-processing stage, which is then saved as the background image. Only the time-varying images are computed from the time-varying volume data set during the actual simulation. This involves relatively small computation compared with the background image. The time-varying images are then overlaid onto the background image to obtain the complete images. This method reduces computational overhead by removing redundant computations. A simplified particle dynamics model is employed for fast simulation of the fluid flow. The fluid model, a collection of particles, interacts only with the ducts based on principles of a complete elastic collision. Hence, the velocity of the particles, when they collide with the duct, can be computed by using simple algebraic equations. The methods are implemented for fast simulation of the ERCP.
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. PMID:26751047
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.
Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M; Benedict, L; Hau-Riege, S; Langdon, A; London, R
2008-02-14
The temperature equilibration rate in dense hydrogen (for both T{sub i} > T{sub e} and T{sub i} < T{sub e}) has been calculated with large-scale molecular dynamics simulations for temperatures between 10 and 300 eV and densities between 10{sup 20}/cc to 10{sup 24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L {approx}> 1, Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] with the sub-leading corrections and the fit of Gericke-Murillo-Schlanges [Gericke et al., PRE 65, 036418 (2003)] to the T-matrix evaluation of the collision operator, agrees with the MD data to within the error bars of the simulation. For more strongly-coupled plasmas where L {approx}< 1, our numerical results are consistent with the fit of Gericke-Murillo-Schlanges.
Dynamics in a supercooled molecular liquid: Theory and simulations
Rinaldi, Adele; Sciortino, Francesco; Tartaglia, Piero
2001-06-01
We report extensive simulations of liquid supercooled states for a simple three-site molecular model, introduced by Lewis and Wahnstrom [Phys. Rev. E >50, 3865 (1994)] to mimic the behavior of ortho-terphenyl. The large system size and the long simulation length allow us to calculate very precisely (in a large q-vector range) self-correlation and collective correlation functions, providing a clean and simple reference model for theoretical descriptions of molecular liquids in supercooled states. The time and wave-vector dependence of the site-site correlation functions are compared (neglecting the molecular constraints) with detailed ideal mode-coupling theory predictions. Except for the wave-vector region where the dynamics are controlled by the center of mass (around 9 nm{sup {minus}1}), the theoretical predictions compare very well with the simulation data.
Dynamical Simulations of Terrestrial Planet Formation During Giant Planet Migration
NASA Astrophysics Data System (ADS)
Mandell, A. M.; Raymond, S. N.; Sigurdsson, S.
2005-12-01
We present preliminary results of dynamical simulations of young planetary systems undergoing migration of a Jovian-type planet through the terrestrial region. We find that a significant fraction (10-40%) of the initial planetary embryos remain after giant planet migration, and subsequent evolution of the system results in the formation of terrestrial planets in various configurations, often including a planet in the Habitable Zone. In simulations with gas drag, 3-6 Earth mass planets are formed interior to the migrating Jovian planet, swept inward through moving resonances, and eccentricities are damped for all planets. Systematic variations are seen between simulations with and without gas drag. The presence of a second, non-migrating giant planet reduces the water content and mass of the planets formed throughout the system. This research was supported in part by the Penn State Astrobiology Research Center and the Goddard Center for Astrobiology.
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.
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.
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.
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.
Implementation of the force decomposition machine for molecular dynamics simulations.
Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka
2012-09-01
We present the design and implementation of the force decomposition machine (FDM), a cluster of personal computers (PCs) that is tailored to running molecular dynamics (MD) simulations using the distributed diagonal force decomposition (DDFD) parallelization method. The cluster interconnect architecture is optimized for the communication pattern of the DDFD method. Our implementation of the FDM relies on standard commodity components even for networking. Although the cluster is meant for DDFD MD simulations, it remains general enough for other parallel computations. An analysis of several MD simulation runs on both the FDM and a standard PC cluster demonstrates that the FDM's interconnect architecture provides a greater performance compared to a more general cluster interconnect. PMID:23085166
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.
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
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
Recovering position-dependent diffusion from biased molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-01
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.
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. PMID:24588150
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
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.
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
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
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.
Shimamura, K; Shibuta, Y; Ohmura, S; Arifin, R; Shimojo, F
2016-04-13
The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed. PMID:26953616
NASA Astrophysics Data System (ADS)
Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.
2016-04-01
The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.
Verhaegen, F; Liu, H H
2001-02-01
In radiation therapy, new treatment modalities employing dynamic collimation and intensity modulation increase the complexity of dose calculation because a new dimension, time, has to be incorporated into the traditional three-dimensional problem. In this work, we investigated two classes of sampling technique to incorporate dynamic collimator motion in Monte Carlo simulation. The methods were initially evaluated for modelling enhanced dynamic wedges (EDWs) from Varian accelerators (Varian Medical Systems, Palo Alto, USA). In the position-probability-sampling or PPS method, a cumulative probability distribution function (CPDF) was computed for the collimator position, which could then be sampled during simulations. In the static-component-simulation or SCS method, a dynamic field is approximated by multiple static fields in a step-shoot fashion. The weights of the particles or the number of particles simulated for each component field are computed from the probability distribution function (PDF) of the collimator position. The CPDF and PDF were computed from the segmented treatment tables (STTs) for the EDWs. An output correction factor had to be applied in this calculation to account for the backscattered radiation affecting monitor chamber readings. Comparison of the phase-space data from the PPS method (with the step-shoot motion) with those from the SCS method showed excellent agreement. The accuracy of the PPS method was further verified from the agreement between the measured and calculated dose distributions. Compared to the SCS method, the PPS method is more automated and efficient from an operational point of view. The principle of the PPS method can be extended to simulate other dynamic motions, and in particular, intensity-modulated beams using multileaf collimators. PMID:11229715
Thermostat artifacts in replica exchange molecular dynamics simulations.
Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard
2009-01-01
We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980
Thermostat artifacts in replica exchange molecular dynamics simulations
Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard
2009-01-01
We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980
MHD Simulations of Plasma Dynamics with Non-Axisymmetric Boundaries
NASA Astrophysics Data System (ADS)
Hansen, Chris; Levesque, Jeffrey; Morgan, Kyle; Jarboe, Thomas
2015-11-01
The arbitrary geometry, 3D extended MHD code PSI-TET is applied to linear and non-linear simulations of MCF plasmas with non-axisymmetric boundaries. Progress and results from simulations on two experiments will be presented: 1) Detailed validation studies of the HIT-SI experiment with self-consistent modeling of plasma dynamics in the helicity injectors. Results will be compared to experimental data and NIMROD simulations that model the effect of the helicity injectors through boundary conditions on an axisymmetric domain. 2) Linear studies of HBT-EP with different wall configurations focusing on toroidal asymmetries in the adjustable conducting wall. HBT-EP studies the effect of active/passive stabilization with an adjustable ferritic wall. Results from linear verification and benchmark studies of ideal mode growth with and without toroidal asymmetries will be presented and compared to DCON predictions. Simulations of detailed experimental geometries are enabled by use of the PSI-TET code, which employs a high order finite element method on unstructured tetrahedral grids that are generated directly from CAD models. Further development of PSI-TET will also be presented including work to support resistive wall regions within extended MHD simulations. Work supported by DoE.
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.
Polymer Brushes under Shear: Molecular Dynamics Simulations Compared to Experiments.
Singh, Manjesh K; Ilg, Patrick; Espinosa-Marzal, Rosa M; Kröger, Martin; Spencer, Nicholas D
2015-04-28
Surfaces coated with polymer brushes in a good solvent are known to exhibit excellent tribological properties. We have performed coarse-grained equilibrium and nonequilibrium molecular dynamics (MD) simulations to investigate dextran polymer brushes in an aqueous environment in molecular detail. In a first step, we determined simulation parameters and units by matching experimental results for a single dextran chain. Analyzing this model when applied to a multichain system, density profiles of end-tethered polymer brushes obtained from equilibrium MD simulations compare very well with expectations based on self-consistent field theory. Simulation results were further validated against and correlated with available experimental results. The simulated compression curves (normal force as a function of surface separation) compare successfully with results obtained with a surface forces apparatus. Shear stress (friction) obtained via nonequilibrium MD is contrasted with nanoscale friction studies employing colloidal-probe lateral force microscopy. We find good agreement in the hydrodynamic regime and explain the observed leveling-off of the friction forces in the boundary regime by means of an effective polymer-wall attraction. PMID:25830715
Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations
Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C.
2013-01-01
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. PMID:24081985
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.
NASA Astrophysics Data System (ADS)
Grest, Gary S.
2008-03-01
Twenty years ago at the APS March Meeting, Kurt Kremer and I presented the first numerical evidence from computer simulations that the reptation model of Edwards and de Gennes correctly describes the dynamics of entangled linear polymer melts. For chains longer than the entanglement length Ne, the monomers of a chain move predominantly along their own contour. The distinctive signature of reptation dynamics, which we observed, was that on intermediate time scales, the mean squared displacement of a monomer increases with time as t^ 1/4. Though these early simulations were limited to chains of a few Ne, they demonstrated the potential of computer simulations to contribute to our understanding of polymer dynamics. Here I will review the progress over the past twenty years and present an outlook for the future in modeling entangled polymer melts and networks. With present day computers coupled with efficient parallel molecular dynamics codes, it is now possible to follow the equilibrium dynamics of chains of length 10-20Ne from the early Rouse regime to the long time diffusive regime. Result of these simulations support the earlier results obtained on chains of only a few Ne. Further evidence for the tube models of polymer dynamics has been obtained by identifying the primitive path mesh that characterizes the microscopic topological state of the computer- generated conformations of the chains. In particular, the plateau moduli derived on the basis of this analysis quantitatively reproduce experimental data for a wide spectrum of entangled polymer liquids including semi-dilute theta solutions of synthetic polymers, the corresponding dense melts, and solutions of semi-flexible (bio)polymers such as f-actin or suspensions of rodlike viruses. We also find that in agreement with the reptation model, the stress, end-to-end distance and entanglement length of an entangled melt subjected to uniaxial elongation, all relax on the same time scale.
Molecular dynamics simulations of hydrogen diffusion in aluminum
Zhou, X. W.; El Gabaly, F.; Stavila, V.; Allendorf, M. D.
2016-03-23
In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less
All-atom simulations of crowding effects on ubiquitin dynamics
NASA Astrophysics Data System (ADS)
Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo
2013-08-01
It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (˜0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.
Brownian dynamics simulations of ellipsoidal magnetizable particle suspensions
NASA Astrophysics Data System (ADS)
Torres-Díaz, I.; Rinaldi, C.
2014-06-01
The rotational motion of soft magnetic tri-axial ellipsoidal particles suspended in a Newtonian fluid has been studied using rotational Brownian dynamics simulations by solving numerically the stochastic angular momentum equation in an orientational space described by the quaternion parameters. The model is applicable to particles where the effect of shape anisotropy is dominant. The algorithm quantifies the magnetization of a monodisperse suspension of tri-axial ellipsoids in dilute limit conditions under applied constant and time-varying magnetic fields. The variation of the relative permeability with the applied magnetic field of the particle's bulk material was included in the simulations. The results show that the equilibrium magnetization of a suspension of magnetizable tri-axial ellipsoids saturates at high magnetic field amplitudes. Additionally, the dynamic susceptibility at low magnetic field intensity presents a peak in the out-of-phase component, which is significantly smaller than the in-phase component and depends on the Langevin parameter. The dynamic magnetization of the particle suspension is in phase with the magnetic field at low and high frequencies far from the peak of the out-of-phase component.
Visualizing microscopic structure and dynamics of simulated silicate melts
NASA Astrophysics Data System (ADS)
Karki, B. B.; Bohara, B.
2013-12-01
We perform a detailed visualization-based analysis of atomic-position series data for silicate melts obtained from first-principles (quantum mechanical) molecular dynamics simulations. This involves processing atomic trajectories as well as relevant structural and dynamical information. Clutter associated with trajectory rendering can be reduced with an adaptive position-merging scheme. To gain insight into the short- and mid-range order of the melt structure, we extract and visualize the details of radial distribution function (RDF) and coordination environment. The first peaks of all partial RDFs lie in the distance range of 1.6 to 4 Å and the corresponding mean coordination numbers vary from less than 1 to more than 9. The coordination environments involving cations and anions differ substantially from each other, each consisting of a rich set of coordination states. These states vary both spatially and temporally: The per-atom coordination information extracted on the fly is rendered instantaneously as the spheres and polyhedra as well as along the corresponding trajectories using a color-coding scheme. The information is also visualized as clusters formed by atoms that are coordinated at different time intervals during the entire simulation. The animated visualization suggests that the melt structure can be viewed as a dynamic (partial) network of Al/Si-O coordination polyhedra connected via bridging oxygen in an inhomogeneous distribution of mobile cations including magnesium, calcium, and protons.
