Computational Fluid Dynamics Simulations of the Transonic Dynamics Tunnel Airstream Oscillator System
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Robert E Bartels↗
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Results for “dynamic simulations”
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General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.
60 APPLIED LIFE SCIENCES↗
Dynamic Simulation and Stability Analysis
Dynamic Interaction Simulation of Controls and Structure (DISCOS) program developed for dynamic simulation and stability analysis of passive and actively controlled spacecraft. In use of DISCOS, physical system undergoing analysis generally described as cluster of contiguous flexible structures (bodies) that comprise mechanical system, such as spacecraft.
Frisch, H. P.↗
Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations
Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Dynamic simulation and stability analysis
Dynamic Interaction Simulation of Controls and Structure (DISCOS) program was developed for dynamic simulation and stability analysis of passive and actively controlled spacecraft. Program is written in FORTRAN IV for batch execution and requires access to finite-element structures program as NASTRAN for flexible-body input data.
Frisch, H. P.↗
Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments
Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.
dynamic simulation↗
Efficient and Robust Dynamic Simulation of Power Systems With Holomorphic Embedding
Dynamic simulation is vitally important in power system analysis, but traditional approaches based on numerical integration over small time steps are time-consuming. Also, the Newton-Raphson method suffers from difficulty in convergence when solving nonlinear algebraic equations. In this paper, we propose a novel dynamic simulation approach based on holomorphic embedding. By obtaining a high-order approximation of system dynamics, it achieves a much larger time step and thus enhances the computational efficiency significantly. In addition, the new approach avoids non-convergence issues in solving algebraic equations, which improves robustness. The approach includes flexible modeling of synchronous generators and controllers, and we propose a method for modeling generator coordinate transformations. The approach is tested on the IEEE 39-bus, 10-generator system and a Polish 2383-bus, 327-generator system. The results demonstrate promising computational efficiency and satisfactory numerical robustness for the analysis of large-scale power systems.
42 ENGINEERING↗
Guest–Host Interactions in Mixed CH 4 –CO 2 Hydrates: Insights from Molecular Dynamics Simulations
Here, classical molecular dynamics simulations of mixed CH 4 –CO 2 gas hydrates provide a thorough analysis of the energetics of both pure CH 4 and CO 2 hydrates and three intermediate compositions along the (CH 4 ) 1–x (CO 2 ) x ·5.75(H 2 O) solid solution. The energy is broken into guest–guest, guest–