Computer Simulation of Flow Dynamics in Paraclinoidal Aneurysms
Kobayashi, N.; Miyachi, S.; Okamoto, T.; Kojima, T.; Hattori, K.; Qian, S.; Takeda, H.; Yoshida, J.
2005-01-01
Summary Endovascular treatment, which is very useful method especially for paraclinoidal aneurysms, has the limitations of coil compaction and recanalization, which are difficult to predict. We tried to understand flow dynamic features, one of the important factors of such problems, using computer flow dynamics (CFD) simulations. CFD simulations were made in paraclinoidal aneurysm model of different size and protruded directions. Flow patterns, flow velocities and pressure are analyzed. Although the pressure on the aneurismal orifice is highest in the aneurysm protruding vertically upward, the flow velocity is highest in the superior-medial protruding one. Significant difference is not observed in either flow patterns, flow velocities or pressures on the aneurismal orifices between the sizes of aneurismal sac. Among paraclinoidal aneurysms, an aneurysm protruding to superior-medially receives the most severe haemodynamic stresses at the orifice and the aneurysm size does not cause significant differences in the aspect of flow dynamics. It should be considered in the treatment of such aneurysms. PMID:20584475
Pattern Recognition for a Flight Dynamics Monte Carlo Simulation
NASA Technical Reports Server (NTRS)
Restrepo, Carolina; Hurtado, John E.
2011-01-01
The design, analysis, and verification and validation of a spacecraft relies heavily on Monte Carlo simulations. Modern computational techniques are able to generate large amounts of Monte Carlo data but flight dynamics engineers lack the time and resources to analyze it all. The growing amounts of data combined with the diminished available time of engineers motivates the need to automate the analysis process. Pattern recognition algorithms are an innovative way of analyzing flight dynamics data efficiently. They can search large data sets for specific patterns and highlight critical variables so analysts can focus their analysis efforts. This work combines a few tractable pattern recognition algorithms with basic flight dynamics concepts to build a practical analysis tool for Monte Carlo simulations. Current results show that this tool can quickly and automatically identify individual design parameters, and most importantly, specific combinations of parameters that should be avoided in order to prevent specific system failures. The current version uses a kernel density estimation algorithm and a sequential feature selection algorithm combined with a k-nearest neighbor classifier to find and rank important design parameters. This provides an increased level of confidence in the analysis and saves a significant amount of time.
Molecular dynamics simulations of solutions at constant chemical potential
NASA Astrophysics Data System (ADS)
Perego, C.; Salvalaglio, M.; Parrinello, M.
2015-04-01
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.
A dynamic motion simulator for future European docking systems
NASA Technical Reports Server (NTRS)
Brondino, G.; Marchal, PH.; Grimbert, D.; Noirault, P.
1990-01-01
Europe's first confrontation with docking in space will require extensive testing to verify design and performance and to qualify hardware. For this purpose, a Docking Dynamics Test Facility (DDTF) was developed. It allows reproduction on the ground of the same impact loads and relative motion dynamics which would occur in space during docking. It uses a 9 degree of freedom, servo-motion system, controlled by a real time computer, which simulates the docking spacecraft in a zero-g environment. The test technique involves and active loop based on six axis force and torque detection, a mathematical simulation of individual spacecraft dynamics, and a 9 degree of freedom servomotion of which 3 DOFs allow extension of the kinematic range to 5 m. The configuration was checked out by closed loop tests involving spacecraft control models and real sensor hardware. The test facility at present has an extensive configuration that allows evaluation of both proximity control and docking systems. It provides a versatile tool to verify system design, hardware items and performance capabilities in the ongoing HERMES and COLUMBUS programs. The test system is described and its capabilities are summarized.
Plimpton, Steve; Thompson, Aidan; Crozier, Paul
LAMMPS (http://lammps.sandia.gov/index.html) stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a code that can be used to model atoms or, as the LAMMPS website says, as a parallel particle simulator at the atomic, meso, or continuum scale. This Sandia-based website provides a long list of animations from large simulations. These were created using different visualization packages to read LAMMPS output, and each one provides the name of the PI and a brief description of the work done or visualization package used. See also the static images produced from simulations at http://lammps.sandia.gov/pictures.html The foundation paper for LAMMPS is: S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995), but the website also lists other papers describing contributions to LAMMPS over the years.
Parallel methods for dynamic simulation of multiple manipulator systems
NASA Technical Reports Server (NTRS)
Mcmillan, Scott; Sadayappan, P.; Orin, David E.
1993-01-01
In this paper, efficient dynamic simulation algorithms for a system of m manipulators, cooperating to manipulate a large load, are developed; their performance, using two possible forms of parallelism on a general-purpose parallel computer, is investigated. One form, temporal parallelism, is obtained with the use of parallel numerical integration methods. A speedup of 3.78 on four processors of CRAY Y-MP8 was achieved with a parallel four-point block predictor-corrector method for the simulation of a four manipulator system. These multi-point methods suffer from reduced accuracy, and when comparing these runs with a serial integration method, the speedup can be as low as 1.83 for simulations with the same accuracy. To regain the performance lost due to accuracy problems, a second form of parallelism is employed. Spatial parallelism allows most of the dynamics of each manipulator chain to be computed simultaneously. Used exclusively in the four processor case, this form of parallelism in conjunction with a serial integration method results in a speedup of 3.1 on four processors over the best serial method. In cases where there are either more processors available or fewer chains in the system, the multi-point parallel integration methods are still advantageous despite the reduced accuracy because both forms of parallelism can then combine to generate more parallel tasks and achieve greater effective speedups. This paper also includes results for these cases.
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel
Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.
2011-12-12
This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12{sigma}, 14{sigma} and 16{sigma} and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.
Molecular dynamics simulations through GPU video games technologies
Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia
2016-01-01
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251
Direct Numerical Simulation of Soot Particle Dynamics using DQMOM
NASA Astrophysics Data System (ADS)
Blanquart, Guillaume; Pitsch, Heinz; Fox, Rodney
2006-11-01
The understanding of soot particle dynamics in combustion systems is a key issue in the development of low emission engines. Of particular importance are the processes shaping the soot particle size distribution function (PSDF). However, it is not always necessary to represent exactly the full distribution but rather some of its moments. The Direct Quadrature Method of Moments (DQMOM) allows for a very accurate prediction of the moments of the soot PSDF without the cost of expensive methods like Direct Simulation Monte-Carlo (DSMC). This method has been validated for laminar premixed and diffusion flames with detailed chemistry and is now implemented in a semi-implicit low Mach number Navier-Stokes solver. A Direct Numerical Simulation (DNS) of an ethylene jet diffusion flame is performed to study the dynamics of soot particles in a turbulent environment. Soot particles are formed in very rich regions of the flames and are then transported to lean regions where they get oxidized. The time evolution of the soot PSDF will be analyzed and compared to similar distributions from laminar simulations.
Parareal in Time for Dynamic Simulations of Power Systems
Gurrala, Gurunath; Dimitrovski, Aleksandar D; Pannala, Sreekanth; Simunovic, Srdjan; Starke, Michael R
2015-01-01
In recent years, there have been significant developments in parallel algorithms and high performance parallel computing platforms. Parareal in time algorithm has become popular for long transient simulations (e.g., molecular dynamics, fusion, reacting flows). Parareal is a parallel algorithm which divides the time interval into sub-intervals and solves them concurrently. This paper investigates the applicability of the parareal algorithm to power system dynamic simulations. Preliminary results on the application of parareal for multi-machine power systems are reported in this paper. Two widely used test systems, WECC 3-generator 9-bus system, New England 10-generator 39- bus system, is used to explore the effectiveness of the parareal. Severe 3 phase bus faults are simulated using both the classical and detailed models of multi-machine power systems. Actual Speedup of 5-7 times is observed assuming ideal parallelization. It has been observed that the speedup factors of the order of 20 can be achieved by using fast coarse approximations of power system models. Dependency of parareal convergence on fault duration and location has been observed.
Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Levine, Zachary Alan
Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant
Emulation of dynamic simulators with application to hydrology
NASA Astrophysics Data System (ADS)
Machac, David; Reichert, Peter; Albert, Carlo
2016-05-01
Many simulation-intensive tasks in the applied sciences, such as sensitivity analysis, parameter inference or real time control, are hampered by slow simulators. Emulators provide the opportunity of speeding up simulations at the cost of introducing some inaccuracy. An emulator is a fast approximation to a simulator that interpolates between design input-output pairs of the simulator. Increasing the number of design data sets is a computationally demanding way of improving the accuracy of emulation. We investigate the complementary approach of increasing emulation accuracy by including knowledge about the mechanisms of the simulator into the formulation of the emulator. To approximately reproduce the output of dynamic simulators, we consider emulators that are based on a system of linear, ordinary or partial stochastic differential equations with a noise term formulated as a Gaussian process of the parameters to be emulated. This stochastic model is then conditioned to the design data so that it mimics the behavior of the nonlinear simulator as a function of the parameters. The drift terms of the linear model are designed to provide a simplified description of the simulator as a function of its key parameters so that the required corrections by the conditioned Gaussian process noise are as small as possible. The goal of this paper is to compare the gain in accuracy of these emulators by enlarging the design data set and by varying the degree of simplification of the linear model. We apply this framework to a simulator for the shallow water equations in a channel and compare emulation accuracy for emulators based on different spatial discretization levels of the channel and for a standard non-mechanistic emulator. Our results indicate that we have a large gain in accuracy already when using the simplest mechanistic description by a single linear reservoir to formulate the drift term of the linear model. Adding some more reservoirs does not lead to a significant
Molecular Dynamics Simulation on Stability of Insulin on Graphene
NASA Astrophysics Data System (ADS)
Liang, Li-jun; Wang, Qi; Wu, Tao; Shen, Jia-wei; Kang, Yu
2009-12-01
The adsorption dynamics of a model protein (the human insulin) onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some α-helices in non-fixed systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.
Micellar crystals in solution from molecular dynamics simulations
Anderson, J.; Lorenz, C.; Travesset, A.
2008-05-14
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers.
Phase portrait methods for verifying fluid dynamic simulations
Stewart, H.B.
1989-01-01
As computing resources become more powerful and accessible, engineers more frequently face the difficult and challenging engineering problem of accurately simulating nonlinear dynamic phenomena. Although mathematical models are usually available, in the form of initial value problems for differential equations, the behavior of the solutions of nonlinear models is often poorly understood. A notable example is fluid dynamics: while the Navier-Stokes equations are believed to correctly describe turbulent flow, no exact mathematical solution of these equations in the turbulent regime is known. Differential equations can of course be solved numerically, but how are we to assess numerical solutions of complex phenomena without some understanding of the mathematical problem and its solutions to guide us
Dynamic simulation of tibial tuberosity realignment: model evaluation.
Purevsuren, Tserenchimed; Elias, John J; Kim, Kyungsoo; Kim, Yoon Hyuk
2015-01-01
This study was performed to evaluate a dynamic multibody model developed to characterize the influence of tibial tuberosity realignment procedures on patellofemoral motion and loading. Computational models were created to represent four knees previously tested at 40°, 60°, and 80° of flexion with the tibial tuberosity in a lateral, medial and anteromedial positions. The experimentally loaded muscles, major ligaments of the knee, and patellar tendon were represented. A repeated measures ANOVA with post-hoc testing was performed at each flexion angle to compare data between the three positions of the tibial tuberosity. Significant experimental trends for decreased patella flexion due to tuberosity anteriorization and a decrease in the lateral contact force due to tuberosity medialization were reproduced computationally. The dynamic multibody modeling technique will allow simulation of function for symptomatic knees to identify optimal surgical treatment methods based on parameters related to knee pathology and pre-operative kinematics. PMID:25025488
Dynamic Simulation and Optimization of Nuclear Hydrogen Production Systems
Paul I. Barton; Mujid S. Kaximi; Georgios Bollas; Patricio Ramirez Munoz
2009-07-31
This project is part of a research effort to design a hydrogen plant and its interface with a nuclear reactor. This project developed a dynamic modeling, simulation and optimization environment for nuclear hydrogen production systems. A hybrid discrete/continuous model captures both the continuous dynamics of the nuclear plant, the hydrogen plant, and their interface, along with discrete events such as major upsets. This hybrid model makes us of accurate thermodynamic sub-models for the description of phase and reaction equilibria in the thermochemical reactor. Use of the detailed thermodynamic models will allow researchers to examine the process in detail and have confidence in the accurary of the property package they use.
Simulation of the photogrammetric appendage structural dynamics experiment
NASA Technical Reports Server (NTRS)
Pappa, Richard S.; Gilbert, Michael G.; Welch, Sharon S.
1995-01-01
The Photogrammetric Appendage Structural Dynamics Experiment (PASDE) uses six video cameras in the Space Shuttle cargo bay to measure vibration of the Russian Mir space station Kvant-ll solar array. It occurs on Shuttle/Mir docking mission STS-74 scheduled for launch in November 1995. The objective of PASDE is to demonstrate photogrammetric technology for measuring 'untargeted' spacecraft appendage structural dynamics. This paper discusses a pre-flight simulation test conducted in July 1995, focusing on the image processing aspects. The flight camera system recorded vibrations of a full-scale structural test article having grids of white lines on black background, similar in appearance to the Mir solar array. Using image correlation analysis, line intersections on the structure are tracked in the video recordings to resolutions of less than 0.1 pixel. Calibration and merging of multiple camera views generated 3-dimensional displacements from which structural modal parameters are then obtained.
Molecular dynamic simulation of non-melt laser annealing process
NASA Astrophysics Data System (ADS)
Liren, Yan; Dai, Li; Wei, Zhang; Zhihong, Liu; Wei, Zhou; Quan, Wang
2016-03-01
Molecular dynamic simulation is performed to study the process of material annealing caused by a 266 nm pulsed laser. A micro-mechanism describing behaviors of silicon and impurity atoms during the laser annealing at a non-melt regime is proposed. After ion implantation, the surface of the Si wafer is acted by a high energy laser pulse, which loosens the material and partially frees both Si and impurity atoms. While the residual laser energy is absorbed by valence electrons, these atoms are recoiled and relocated to finally form a crystal. Energy-related movement behavior is observed by using the molecular dynamic method. The non-melt laser anneal appears to be quite sensitive to the energy density of the laser, as a small excess energy may causes a significant impurity diffusion. Such a result is also supported by our laser anneal experiment.
Gas adsorption and accumulation on hydrophobic surfaces: Molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Luo, Qing-Qun; Yang, Jie-Ming
2015-09-01
Molecular dynamics simulations show that the gas dissolved in water can be adsorbed at a hydrophobic interface and accumulates thereon. Initially, a water depletion layer appears on the hydrophobic interface. Gas molecules then enter the depletion layer and form a high-density gas-enriched layer. Finally, the gas-enriched layer accumulates to form a nanobubble. The radian of the nanobubble increases with time until equilibrium is reached. The equilibrium state arises through a Brenner-Lohse dynamic equilibrium mechanism, whereby the diffusive outflux is compensated by an influx near the contact line. Additionally, supersaturated gas also accumulates unsteadily in bulk water, since it can diffuse back into the water and is gradually adsorbed by a solid substrate. Project supported by the National Natural Science Foundation of China (Grant No. 21376161).
Clustering effects in ionic polymers: Molecular dynamics simulations
Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.
2015-08-18
Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing themore » electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.« less
Clustering effects in ionic polymers: Molecular dynamics simulations
Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.
2015-08-18
Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.
Dynamic simulation of a smart crank and slider mechanism
NASA Astrophysics Data System (ADS)
Zhu, Hai-Tao; Zhang, Xu; Zhang, Jia-Tai; Hu, Sheng-Hai
2002-12-01
In this paper, a smart crank and slider mechanism is analyzed mostly from a dynamic view. By means of dynamic explicit finite element method, 3D nonlinear structure is simulated. It is proved that the mechanism can effectively accomplish smart movement prescribed. And in order to ensure reciprocal movement with higher frequency, measures should be taken to avoid over heating of parts. Compared with internal energy, kinetic energy of total rigid body is dominating, and Y direction equivalent rigid velocity is much higher than X direction velocity. Equivalent rigid velocity of all parts is consistent with respective movement condition. For both energy and velocity, slider effect is dominating. Three direction equivalent inertia force oscillates. Force amplitude in Y-direction is comparitively the greatest.
Accurate direct Eulerian simulation of dynamic elastic-plastic flow
Kamm, James R; Walter, John W
2009-01-01
The simulation of dynamic, large strain deformation is an important, difficult, and unsolved computational challenge. Existing Eulerian schemes for dynamic material response are plagued by unresolved issues. We present a new scheme for the first-order system of elasto-plasticity equations in the Eulerian frame. This system has an intrinsic constraint on the inverse deformation gradient. Standard Godunov schemes do not satisfy this constraint. The method of Flux Distributions (FD) was devised to discretely enforce such constraints for numerical schemes with cell-centered variables. We describe a Flux Distribution approach that enforces the inverse deformation gradient constraint. As this approach is new and novel, we do not yet have numerical results to validate our claims. This paper is the first installment of our program to develop this new method.
Molecular Dynamics Simulations of the Photoactive Protein Nitrile Hydratase
Kubiak, Karina; Nowak, Wieslaw
2008-01-01
Nitrile hydratase (NHase) is an enzyme used in the industrial biotechnological production of acrylamide. The active site, which contains nonheme iron or noncorrin cobalt, is buried in the protein core at the interface of two domains, α and β. Hydrogen bonds between βArg-56 and αCys-114 sulfenic acid (αCEA114) are important to maintain the enzymatic activity. The enzyme may be inactivated by endogenous nitric oxide (NO) and activated by absorption of photons of wavelength λ < 630 nm. To explain the photosensitivity and to propose structural determinants of catalytic activity, differences in the dynamics of light-active and dark-inactive forms of NHase were investigated using molecular dynamics (MD) modeling. To this end, a new set of force field parameters for nonstandard NHase active sites have been developed. The dynamics of the photodissociated NO ligand in the enzyme channel was analyzed using the locally enhanced sampling method, as implemented in the MOIL MD package. A series of 1 ns trajectories of NHases shows that the protonation state of the active site affects the dynamics of the catalytic water and NO ligand close to the metal center. MD simulations support the catalytic mechanism in which a water molecule bound to the metal ion directly attacks the nitrile carbon. PMID:18234830
A family of dynamic models for large-eddy simulation
NASA Technical Reports Server (NTRS)
Carati, D.; Jansen, K.; Lund, T.
1995-01-01
Since its first application, the dynamic procedure has been recognized as an effective means to compute rather than prescribe the unknown coefficients that appear in a subgrid-scale model for Large-Eddy Simulation (LES). The dynamic procedure is usually used to determine the nondimensional coefficient in the Smagorinsky (1963) model. In reality the procedure is quite general and it is not limited to the Smagorinsky model by any theoretical or practical constraints. The purpose of this note is to consider a generalized family of dynamic eddy viscosity models that do not necessarily rely on the local equilibrium assumption built into the Smagorinsky model. By invoking an inertial range assumption, it will be shown that the coefficients in the new models need not be nondimensional. This additional degree of freedom allows the use of models that are scaled on traditionally unknown quantities such as the dissipation rate. In certain cases, the dynamic models with dimensional coefficients are simpler to implement, and allow for a 30% reduction in the number of required filtering operations.
Decoherence Allows Model Reduction in Nonadiabatic Dynamics Simulations.
Trivedi, Dhara J; Prezhdo, Oleg V
2015-08-20
A nonadiabatic (NA) molecular dynamics (MD) simulation requires calculation of NA coupling matrix elements, the number of which scales as a square of the number of basis states. The basis size can be huge in studies of nanoscale materials, and calculation of the NA couplings can present a significant bottleneck. A quantum-classical approximation, NAMD overestimates coherence in the quantum, electronic subsystem, requiring decoherence correction. Generally, decoherence times decrease with increasing energy separation between pairs of states forming coherent superpositions. Since rapid decoherence stops quantum dynamics, one expects that decoherence-corrected NAMD can eliminate the need for calculation of NA couplings between energetically distant states, notably reducing the computational cost. Considering several types of dynamics in a semiconductor quantum dot, we demonstrate that indeed, decoherence allows one to reduce the number of needed NA coupling matrix elements. If the energy levels are spaced closer than 0.1 eV, one obtains good results while including only three nearest-neighbor couplings, and in some cases even with just the first nearest-neighbor coupling scheme. If the energy levels are spaced by about 0.4 eV, the nearest-neighbor model fails, while three or more nearest-neighbor schemes also provide good results. In comparison, the results of NAMD simulation without decoherence vary continuously with changes in the number of NA couplings. Thus, decoherence effects induced by coupling to a quantum-mechanical environment not only provide the physical mechanism for NAMD trajectory branding and improve the accuracy of NAMD simulations, but also afford significant computational savings. PMID:26221974
New insights into photodissociation dynamics of cyclobutanone from the AIMS dynamic simulation
NASA Astrophysics Data System (ADS)
Liu, Lihong; Fang, Wei-Hai
2016-04-01
In this work, the combined electronic structure calculations and non-adiabatic dynamics simulations were performed for understanding mechanistic photodissociation of cyclobutanone at ˜248 nm. Besides the stationary and intersection structures reported before, two new conical intersections between the ground (S0) and the first excited singlet (S1) states were determined in the present study, which were confirmed to be the new S1 → S0 funnels by the ab initio multiple spawning dynamic simulation, giving rise to products in the S0 state selectively. The time evolution of the S1 electronic population was fitted with the pure exponential formulae, from which the S1 lifetime was estimated to be 484.0 fs. The time constant for the S1 α-cleavage is calculated to be 176.6 fs, which is based on the present dynamics simulation. As a result of the ultrafast S1 processes, the statistical distribution of the excess energies is prevented in the S1 state. The S1 dynamic effect (the nonergodic behavior) was predicted to be an important factor that is responsible for the wavelength dependence of the branching ratio of photodissociation products, which will be discussed in detail.
Coupled Radiative-Dynamical GCM Simulations of Hot Jupiters
NASA Astrophysics Data System (ADS)
Showman, Adam P.; Fortney, J. J.; Lian, Y.; Marley, M. S.
2007-10-01
The stellar flux incident on hot Jupiters is expected to drive an atmospheric circulation that shapes the day-night temperature difference, infrared lightcurve, spectra, albedo, and atmospheric composition. Recent Spitzer lightcurve observations show that on some hot Jupiters, including HD189733b and HD209458b, the circulation efficiently homogenizes the temperature, whereas other planets such as Ups And b may exhibit large day-night temperature differences. Moreover, Spitzer infrared photometry and spectra constrain the vertical temperature structure in the atmosphere, which may deviate strongly from radiative equilibrium. Several groups have investigated the atmospheric circulation with a variety of 2D and 3D models (Showman and Guillot 2002; Cho et al. 2003, 2006; Langton and Laughlin 2007; Cooper and Showman 2005, 2006; Dobbs-Dixon and Lin 2007). However, all of these models drive the dynamics with simplified heating/cooling schemes that preclude robust predictions for the 3D temperature patterns, spectra, and lightcurves. Here, we present the first simulations of cloud-free hot Jupiters from a 3D general circulation model (GCM) that couples the atmospheric dynamics to a realistic representation of radiative transfer. For the dynamics, we adopt the MITgcm, which is a state-of-the-art circulation model that solves the 3D primitive equations of meteorology. Our radiation model is that of Marley and McKay (1999), which solves the two-stream radiative-transfer equations using the correlated-k method for the opacities; this radiative-transfer model has been extensively applied to brown dwarfs and extrasolar planets by Marley, Fortney, and collaborators. By coupling these components, the GCM provides a much more realistic representation of the radiative-dynamical interaction than possible with previous models. Here, we will present simulations of HD209458b and HD189733b, compare the predicted temperatures, spectra, and lightcurves with existing data, and make
Digital simulation of dynamic processes in radiometer systems. [microwave radiometers
NASA Technical Reports Server (NTRS)
Stanley, W. D.
1980-01-01
The development and application of several computer programs for simulating different classes of microwave radiometers are described. The programs are dynamic in nature, and they may be used to determine the instantaneous behavior of system variables as a function of time. Some of the programs employ random variable models in the simulations so that the statistical nature of the results may be investigated. The programs have been developed to utilize either the Continuous System Modeling Program or the Advanced Continuous System Language. The validity of most of the programs was investigated using statistical tests, and the results show excellent correlation with theoretical predictions. The programs are currently being used in the investigation of new design techniques for microwave radiometers.
A model for including thermal conduction in molecular dynamics simulations
NASA Technical Reports Server (NTRS)
Wu, Yue; Friauf, Robert J.
1989-01-01
A technique is introduced for including thermal conduction in molecular dynamics simulations for solids. A model is developed to allow energy flow between the computational cell and the bulk of the solid when periodic boundary conditions cannot be used. Thermal conduction is achieved by scaling the velocities of atoms in a transitional boundary layer. The scaling factor is obtained from the thermal diffusivity, and the results show good agreement with the solution for a continuous medium at long times. The effects of different temperature and size of the system, and of variations in strength parameter, atomic mass, and thermal diffusivity were investigated. In all cases, no significant change in simulation results has been found.
Molecular Dynamics Simulations of Homogeneous Crystallization in Polymer Melt
NASA Astrophysics Data System (ADS)
Kong, Bin
2015-03-01
Molecular mechanisms of homogeneous nucleation and crystal growth from the melt of polyethylene-like polymer were investigated by molecular dynamics simulations. The crystallinity was determined by using the site order parameter method (SOP), which described local order degree around an atom. Snapshots of the simulations showed evolution of the nucleation and the crystal growth through SOP images clearly. The isothermal crystallization kinetics was determined at different temperatures. The rate of crystallization, Kc, and the Avrami exponents, n, were determined as a function of temperature. The forming of nucleis was traced to reveal that the nucleis were formed with more ordered cores and less ordered shells. A detailed statistical analysis of the MD snapshots and trajectories suggested conformations of the polymer chains changed smoothly from random coil to chain folded lamella in the crystallization processes.
Molecular dynamics simulations of field emission from a planar nanodiode
Torfason, Kristinn; Valfells, Agust; Manolescu, Andrei
2015-03-15
High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space-charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current [Y. Y. Lau, Y. Liu, and R. K. Parker, Phys. Plasmas 1, 2082 (1994) and Y. Feng and J. P. Verboncoeur, Phys. Plasmas 13, 073105 (2006)]. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.
Phase transitions in electrorheological fluids using molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Lapenta, Giovanni; Maizza, Giovanni; Palmieri, Antonio; Boretto, Gianmarco; Debenedetti, Massimo
1999-10-01
A parametric study of the properties of electrorheological fluids is conducted using molecular dynamics (MD) simulations. The MD model is based on the solution of the Langevin equation for a number of suspended particles. The equations of motion include inertial effects, polarization forces, Stokes' drag, short range repulsion, and Brownian forces. Different polarization forces are considered to include the effect of enhancements at short range due to multipole moments induced by the suspended particles and other effects. The model is used to investigate the structural changes induced by external electric fields and by shear strains imposed on the system. The response times are studied as a function of two characteristic parameters describing the physical status of the system (temperature and external electric field). Finally, the stress-strain characteristics are studied and the yield stress is calculated as a function of the external electric field. The simulated response is compared with experimental findings.
Molecular Dynamics Simulation of MgSiO3 Perovskite
NASA Astrophysics Data System (ADS)
Lin-xiang, Zhou; L, Zhou X.; J, Hardy R.; Xin, Xu; X, Xu
1998-06-01
Using molecular dynamics to simulate MgSiO3 perovskite is performed to investigate its phase transitions and superionicity. These simulations has used parameter-free Gordon-Kim potentials and a novel technique to monitor the motion of ions which clearly demonstrates the sublattice melting of ions O2- and the rotations of SiO6 octahedra. MgSiO3 has to undergo a few of phase transitions, then enter into the cubic phase. In particular, there is a transitional phase between orthorhombic phase and cubic phase. There are a superionic phase and the cubic phase in magnesium-rich silicate perovskite. This superionic phase occurs after the onset of cubic phase before the melting point. The onset temparature Tc for superionicity is about 200-700 K below the melting point Tm, Tc / Tm similar 0.92.
A molecular dynamics simulation study of defect production in vanadium
Morishita, K. |; Diaz de la Rubia, T.
1995-01-23
We performed molecular dynamics simulations to investigate the process of defect production in pure vanadium. The interaction of atoms was described by the EAM interatomic potential modified at short range to merge smoothly with the universal potential for description of the high energy recoils in cascades. The melting point of this EAM model of vanadium was found to be consistent with the experimental melting temperature. The threshold energies of displacement events in the model system are also consistent with experimental minimum threshold in vanadium, and its average was found to be 44 eV. We evaluated the efficiencies of defect production in the displacement events initiated by recoils with kinetic energy up to 5 keV, and found that the probability of cluster formation is smaller than that of simulated events in fcc metals reported in the literature.
Observed and Simulated Regional North American Vegetation Dynamics: 1982- 2005
NASA Astrophysics Data System (ADS)
Neigh, C. S.; Tucker, C. J.; Townshend, J. R.; Collatz, G. J.
2006-12-01
Normalized difference vegetation index data from the NOAA series of Advanced Very High Resolution Radiometers (AVHRR) revealed regions in North America that experienced marked increases in annual photosynthetic capacity at various times from 1982 to 2005. Inspection of these anomalous areas with Landsat, Ikonos, aerial photography, and ancillary statistical datasets revealed a range of causes: climatic influences; drought and subsequent recovery; irrigated agriculture expansion; herbivores insect outbreaks followed by logging and subsequent regeneration; and forest fires with subsequent regeneration. We describe an efficient continental monitoring system that simulates biogeochemistry dynamics to quantify changing carbon content of ecosystems.
Molecular dynamics simulation of bicrystalline metal surface treatment
Nikonov, A. Yu.
2015-10-27
The paper reports the molecular dynamics simulation results on the behavior of a copper crystallite in local frictional contact. The crystallite has a perfect defect-free structure and contains a high-angle grain boundary of type Σ5. The influence of the initial structure on the specimen behavior under loading was analyzed. It is shown that nanoblocks are formed in the subsurface layer. The atomic mechanism of nanofragmentation was studied. A detailed analysis of atomic displacements in the blocks showed that the displacements are rotational. Calculations revealed that the misorientation angle of formed nanoblocks along different directions does not exceed 2 degrees.
Investigations of Solar Prominence Dynamics Using Laboratory Simulations
Paul M Bellan
2008-05-28
Laboratory experiments simulating many of the dynamical features of solar coronal loops have been carried out. These experiments manifest collimation, kinking, jet flows, and S-shapes. Diagnostics include high-speed photography and x-ray detectors. Two loops having opposite or the same magnetic helicity polarities have been merged and it is found that counter-helicity merging provides much greater x-ray emission. A non-MHD particle orbit instability has been discovered whereby ions going in the opposite direction of the current flow direction can be ejected from a magnetic flux tube.
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
Mugnai, Mauro L.; Elber, Ron
2015-01-07
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.
Molecular dynamics simulation of hollow thick-walled cylinder collapse
Nikonov, A. Yu.
2015-10-27
The generation and evolution of plastic deformation in a hollow single-crystal cylinder under high-rate axisymmetric loading were studied. An advantage of the proposed loading scheme is that all loading modes are applied simultaneously within the chosen crystallographic plane of the cylinder base and different strain degrees are achieved along the specimen cross section. Molecular dynamics simulation was performed to show that the achievement of a certain strain causes the formation of structural defects on the inner surface of the specimen. The obtained results can be used to explain the main plastic deformation mechanisms of crystalline solids.
Molecular Dynamics Simulations Of Nanometer-Scale Feature Etch
Vegh, J. J.; Graves, D. B.
2008-09-23
Molecular dynamics (MD) simulations have been carried out to examine fundamental etch limitations. Beams of Ar{sup +}, Ar{sup +}/F and CF{sub x}{sup +} (x = 2,3) with 2 nm diameter cylindrical confinement were utilized to mimic 'perfect' masks for small feature etching in silicon. The holes formed during etch exhibit sidewall damage and passivation as a result of ion-induced mixing. The MD results predict a minimum hole diameter of {approx}5 nm after post-etch cleaning of the sidewall.
Polymer chain simulations in microchannels with Dissipative Particle Dynamics
NASA Astrophysics Data System (ADS)
Symeonidis, Vasileios; Karniadakis, George; Caswell, Bruce
2006-03-01
In this work we employ Dissipative Particle Dynamics (dpd) for simulations of dilute polymer solutions using bead-spring representations. We present comparison of two time-marching schemes: the popular velocity-Verlet and Lowe's scheme. Schmidt number effects are investigated for a series of cases, including λ-dna molecules under shear (using the Marko-Siggia wormlike chain spring law) and Poiseuille flow in microchannels. Effects on the polymer depletion layer, power-law profiles and apparent viscosities are presented as a function of the number of beads per polymer chain.
Tight-binding molecular-dynamics simulation of buckyball collisions
Zhang, B.L.; Wang, C.Z.; Chan, C.T.; Ho, K.M. )
1993-04-01
The collisions between C[sub 60] molecules are studied by tight-binding molecular-dynamics simulations. We observe three different regimes of behavior as the collisions become more and more energetic: bouncing, fusion, and fragmentation. The critical energies for fusion and fragmentation as well as details of the energy transfer during the collision process for the bouncing regime are investigated. The collisions at several specific energies and orientations produce interesting novel molecules, such as small baby cages, caps, and even a Russian-Doll molecule in which a small cage is trapped in a bigger one. 28 refs., 5 figs., 2 tabs.
A sampling problem in molecular dynamics simulations of macromolecules.
Clarage, J B; Romo, T; Andrews, B K; Pettitt, B M; Phillips, G N
1995-01-01
Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled. Images Fig. 1 Fig. 2 Fig. 3 PMID:7724554
Molecular dynamics simulations of nanoidentation of silicon nitride
Walsh, P.; Omeltchenko, A.; Kikuchi, Hideaki; Kalia, R.K.; Nakano, Aiichiro; Vashishta, P.
1999-08-01
This is a report of work in progress on 10 million atom Molecular Dynamics (MD) simulations of nanoindentation of crystalline and amorphous silicon nitride (Si{sub 3}N{sub 4}). Nanoindentation is used to determine mechanical properties of extremely thin films such as hardness and elastic moduli. The authors report load-displacement curves for several Si{sub 3}N{sub 4} configurations using an idealized non-deformable indenter and analyze the local stress distributions in the vicinity of the indenter tip. Preliminary results for surface adhesion using Si{sub 3}N{sub 4} for both tip and substrate are also reported.
Dissipative particle dynamics simulation of a colloidal micropump
NASA Astrophysics Data System (ADS)
De Palma, Pietro; Valentini, P.; Napolitano, M.
2006-02-01
Dissipative particle dynamics (DPD) is a recently developed model for computing complex fluid flows at mesoscopic scales. This article provides a novel DPD simulation of complex microfluidic devices involving the momentum exchange between a body moving with a prescribed law of motion and the surrounding fluid. To this purpose, a DPD computational method is developed and equipped with an elastic collision model between the moving body and the DPD fluid particles surrounding it. The method is first validated versus well known theoretical, numerical, and experimental results, providing a sensitivity analysis of the dependence of continuum-flow properties on DPD parameters, as well as verifying its reliability for well known continuum-flow test cases. The method is then applied to its main goal, namely, the simulation of the flow driven by a peristaltic micropump, constructed by assembling several colloidal spheres. The DPD fluid model provides quite accurate results with respect to the experimental data and gives a detailed description of local flow properties. It is found that a careful choice of the DPD parameters is needed to avoid spurious compressibility effects and to match the real fluid characteristics; furthermore, due to the very coarse graining used in the present simulation, the thermal kinetic energy of the DPD particles needs to be reduced, in order to correctly evaluate their displacement, which is determined mainly by the momentum driving the flow. Finally, thanks to such a very coarse graining, the proposed DPD method provides an accurate prediction of local mesoscale flow properties with a dramatic reduction of the computational cost with respect to molecular dynamics simulations.
Nonequilibrium Simulations of Ion Dynamics in Ionomer Melts
NASA Astrophysics Data System (ADS)
Frischknecht, Amalie
Ionomers, polymers containing a small fraction of covalently bound ionic groups, are of interest as possible electrolytes in batteries. However, to date ionomers do not have sufficiently high conductivities for practical application, most likely because the ions tend to form aggregates, leading to slow ion transport. To build a better understanding of the relationships among ionomer chemistry, morphology, and ion transport, we have performed a series of molecular dynamics simulations and connected aspects of these simulations with experiment. In previous work using both atomistic and coarse-grained models, we showed that precise ionomers (with a fixed spacing between ionic groups along the polymer backbone) exhibit a range of ionic aggregate morphologies, from discrete clusters to percolated aggregates. In this talk I will describe recent simulations of our coarse-grained ionomer melts in an applied electric field. From a constant applied field, we are able to extract the ion mobilities and hence conductivities. We find that ionomers with percolated ionic aggregate morphologies have higher ion mobilities and hence higher conductivities. Application of an oscillating electric field enables us to calculate the frequency-dependent conductivity of the model ionomer melts. The real part of the conductivity has a high frequency peak associated with plasma oscillations, and a very broad low frequency peak associated with ion motions in ionic aggregates. I will end with comments on the connections to atomistic simulations and to experimental probes of ion dynamics. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Two-Dimensional Dynamic Simulation of a Continuous Foil Bearing
NASA Technical Reports Server (NTRS)
Braun, M. Jack; Choy, F. K.; Dzodzo, Milorad; Hsu, J.
1996-01-01
In this paper, the two dimensional(radial and circumferential) transient Navier-Stokes equations are used to solve the hydrodynamic problem in conjunction with the time dependent motion of the journal, and the deformable, spring supported foil. The elastic deformation of the foil and its supports are simulated by a finite element model. The time-dependent Navier-Stokes formulation is used to solve for the interaction between the fluid lubricant, the motion of the journal and the deformable foil boundary. The steady state, the quasi-transient and the full transient dynamic simulation of the foil-fluid journal interaction are examined on a comparative basis. For the steady state simulation, the fluid lubricant pressures are evaluated for a particular journal position, by means of an iterative scheme until convergence is achieved in both the fluid pressures and the corresponding foil deformation. For the quasi-transient case, the transient motion of the journal is calculated using a numerical integration scheme for the velocity and displacement of the journal. The deformation of the foil is evaluated through numerical iteration in feedback mode with the fluid film pressure generated by the journal motion until convergence at every time step is achieved. For the full transient simulation, a parallel real-time integration scheme is used to evaluate simultaneously the new journal position and the new deformed shape of the foil at each time step. The pressure of the fluid lubricant is iterated jointly with the corresponding journal position and the deformed foil geometry until convergence is achieved. A variable time-stepping Newmark-Beta integration procedure is used to evaluate the transient dynamics at each time step of the bearing.
Molecular dynamics simulations of pressure shocks in liquid phase nitromethane
NASA Astrophysics Data System (ADS)
McNatt, Michael David
The dynamic energy transfer processes present in liquid nitromethane (NM) under pressure shock loading conditions have been investigated by nonequilibrium molecular dynamics methods using a previously developed, fully flexible NM force field (Sorescu, D. C.; Rice, B. M.; Thompson, D. L. J. Phys. Chem. B 2000, 104, 8406). Generally good qualitative agreement with the corresponding experimental values was found for sound speeds (C) as a function of temperature. This is true as well for the PVT Hugoniot data calculated for the shock compressed zones behind our simulated shock fronts. The predicted C( T) are, however, ˜13--30% higher than experiment (Lysne, P. C.; Hardesty, D. R. J. Chem. Phys. 1973, 59, 6512) and our predicted densities for the shock compressed area behind fronts are consistently 4--10% lower than experiment (Winey, J. M.; Duvall, G. E.; Knudson, M. D.; Gupta, Y. M. J. Chem. Phys. 2000, 113, 7492). Accurate Hugoniot pressures are predicted by our simulations at all three initial temperatures (T i) studied. The Ti simulated for this work (255, 300, 350 K) span virtually the entire experimental ambient pressure liquid temperature range of NM (˜ 244--373 K). Thus combining and comparing our results with those of Winey et al. based on empirical equations of state work, opens up a considerable range of possible further tests and developments of our NM force field. This is particularly important in regards to the intermolecular force field due to its intended purpose of being applicable to a wide range of nitro and nitramine energetic compounds. Also, within the timeframes of our simulations (< 10 ps) the kinetic energy behind our shock fronts does not achieve equilibrium conditions as determined by the classical theory of equipartition.
Magnetoviscosity in dilute ferrofluids from rotational brownian dynamics simulations.
Soto-Aquino, D; Rinaldi, C
2010-10-01
Ferrofluids are suspensions of magnetic nanoparticles which respond to imposed magnetic fields by changing their viscosity without losing their fluidity. Prior work on modeling the behavior of ferrofluids has focused on using phenomenological suspension-scale continuum equations. A disadvantage of this approach is the controversy surrounding the equation describing the rate of change of the ferrofluid magnetization, the so-called magnetization relaxation equation. In this contribution the viscosity of dilute suspensions of spherical magnetic nanoparticles suspended in a Newtonian fluid and under applied shear and constant magnetic fields is studied through rotational brownian dynamics simulations. Simulation results are compared with the predictions of suspension-scale models based on three magnetization relaxation equations. Excellent agreement is observed between simulation results and the predictions of an equation due to Martsenyuk, Raikher, and Shliomis. Good qualitative agreement is observed with predictions of other equations, although these models fail to accurately predict the magnitude and shear rate dependence of the magnetic-field-dependent effective viscosity. Finally, simulation results over a wide range of conditions are collapsed into master curves using a Mason number defined based on the balance of hydrodynamic and magnetic torques. PMID:21230393
Thermocapillary simulation of single bubble dynamics in zero gravity
NASA Astrophysics Data System (ADS)
Alhendal, Yousuf; Turan, Ali; Hollingsworth, Peter
2013-07-01
The lack of significant buoyancy effects in zero gravity conditions poses an issue with fluid transfer in a stagnant liquid. In this paper bubble movement in a stagnant liquid is analysed and presented numerically using a computational fluid dynamics (CFD) approach. The governing continuum conservation equations for two phase flow are solved using the commercial software package Ansys-Fluent v.13 and the Volume of Fluid (VOF) method is used to track the liquid/gas interface in 2D and 3D domains. The simulation results are in reasonable agreement with the earlier experimental observations, the VOF algorithm is found to be a valuable tool for studying the phenomena of gas-liquid interaction. The flow is driven via Marangoni influence induced by the temperature difference which in turn drives the bubble from the cold to the hot region. A range of thermal Reynolds (ReT) and Marangoni numbers (MaT) are selected for the numerical simulations, specifically ReT=13-658 and MaT=214-10,721 respectively. The results indicate that the inherent velocity of bubbles decreases with an increase of the Marangoni number, a result that is line with the results of previous space experiments (Kang et al., 2008) [1]. An expression for predicting the scaled velocity of bubble has been derived based on the data obtained in the present numerical study. Some three-dimensional simulations are also performed to compare and examine the results with two-dimensional simulations.
Accurate Langevin approaches to simulate Markovian channel dynamics
NASA Astrophysics Data System (ADS)
Huang, Yandong; Rüdiger, Sten; Shuai, Jianwei
2015-12-01
The stochasticity of ion-channels dynamic is significant for physiological processes on neuronal cell membranes. Microscopic simulations of the ion-channel gating with Markov chains can be considered to be an accurate standard. However, such Markovian simulations are computationally demanding for membrane areas of physiologically relevant sizes, which makes the noise-approximating or Langevin equation methods advantageous in many cases. In this review, we discuss the Langevin-like approaches, including the channel-based and simplified subunit-based stochastic differential equations proposed by Fox and Lu, and the effective Langevin approaches in which colored noise is added to deterministic differential equations. In the framework of Fox and Lu’s classical models, several variants of numerical algorithms, which have been recently developed to improve accuracy as well as efficiency, are also discussed. Through the comparison of different simulation algorithms of ion-channel noise with the standard Markovian simulation, we aim to reveal the extent to which the existing Langevin-like methods approximate results using Markovian methods. Open questions for future studies are also discussed.
Dynamic simulation of sulfur-removal systems. Final report
Alexander, J.H.; Blake, T.R.; Brownell, D.H. Jr.; Henline, W.D.; Wilkins, D.E.
1982-01-01
A generalized computer simulation has been developed to predict the dynamic response of alternate gas absorption systems for selective removal of sulfur compounds or ammonia from fuel gas or synthesis gas produced from coal or other fossil fuels. The models use numerical methods based upon finite difference techniques to determine the spatial distribution of process variables within both the absorption and regeneration columns of such gas cleanup processes. The simulator may be applied to systems for selective gas absorption based on either chemical or physical principles. Examples of such systems include the Benfield process based on absorption by chemical reaction with an activated alkali carbonate solvent, and the Allied SELEXOL Solvent Process based on physical absorption as a result of partial pressure differences of the gas components above an organic solvent system. Simulations of either individual process units or an entire integrated plant can be performed. This computer program has specifically been structured to permit convenient flow sheet modification, as well as addition of new units. This research has emphasized the development of a general theoretical structure which can be easily modified by substituting alternate sets of data on the physicochemical properties of the appropriate liquid solvent. This model has been applied to Selexol Solvent Processes using both published and proprietary data on solvent properties. Test calculations have been performed to simulate open loop response of individual scrubber towers, and the complete system, to input composition and flow rate transients.
Computer simulations of solvation dynamics in lithium clay materials
Greathouse, J.A.
1997-12-31
Monte Carlo and molecular dynamics computer simulations were performed concurrently for the first time on lithium-smectites (montmorillonite, beidellite, and hectorite) at very low water content (about 0.5 monolayer). These simulation conditions were selected to provide a comparison with existing NMR, IR, neutron scattering, and X-ray diffraction data which have been interpreted in terms of inner-sphere (IS) Li surface complexes solvated by three water molecules exhibiting hindered rotational degrees of freedom. Our simulations predicted layer spacings (c-axis direction) ranging from 10.32 {angstrom} (Hectorite) to 11.93 {angstrom} (beidellite). Both IS and outer-sphere (OS) Li surface complexes formed in the interlayers of montmorillonite, whereas only one type of surface complex formed in the interlayers of beidellite (IS) and hectorite (OS). Lithium ions were solvated by 2, 3, or 4 water molecules. Some evidence of Li-hydrate rotation was seen for beidellite, but the other smectites showed no Li-hydrate rotational motion. However water molecules were observed to rotate about their C{sub 2} axes of symmetry in montmorillonite. Additional spectroscopic data are needed to resolve the differences between the simulation predictions and current experimental interpretations.
Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies
NASA Astrophysics Data System (ADS)
Oh, Kwang-Im; Choi, Jun-Ho; Lee, Joo-Hyun; Han, Jae-Beom; Lee, Hochan; Cho, Minhaeng
2008-04-01
Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9cm-1, respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, β-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.
RIAPMTQ/Impact : beam-dynamics simulation tool for RIA.
Wangler, T. P.; Billen, J. H.; Garnett, R. W.; Qiang, J.; Ryne, R.; Crandall, K. R.; Ostroumov, P.; Aseev, V. N.; Mustapha, B.; York, R. C.; Wu, X.; Zhao, Q.; Gorelov, D.; Doleans, M.; Physics; LANL; Tech Source; Michigan State Univ.
2006-01-01
We have developed a pair of multiparticle beam dynamics codes for end-to-end computer simulations of the proposed RIA heavy-ion driver linac. The two codes are: (1) an adaptation of PARMTEQ called RIAPMTQ for the normal-conducting-linac front end, and (2) IMPACT for the superconducting linac. The codes run on a PC as well as on parallel supercomputing platforms such as NERSC at LBNL. The parallel capability allows us to run simulations with large numbers of macroparticles for the computation of beam halo and beam-losses. The codes are being benchmarked for rms beam properties against previously existing codes at ANL and MSU. The work is being performed by a collaboration including LANL, LBNL, ANL, and Michigan State University (MSU). In this paper we present an overview, the status of the work, comparison of simulation results from RIAPMTQ and the ANL code TRACK for the ANL front-end design, and the first RIAPMTQ/IMPACT end-to-end multiprocessor simulation for the MSU design.
Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation
NASA Technical Reports Server (NTRS)
Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.
2007-01-01
The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.
Kwon, Taekyung; Harris, Andrew L.; Rossi, Angelo
2011-01-01
The recently published crystal structure of the Cx26 gap junction channel provides a unique opportunity for elucidation of the structure of the conductive connexin pore and the molecular determinants of its ion permeation properties (conductance, current–voltage [I-V] relations, and charge selectivity). However, the crystal structure was incomplete, most notably lacking the coordinates of the N-terminal methionine residue, which resides within the pore, and also lacking two cytosolic domains. To allow computational studies for comparison with the known channel properties, we completed the structure. Grand canonical Monte Carlo Brownian dynamics (GCMC/BD) simulations of the completed and the published Cx26 hemichannel crystal structure indicate that the pore is too narrow to permit significant ion flux. The GCMC/BD simulations predict marked inward current rectification and almost perfect anion selectivity, both inconsistent with known channel properties. The completed structure was refined by all-atom molecular dynamics (MD) simulations (220 ns total) in an explicit solvent and POPC membrane system. These MD simulations produced an equilibrated structure with a larger minimal pore diameter, which decreased the height of the permeation barrier formed by the N terminus. GCMC/BD simulations of the MD-equilibrated structure yielded more appropriate single-channel conductance and less anion/cation selectivity. However, the simulations much more closely matched experimentally determined I-V relations when the charge effects of specific co- and posttranslational modifications of Cx26 previously identified by mass spectrometry were incorporated. We conclude that the average equilibrated structure obtained after MD simulations more closely represents the open Cx26 hemichannel structure than does the crystal structure, and that co- and posttranslational modifications of Cx26 hemichannels are likely to play an important physiological role by defining the conductance and ion
NASA Astrophysics Data System (ADS)
Messing, Rene
2012-07-01
To simulate environmental space conditions for space- craft qualification testing the European Space Agency ESA uses a Large Space Simulator (LSS) in its Test Centre in Noordwijk, the Netherlands. In the LSS a motion system is used, to provide the orientation of an up to five tons heavy spacecraft with respect to an artificial solar beam. The existing motion simulation will be replaced by a new motion system. The new motion system shall be able to orient a spacecraft, defined by its elevation and azimuth angle and provide an eclipse simulation (continuous spinning) around the spacecraft rotation axis. The development of the new motion system has been contracted to APCO Technologies in Switzerland. In addition to the design development done by the con- tractor the Engineering section of the ESTEC Test Centre is in parallel developing a mathematical model simulating the dynamic behaviour of the system. The model shall to serve, during the preliminary design, to verify the selection of the drive units and define the specimen trajectory speed and acceleration profiles. In the further design phase it shall verify the dynamic response, at the spacecraft mounting interface of the unloaded system, against the requirements. In the future it shall predict the dynamic responses of the implemented system for different spacecraft being mounted and operated onto the system. The paper shall give a brief description of the investment history and design developments of the new motion system for the LSS and then give a brief description the different developments steps which are foreseen and which have been already implemented in the mathematical simulation model.
Spatially resolved dynamic structure factor of finite systems from molecular dynamics simulations
Raitza, Thomas; Roepke, Gerd; Reinholz, Heidi; Morozov, Igor
2011-09-15
The dynamical response of metallic clusters up to 10{sup 3} atoms is investigated using the restricted molecular dynamics simulations scheme. Exemplarily, a sodium like material is considered. Correlation functions are evaluated to investigate the spatial structure of collective electron excitations and the optical response of laser-excited clusters. In particular, the spectrum of bilocal correlation functions shows resonances representing different modes of collective excitations inside the nano plasma. The spatial structure, the resonance energy, and the width of the eigenmodes have been investigated for various values of electron density, temperature, cluster size, and ionization degree. Comparison with bulk properties is performed and the dispersion relation of collective excitations is discussed.
Hall, Benjamin A; Halim, Khairul Abd; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S P
2016-01-01
The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analysed via coarse-grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. To facilitate the running and analysis of such ensembles of simulations we have developed Sidekick, an automated pipeline software for performing high throughput CGMD simulations of α-helical peptides in lipid bilayer membranes. Through an end-to-end approach, which takes as input a helix sequence and outputs analytical metrics derived from CGMD simulations, we are able to predict the orientation and likelihood of insertion into a lipid bilayer of a given helix of family of helix sequences. We illustrate this software via analysis of insertion into a membrane of short hydrophobic TM helices containing a single cationic arginine residue positioned at different positions along the length of the helix. From analysis of these ensembles of simulations we estimate apparent energy barriers to insertion which are comparable to experimentally determined values. In a second application we use CGMD simulations to examine self-assembly of dimers of TM helices from the ErbB1 receptor tyrosine kinase, and analyse the numbers of simulation repeats necessary to obtain convergence of simple descriptors of the mode of packing of the two helices within a dimer. Our approach offers proof-of-principle platform for the further employment of automation in large ensemble CGMD simulations of membrane proteins. PMID:26580541
Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology
Byrne, Michael J.; Waxham, M. Neal; Kubota, Yoshihisa
2010-01-01
In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations. PMID:20361275
Lattice gas simulations of dynamical geometry in two dimensions
NASA Astrophysics Data System (ADS)
Klales, Anna; Cianci, Donato; Needell, Zachary; Meyer, David A.; Love, Peter J.
2010-10-01
We present a hydrodynamic lattice gas model for two-dimensional flows on curved surfaces with dynamical geometry. This model is an extension to two dimensions of the dynamical geometry lattice gas model previously studied in one dimension. We expand upon a variation of the two-dimensional flat space Frisch-Hasslacher-Pomeau (FHP) model created by Frisch [Phys. Rev. Lett.PRLTAO0031-9007 56, 1505 (1986)]10.1103/PhysRevLett.56.1505 and independently by Wolfram, and modified by Boghosian [Philos. Trans. R. Soc. London, Ser. A 360, 333 (2002)]10.1098/rsta.2001.0933. We define a hydrodynamic lattice gas model on an arbitrary triangulation whose flat space limit is the FHP model. Rules that change the geometry are constructed using the Pachner moves, which alter the triangulation but not the topology. We present results on the growth of the number of triangles as a function of time. Simulations show that the number of triangles grows with time as t1/3 , in agreement with a mean-field prediction. We also present preliminary results on the distribution of curvature for a typical triangulation in these simulations.
Lattice gas simulations of dynamical geometry in two dimensions.
Klales, Anna; Cianci, Donato; Needell, Zachary; Meyer, David A; Love, Peter J
2010-10-01
We present a hydrodynamic lattice gas model for two-dimensional flows on curved surfaces with dynamical geometry. This model is an extension to two dimensions of the dynamical geometry lattice gas model previously studied in one dimension. We expand upon a variation of the two-dimensional flat space Frisch-Hasslacher-Pomeau (FHP) model created by Frisch [Phys. Rev. Lett. 56, 1505 (1986)] and independently by Wolfram, and modified by Boghosian [Philos. Trans. R. Soc. London, Ser. A 360, 333 (2002)]. We define a hydrodynamic lattice gas model on an arbitrary triangulation whose flat space limit is the FHP model. Rules that change the geometry are constructed using the Pachner moves, which alter the triangulation but not the topology. We present results on the growth of the number of triangles as a function of time. Simulations show that the number of triangles grows with time as t(1/3), in agreement with a mean-field prediction. We also present preliminary results on the distribution of curvature for a typical triangulation in these simulations. PMID:21230410
Molecular dynamics simulations of ionic liquid nanodroplets in electric fields
NASA Astrophysics Data System (ADS)
Tiruppathi, Pavithra C.
2011-12-01
Ionic liquids are appropriate for the application of electrospray thruster propulsion due to their physical properties such as low volatility and high electrical conductivity. The behavior of ionic liquid droplets and resulting ion and cluster emission in the presence of an electric field impacts the efficiency and thrust of the electrospray thruster. The technique of molecular simulation allows for the study of ionic liquid nanodroplets in atomic detail which is a limitation in mass spectrometric experiments. This thesis discusses the investigation of nanodroplets of the ionic liquid 1-ethyl-3- methylimidaziolium bis(triuoromethylsulfonyl)imide ([Emim+][Tf2n -]) in the presence of an electric field using molecular dynamics simulations. The ratio of the single ions to large clusters emitted from the droplet are observed and compared with experiment. The critical field strength required for ion emission from the droplet agrees with experiment. The critical field strength is also computed as a function of droplet size. The thermal stabilities, structural and dynamical properties are analyzed for the ([Emim +][Tf2n-]) nanodroplets.
Molecular dynamics simulation of complex plasmas: interaction of nonlinear waves
NASA Astrophysics Data System (ADS)
Durniak, Celine; Samsonov, Dmitry
2008-11-01
Complex plasmas consist of micron sized microspheres immersed into ordinary ion-electron plasmas. They exist in solid, liquid, gaseous states and exhibit a range of dynamic phenomena such as waves, solitons, phase transitions, heat transfer. These phenomena can be modelled in complex plasmas at the microscopic or ``molecular'' scale, which is almost impossible in ordinary solids and liquids. We simulate a monolayer complex plasma consisting of 3000 negatively-charged particles (or grains) with the help of molecular dynamics computer simulations. The equations of grain motion are solved using a 5^th order Runge Kutta method taking into account interaction of every grain with each other via a Yukawa potential. The grains are confined more strongly in the vertical direction than in the horizontal. After seeding the grains randomly the code is run until the equilibrium is reached as the grain kinetics energy reduces due to damping force equal to the neutral friction in the experiments and a monolayer crystal lattice is formed. Then we investigate interactions between nonlinear waves in a monolayer strongly coupled complex plasma moving in three dimensions. Different excitations are applied during a short time symmetrically on both sides of the lattice. Structural properties and nonlinear waves characteristics are examined as the pulses propagate across the complex plasma in opposite directions.
Molecular Dynamics Simulation of Carbon Nanotube Based Gears
NASA Technical Reports Server (NTRS)
Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)
1996-01-01
We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.
Non-steady Reconnection in Global Simulations of Magnetosphere Dynamics
NASA Technical Reports Server (NTRS)
Kuznetsova, M. M.; Hesse, M.; Sibeck, D.; Rastaetter, L.; Toth, G.; Ridley, A.
2008-01-01
To analyze the non-steady magnetic reconnection during quasi-steady solar wind driving we employed high resolution global MHD model BATSRUS with non-MHD corrections in diffusion regions around the reconnection sites. To clarify the role of small-scale non-MHD effects on the global magnetospheric dynamic we performed simulations with different models of dissipation. We found that magnetopause surface is not in steady state even during extended periods of steady solar wind conditions. The so-called tilted reconnection lines become unstable due to formation of pressure bubbles, strong core field flux tubes, vortices, and traveling magnetic field cavities. Non-steady dayside reconnection results in formation of flux tubes with bended axis magnetically connecting magnetic field cavities generated at flanks and strong core segments formed near the subsolar region. We found that the rate of magnetic flux loading to the tail lobes is not very sensitive to the dissipation mechanism and details of the dayside reconnection. On the other hand the magnetotail reconnection rate, the speed of the reconnection site retreat and the global magnetotail dynamics strongly depend on the model of dissipation. THEMIS and Cluster observations are consistent with signatures predicted by simulations.
Molecular Dynamics Simulations of Adhesion at Epoxy Interfaces
NASA Technical Reports Server (NTRS)
Frankland, Sarah-Jane V.; Clancy, Thomas C.; Hinkley, J. A.; Gates. T. S.
2008-01-01
The effect of moisture on adhesives used in aerospace applications can be modeled with chemically specific techniques such as molecular dynamics simulation. In the present study, the surface energy and work of adhesion are calculated for epoxy surfaces and interfaces, respectively, by using molecular dynamics simulation. Modifications are made to current theory to calculate the work of adhesion at the epoxy-epoxy interface with and without water. Quantitative agreement with experimental values is obtained for the surface energy and work of adhesion at the interface without water. The work of adhesion agrees qualitatively with the experimental values for the interface with water: the magnitude is reduced 15% with respect to the value for the interface without water. A variation of 26% in the magnitude is observed depending on the water configuration at a concentration of 1.6 wt%. The methods and modifications to the method that are employed to obtain these values are expected to be applicable for other epoxy adhesives to determine the effects of moisture uptake on their work of adhesion.
GPU-enabled molecular dynamics simulations of ankyrin kinase complex
NASA Astrophysics Data System (ADS)
Gautam, Vertika; Chong, Wei Lim; Wisitponchai, Tanchanok; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.; Tayapiwatana, Chatchai; Lee, Vannajan Sanghiran
2014-10-01
The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein-protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.
Droplets impact on textured surfaces: Mesoscopic simulation of spreading dynamics
NASA Astrophysics Data System (ADS)
Wang, Yuxiang; Chen, Shuo
2015-02-01
Superhydrophobic surfaces have attracted much attention due to their excellent water-repellent property. In the present study, droplets in the ideal Cassie state were focused on, and a particle-based numerical method, many-body dissipative particle dynamics, was employed to explore the mechanism of droplets impact on textured surfaces. A solid-fluid interaction with three linear weight functions was used to generate different wettability and a simple but efficient method was introduced to compute the contact angle. The simulated results show that the static contact angle is in good agreement with the Cassie-Baxter formula for smaller ∅S and Fa, but more deviation will be produced for larger ∅S and Fa, and it is related to the fact that the Cassie-Baxter theory does not consider the contact angle hysteresis effect in their formula. Furthermore, high impact velocity can induce large contact angle hysteresis on textured surfaces with larger ∅S and Fa. The typical time-based evolutions of the spreading diameter were simulated, and they were analyzed from an energy transformation viewpoint. These results also show that the dynamical properties of droplet, such as rebounding or pinning, contact time and maximum spreading diameters, largely depend on the comprehensive effects of the material wettability, fraction of the pillars and impact velocities of the droplets.
Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations
2013-01-01
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176
Pastor, Nina; Amero, Carlos
2015-01-01
Proteins participate in information pathways in cells, both as links in the chain of signals, and as the ultimate effectors. Upon ligand binding, proteins undergo conformation and motion changes, which can be sensed by the following link in the chain of information. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations represent powerful tools for examining the time-dependent function of biological molecules. The recent advances in NMR and the availability of faster computers have opened the door to more detailed analyses of structure, dynamics, and interactions. Here we briefly describe the recent applications that allow NMR spectroscopy and MD simulations to offer unique insight into the basic motions that underlie information transfer within and between cells. PMID:25999971
Pastor, Nina; Amero, Carlos
2015-01-01
Proteins participate in information pathways in cells, both as links in the chain of signals, and as the ultimate effectors. Upon ligand binding, proteins undergo conformation and motion changes, which can be sensed by the following link in the chain of information. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations represent powerful tools for examining the time-dependent function of biological molecules. The recent advances in NMR and the availability of faster computers have opened the door to more detailed analyses of structure, dynamics, and interactions. Here we briefly describe the recent applications that allow NMR spectroscopy and MD simulations to offer unique insight into the basic motions that underlie information transfer within and between cells. PMID:25999971
Xie, Jun Yu; Ding, Guang Hong; Karttunen, Mikko
2014-03-01
Membranes' response to lateral tension, and eventual rupture, remains poorly understood. In this study, pure dipalmitoylphosphatidylcholine (DPPC) lipid bilayers, under tension/pressure, were studied using molecular dynamics (MD) simulations. The irreversible membrane breakdown is demonstrated to depend on the amplitude of lateral tension, loading rate, and the size of the bilayer. In all of our simulations, -200bar lateral pressure was found to be enough to rupture lipid membrane regardless of the loading rate or the membrane size. Loading rate and membrane size had a significant impact on rupture. A variety of dynamic properties of lipid molecules, probability distribution of area per lipid particularly, have been determined, and found to be fundamental for describing membrane behavior in detail, thus providing the quantitative description for the requirement of membrane rupture. PMID:24374317
Combined Molecular Dynamics-Spin Dynamics Simulation of α-Iron in an External Magnetic Field
NASA Astrophysics Data System (ADS)
Mudrick, Mark; Perera, Dilina; Landau, David P.
Using an atomistic model that treats both translational and spin degrees of freedom, combined molecular and spin dynamics simulations have been performed to study dynamic properties of α-iron. Atomic interactions are described by an empirical many-body potential while spin-spin interactions are handled with a Heisenberg-like Hamiltonian with a coordinate dependent exchange interaction. Each of these interactions are parameterized by first-principles calculations. These simulations numerically solve equations of motion using an algorithm based on the second-order Suzuki-Trotter decomposition for the time evolution operator. Through calculation of the Fourier transform of space-displaced time-displaced correlation functions, vibrational and magnetic excitations have been studied. The application of an external magnetic field up to 10-T has now been included and has been shown to increase the characteristic frequencies of the single-spin-wave excitations. Two-spin-wave interactions have also been investigated.
The study of dynamics heterogeneity and slow down of silica by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
San, L. T.; Hung, P. K.; Hue, H. V.
2016-06-01
We have numerically studied the diffusion in silica liquids via the SiOx → SiOx±1, OSiy → OSiy±1 reactions and coordination cells (CC). Five models with temperatures from 1000 to 3500 K have been constructed by molecular dynamics simulation. We reveal that the reactions happen not randomly in the space. In addition, the reactions correlated strongly with the mobility of CC atom. Further we examine the clustering of atoms having unbroken bonds and restored bonds. The time evolution of these clusters under temperature is also considered. The simulation shows that both slow down and dynamic heterogeneity (DH) is related not only to the percolation of restored-rigid clusters near glass transition but also to their long lifetime.
Brownian Dynamics Simulation of Macromolecule Diffusion in a Protocell
NASA Astrophysics Data System (ADS)
Ando, Tadashi; Skolnick, Jeffrey
2011-01-01
The interiors of all living cells are highly crowded with macro molecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green fluorescent protein (GFP) in E. coli is ~10-fold slower than in dilute conditions. In this study, we performed Brownian dynamics (BD) simulations of rigid macromolecules in a crowded environment mimicking the cytosol of E. coli to study the motions of macromolecules. The simulation systems contained 35 70S ribosomes, 750 glycolytic enzymes, 75 GFPs, and 392 tRNAs in a 100 nm × 100 nm × 100 nm simulation box, where the macromolecules were represented by rigid-objects of one bead per amino acid or four beads per nucleotide models. Diffusion tensors of these molecules in dilute solutions were estimated by using a hydrodynamic theory to take into account the diffusion anisotropy of arbitrary shaped objects in the BD simulations. BD simulations of the system where each macromolecule is represented by its Stokes radius were also performed for comparison. Excluded volume effects greatly reduce the mobility of molecules in crowded environments for both molecular-shaped and equivalent sphere systems. Additionally, there were no significant differences in the reduction of diffusivity over the entire range of molecular size between two systems. However, the reduction in diffusion of GFP in these systems was still 4-5 times larger than for the in vivo experiment. We will discuss other plausible factors that might cause the large reduction in diffusion in vivo.
NASA Astrophysics Data System (ADS)
Lynch, Gillian C.; Pettitt, B. Montgomery
1997-11-01
The extended system Hamiltonian for carrying out grand canonical ensemble molecular dynamics simulations is reformulated. This new Hamiltonian includes a generalized treatment of the reference state partition function of the total chemical potential that reproduces the ideal gas behavior and various previous partitionings of ideal and excess terms. Initial calculations are performed on a system of Lennard-Jones particles near the triple point and on liquid water at room temperature.
Moritsugu, Kei; Koike, Ryotaro; Yamada, Kouki; Kato, Hiroaki; Kidera, Akinori
2015-01-01
Molecular dynamics (MD) simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a “Motion Tree”, to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC) transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory. PMID:26148295
Metascalable molecular dynamics simulation of nano-mechano-chemistry
NASA Astrophysics Data System (ADS)
Shimojo, F.; Kalia, R. K.; Nakano, A.; Nomura, K.; Vashishta, P.
2008-07-01
We have developed a metascalable (or 'design once, scale on new architectures') parallel application-development framework for first-principles based simulations of nano-mechano-chemical processes on emerging petaflops architectures based on spatiotemporal data locality principles. The framework consists of (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms, (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these scalable algorithms onto hardware. The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics (MD) and 17.7-million-atom (1.56 trillion electronic degrees of freedom) quantum mechanical (QM) MD in the framework of the density functional theory (DFT) on adaptive multigrids, in addition to 201-billion-atom nonreactive MD, on 196 608 IBM BlueGene/L processors. We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on demand and tasks were migrated according to unexpected faults. The paper presents the application of the framework to the study of nanoenergetic materials: (1) combustion of an Al/Fe2O3 thermite and (2) shock initiation and reactive nanojets at a void in an energetic crystal.
Narrowing the gap between real and simulated barchan dune dynamics
NASA Astrophysics Data System (ADS)
Hugenholtz, C.; Barchyn, T. E.
2011-12-01
There are a growing number of computer simulation models capable of reproducing many of the morphological characteristics and dynamics of real barchan sand dunes. While these models offer tremendous insight and opportunities to develop hypotheses, there is a relative paucity of empirical observations to use as a basis for validation. To address this issue we present empirical observations of barchan dune dynamics using high-resolution, multi-temporal satellite imagery from locations in Peru, Namibia, and Mauritania. We highlight the response of barchan dunes to collisions, wind direction variability, interactions with bedrock topography, and depletion of sediment supply. First, we document the process of dunes emerging from the slipfaces of barchan dunes. In the past, this process was only observed in numerical models or interpreted from single-date imagery. We also show that collisions can result in calving or shedding of dunes from the horns. Second, we present the first empirical evidence of barchans changing into dome and "wedge" dunes under the influence of bimodal winds. Third, we show that barchans break down when they encounter uphill topography. However, they can re-form in the lee of a bedrock obstacle if sediment supply is sufficient. Finally, we show that, in the absence of collisions, small barchans can disappear quickly when they lose upwind sediment supply. Altogether, our observations add to the empirical record of barchan dune dynamics and are useful for evaluating the behaviour of numerical models.
Development of a Multibody Dynamics Simulation Tool for Tracked Vehicles
NASA Astrophysics Data System (ADS)
Ryu, Han Sik; Huh, Kun Soo; Bae, Dae Sung; Choi, Jin Hwan
In this paper, the nonlinear dynamic modeling methods for the virtual design of tracked vehicle are investigated by using multibody dynamic simulation techniques. The results include high oscillatory signals resulting from the impulsive contact forces and the use of stiff compliant elements to represent the joints between the track links. Each track link is modeled as a body which has six degrees of freedom, and two compliant bushing elements is used to connect track links. The efficient contact search kinematics and algorithms in the context of the compliance contact model are developed to detect the interactions between track links, rollers, sprockets, and ground for the sake of speedy and robust solutions. In order to validate the developed nonlinear multibody dynamic model against the experimental measurements, several empirical techniques are suggested and applied to the physical proving ground tests of the high mobility tracked vehicle. In this empirical validations, positions, velocities, accelerations and forces of the chassis and the track sub-systems are correlated accordingly.
Simulation of dynamics of hydraulic system with proportional control valve
NASA Astrophysics Data System (ADS)
Bureček, Adam; Hružík, Lumír; Vašina, Martin
2016-03-01
Dynamics of a hydraulic system is influenced by several parameters, in this case mainly by proportional control valve, oil bulk modulus, oil viscosity, mass load etc. This paper will be focused on experimental measurement and mathematical simulation of dynamics of a hydraulic system with proportional control valve, linear hydraulic cylinder and mass load. The measurement is performed on experimental equipment that enables realization of dynamic processes of the hydraulic system. Linear hydraulic cylinder with mass load is equipped with position sensor of piston. The movement control of piston rod is ensured by the proportional control valve. The equipment enables to test an influence of parameter settings of regulator of the proportional control valve on position and pressure system responses. The piston position is recorded by magnetostrictive sensor that is located in drilled piston rod side of the linear hydraulic cylinder. Pressures are measured by piezoresistive sensors on the piston side and the piston rod side of the hydraulic cylinder. The measurement is performed during movement of the piston rod with mass load to the required position. There is realized and verified a mathematical model using Matlab SimHydraulics software for this hydraulic system.
Extensions to Dynamic System Simulation of Fissile Solution Systems
Klein, Steven Karl; Bernardin, John David; Kimpland, Robert Herbert; Spernjak, Dusan
2015-08-24
Previous reports have documented the results of applying dynamic system simulation (DSS) techniques to model a variety of fissile solution systems. The SUPO (Super Power) aqueous homogeneous reactor (AHR) was chosen as the benchmark for comparison of model results to experimental data for steadystate operation.1 Subsequently, DSS was applied to additional AHR to verify results obtained for SUPO and extend modeling to prompt critical excursions, ramp reactivity insertions of various magnitudes and rate, and boiling operations in SILENE and KEWB (Kinetic Experiment Water Boiler).2 Additional models for pressurized cores (HRE: Homogeneous Reactor Experiment), annular core geometries, and accelerator-driven subcritical systems (ADAHR) were developed and results reported.3 The focus of each of these models is core dynamics; neutron kinetics, thermal hydraulics, radiolytic gas generation and transport are coupled to examine the time-based evolution of these systems from start-up through transition to steady-state. A common characteristic of these models is the assumption that (a) core cooling system inlet temperature and flow and (b) plenum gas inlet pressure and flow are held constant; no external (to core) component operations that may result in dynamic change to these parameters are considered. This report discusses extension of models to include explicit reference to cooling structures and radiolytic gas handling. The accelerator-driven subcritical generic system model described in References 3 and 4 is used as a basis for this extension.
Observations of Crew Dynamics during Mars Analog Simulations
NASA Technical Reports Server (NTRS)
Cusack, Stacy L.
2010-01-01
This presentation reviews the crew dynamics during two simulations of Mars Missions. Using an analog of a Mars habitat in two locations, Flashline Mars Arctic Research Station (FMARS) which is located on Devon Island at 75 deg North in the Canadian Arctic, and the Mars Desert Research Station (MDRS) which is located in the south of Utah, the presentation examines the crew dynamics in relation to the leadership style of the commander of the mission. The difference in the interaction of the two crews were shown to be related to the leadership style and the age group in the crew. As much as possible the habitats and environment was to resemble a Mars outpost. The difference between the International Space Station and a Mars missions is reviewed. The leadership styles are reviewed and the contrast between the FMARS and the MDRS leadership styles were related to crew productivity, and the personal interactions between the crew members. It became evident that leadership styles and interpersonal skill had more affect on mission success and crew dynamics than other characteristics.
Dynamic Deformation of Thermosetting Polymers---All Atomistic Simulations
NASA Astrophysics Data System (ADS)
Tsige, Mesfin; Shenogina, Natalia; Mukhopadhyay, Sharmila; Patnaik, Soumya
2013-03-01
We are using all-atom molecular dynamics simulations to investigate the interconnection between structural and mechanical properties of highly cross-linked polymer networks. In this study we focused on the widely used resin-hardener system composed of DGEBA epoxy oligomers and aromatic amine hardener DETDA. Accurate cross-linked models were developed using the effective cross-linking procedure that enables to generate thermoset structures with realistic structural characteristics. These models were used to examine the elastic properties of thermosetting networks with various degrees of curing and length of resin strands both in glassy and rubbery states. In our recent study we employed static deformation approach to estimate potential energy contribution to the mechanical response. In the present work we are using dynamic deformation approach which takes into account both potential energy and thermal motions in the structure. Uniaxial, volumetric and shear dynamic deformation modes were used to obtain Young's, bulk, shear moduli and Poisson's ratio directly. We also calculated elastic constants using formulae of linear elasticity and analyzed the results obtained by direct deformation and interconversion methods. The elastic properties determined from these two approaches are in good agreement with each other and also with experimental data.
Molecular Dynamics Simulations of Highly Charged Green Fluorescent Proteins
Lau, E Y; Phillips, J L; Colvin, M E
2009-03-26
A recent experimental study showed that green fluorescent protein (GFP) that has been mutated to have ultra-high positive or negative net charges, retain their native structure and fluorescent properties while gaining resistance to aggregation under denaturing conditions. These proteins also provide an ideal test case for studying the effects of surface charge on protein structure and dynamics. They have performed classical molecular dynamics (MD) simulations on the near-neutral wildtype GFP and mutants with net charges of -29 and +35. They analyzed the resulting trajectories to quantify differences in structure and dynamics between the three GFPs. This analyses shows that all three proteins are stable over the MD trajectory, with the near-neutral wild type GFP exhibiting somewhat more flexibility than the positive or negative GFP mutants, as measured by the order parameter and changes in phi-psi angles. There are more dramatic differences in the properties of the water and counter ions surrounding the proteins. The water diffusion constant near the protein surface is closer to the value for bulk water in the positively charged GFP than in the other two proteins. Additionally, the positively charged GFP shows a much greater clustering of the counter ions (CL-) near its surface than corresponding counter ions (Na+) near the negatively charged mutant.
Swimming patterns and dynamics of simulated Escherichia coli bacteria
Zonia, Laura; Bray, Dennis
2009-01-01
A spatially and temporally realistic simulation of Escherichia coli chemotaxis was used to investigate the swimming patterns of wild-type and mutant bacteria within a rectangular arena in response to chemoattractant gradients. Swimming dynamics were analysed during long time series with phase-space trajectories, power spectra and estimations of fractal dimensions (FDs). Cell movement displayed complex trajectories in the phase space owing to interaction of multiple attractors that captured runs and tumbles. Deletion of enzymes responsible for adaptation (CheR and CheB) restricted the pattern of bacterial swimming in the absence of a gradient. In the presence of a gradient, there was a strong increase in trajectories arising from runs and attenuation of those arising from tumbles. Similar dynamics were observed for mutants lacking CheY, which are unable to tumble. The deletion of CheR, CheB and CheY also caused significant shifts in chemotaxis spectral frequencies. Rescaled range analysis and estimation of FD suggest that wild-type bacteria display characteristics of fractional Brownian motion with positive correlation between past and future events. These results reveal an underlying order in bacterial swimming dynamics, which enables a chemotactic search strategy conforming to a fractal walk. PMID:19324687
Flame hole dynamics simulation of Sandia Flame F
NASA Astrophysics Data System (ADS)
Knaus, Robert; Hewson, John; Domino, Stefan; Pantano, Carlos
2014-11-01
The Sandia Flame ``F'' is a piloted methane/air diffusion flame containing high levels of local extinction. These regions of local extinction reduce the efficiency of combustion and can increase the production of certain pollutants (e.g. carbon monoxide) as well as limit the overall stability of the flame. We present a flame hole dynamics model describing evolution of local extinction zones (flame holes) in a turbulent diffusion flame and apply it to perform a direct numerical simulation of the Sandia Flame F using Sandia's ``SIERRA low Mach Module, Nalu.'' The flame hole dynamics model is a phase-field model that describes the state of the flame (burning or extinguished) through a surface partial differential equation modeling extinction, reignition and advection of the flame state on the moving stoichiometric surface using edge flame properties. The solution of the surface equation is then extended away from the surface and used for state evaluations using a flamelet library with steady flamelets in the burning region and a transient solution in the quenched regions. The flame hole dynamics approach allows tracking extinction and reignition in turbulent diffusion flames without using the computationally costly detailed chemistry explicitly.
Dynamics of Vapor-Deposited Polymer Glasses from Simulation
NASA Astrophysics Data System (ADS)
Zhang, Wengang; Starr, Francis; Douglas, Jack
We use molecular dynamics simulations to mimic the physical vapor deposition of glassy polymer films. Like experiments, the deposition results in ''ultrastable glasses'' that have lower energies, and greater kinetic stability than ordinary glasses. It has been suggested that these ultrastable glasses may be equivalent to very highly aged ordinary glasses. To explore this possibility, we contrast both the structure and dynamics of deposited and ordinary glasses. Our modeling indicates that the deposited polymer glass is structurally distinct from the ordinary glass due to anisotropy of chain packing. If the deposited glasses correspond to highly aged ordinary glasses, we would expect vastly larger relaxation times for the deposited glass. Instead, we find that relaxation times of the vapor-deposited glass are nearly the same as that of the ordinary glass. These findings do not support the view that vapor-deposited glassy polymer films are equivalent to highly-aged ordinary glassy polymer films. We further study the dynamical heterogeneity of highly out-of-equilibrium polymer films. Computer time was provided by Wesleyan University. This work was supported in part by NIST Award 70NANB13H202 and ACS-PRF Grant 51983-ND7.
Numerical Simulations of Droplet Dynamics in PEM Fuel Cell Microchannels
NASA Astrophysics Data System (ADS)
Cauble, Eric; Owkes, Mark
2015-11-01
Proton exchange membrane (PEM) fuel cells are of beneficial interest due to their capability of producing clean energy with zero emissions. An important design challenge hindering the performance of fuel cells is controlling water removal to maintain a hydrated membrane while avoiding excess water that may lead to channel blockage. Fuel cell water management requires a detailed knowledge of multiphase flow dynamics within microchannels. Direct observation of gas-liquid flows is difficult due to the small scale and viewing obstructions of the channels within the fuel cell. Instead, this work uses a CFD approach to compute the formation and dynamics of droplets in fuel cell channels. The method leverages a conservative volume-of-fluid (VOF) formulation coupled with a novel methodology to track dynamic contact angles. We present details of the numerical approach and simulation results relevant to water management in PEM fuel cells. In particular, it is shown that variation of the contact hysteresis angle influences the wetting properties of the droplet and significantly impacts water transport throughout the a fuel cell channel.
Rigid body dynamics approach to Stokesian dynamics simulations of nonspherical particles
NASA Astrophysics Data System (ADS)
Kutteh, Ramzi
2010-05-01
We describe an algorithm for performing Stokesian dynamics (SD) simulations of suspensions of arbitrary shape rigid particles with hydrodynamic interactions, modeled as rigid groups of spheres, the hydrodynamic mobility matrix of which is accurately computable by several established schemes for spheres. The algorithm is based on Stokesian rigid body equations of translational and rotational motion, which we have derived by an approach formally analogous to that of Newtonian rigid body dynamics. Particle orientation is represented in terms of Euler parameters (quaternion of rotation). This rigid body SD algorithm (RBSDA) complements recently described constraint SD algorithms [R. Kutteh, J. Chem. Phys. 119, 9280 (2003); R. Kutteh, Phys. Rev. E 69, 011406 (2004)], over which it offers the same computational advantages in imposing total rigidity that the basic rigid body molecular dynamics (MD) algorithm offers over constraint MD algorithms. We show that SD simulation results generated with the RBSDA, in bounded and unbounded geometries, agree very well with those from experiment and other SD and non-SD methods, and are numerically identical to those from a constraint SD algorithm, HSHAKE. Finally, for completeness we also describe a third (additional to the constraint SD and rigid body SD approaches) more traditional approach for SD simulations of arbitrary shape rigid particles modeled as rigid groups of spheres.
Rigid body dynamics approach to Stokesian dynamics simulations of nonspherical particles.
Kutteh, Ramzi
2010-05-01
We describe an algorithm for performing Stokesian dynamics (SD) simulations of suspensions of arbitrary shape rigid particles with hydrodynamic interactions, modeled as rigid groups of spheres, the hydrodynamic mobility matrix of which is accurately computable by several established schemes for spheres. The algorithm is based on Stokesian rigid body equations of translational and rotational motion, which we have derived by an approach formally analogous to that of Newtonian rigid body dynamics. Particle orientation is represented in terms of Euler parameters (quaternion of rotation). This rigid body SD algorithm (RBSDA) complements recently described constraint SD algorithms [R. Kutteh, J. Chem. Phys. 119, 9280 (2003); R. Kutteh, Phys. Rev. E 69, 011406 (2004)], over which it offers the same computational advantages in imposing total rigidity that the basic rigid body molecular dynamics (MD) algorithm offers over constraint MD algorithms. We show that SD simulation results generated with the RBSDA, in bounded and unbounded geometries, agree very well with those from experiment and other SD and non-SD methods, and are numerically identical to those from a constraint SD algorithm, HSHAKE. Finally, for completeness we also describe a third (additional to the constraint SD and rigid body SD approaches) more traditional approach for SD simulations of arbitrary shape rigid particles modeled as rigid groups of spheres. PMID:20459156
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
Yoo, Jejoong; Aksimentiev, Aleksei
2013-01-01
The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840
Animated molecular dynamics simulations of hydrated caesium-smectite interlayers
Sutton, Rebecca; Sposito, Garrison
2002-01-01
Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.
Deringer, J.J. ); Hall, J.D. ); Jones, J.W. ); McKay, H.N. ); Alley, P.K. )
1990-09-01
The primary focus of the Whole-Building Energy Design Targets project is to develop a flexible methodology for setting target guidelines with which to assess energy efficiency in commercial building design. The proposed methodology has several innovative features. In this report, the authors document their work to define the software development concepts upon which the overall Targets methodology will be based. Three task reports are included here. Development of the user interface--that critical connection through which the human end-user (architect, engineer, planner, owner) will apply the methodology--is described in Section 2. In Section 3, the use of the software engineering process in Targets model development efforts is described. Section 4 provides details on the data and system integration task, in which interactions between and among all the major components, termed modules, of the Targets model were examined to determine how to put them together to create a methodology that is effective and easy to use. 4 refs., 26 figs.
Jones, J.W. ); Deringer, J.J. ); McKay, H.N. )
1990-09-01
Since 1985, the Pacific Northwest Laboratory (PNL) has managed the Whole-Building Energy Design Targets project for the US Department of Energy (DOE) Office of Building Technologies (formerly the Office of Buildings and Community Systems). The primary focus of the Targets project is to develop a flexible methodology for buildings industry use in setting energy performance guidelines for commercial buildings and for determining compliance with those guidelines. The project is being conducted as a two-phase effort. In Phase 1, Planning, the project team determined the research that was necessary for developing the Targets methodology. In the concept stage of Phase 2, Development, the team sought to define the technical and software development concepts upon which the overall Targets methodology will be based. The concept stage work is documented in four volumes, of which this summary volume is the first. The three other volumes are Volume 2: Technical Concept Development Task Reports, Volume 3: Workshop Summaries, and Volume 4: Software Concept Development Task Reports. 8 refs., 14 figs.
NASA Astrophysics Data System (ADS)
Calandrini, V.; Hamon, V.; Hinsen, K.; Calligari, P.; Bellissent-Funel, M.-C.; Kneller, G. R.
2008-04-01
This paper presents a study of the influence of non-denaturing hydrostatic pressure on the relaxation dynamics of lysozyme in solution, which combines molecular dynamics simulations and quasielastic neutron scattering experiments. We compare results obtained at ambient pressure and at 3 kbar. Experiments have been performed at pD 4.6 and at a protein concentration of 60 mg/ml. For both pressures we checked the monodispersity of the protein solution by small angle neutron scattering. To interpret the simulation results and the experimental data, we adopt the fractional Ornstein-Uhlenbeck process as a model for the internal relaxation dynamics of the protein. On the experimental side, global protein motions are accounted for by the model of free translational diffusion, neglecting the much slower rotational diffusion. We find that the protein dynamics in the observed time window from about 1 to 100 ps is slowed down under pressure, while its fractal characteristics is preserved, and that the amplitudes of the motions are reduced by about 20%. The slowing down of the relaxation is reduced with increasing q-values, where more localized motions are seen.
Linear interfacial polymerization: theory and simulations with dissipative particle dynamics.
Berezkin, Anatoly V; Kudryavtsev, Yaroslav V
2014-11-21
Step-growth alternating interfacial polymerization between two miscible or immiscible monomer melts is investigated theoretically and by dissipative particle dynamics simulations. In both cases the kinetics for an initially bilayer system passes from the reaction to diffusion control. The polymer composed of immiscible monomers precipitates at the interface forming a film of nearly uniform density. It is demonstrated that the reaction proceeds in a narrow zone, which expands much slower than the whole film, so that newly formed polymer is extruded from the reaction zone. This concept of "reactive extrusion" is used to analytically predict the degree of polymerization and distribution of all components (monomers, polymer, and end groups) within the film in close agreement with the simulations. Increasing the comonomer incompatibility leads to thinner and more uniform films with the higher average degree of polymerization. The final product is considerably more polydisperse than expected for the homogeneous step-growth polymerization. The results extend the previous theoretical reports on interfacial polymerization and provide new insights into the internal film structure and polymer characteristics, which are important for membrane preparation, microencapsulation, and 3D printing technologies. A systematic way of mapping the simulation data onto laboratory scales is discussed. PMID:25416911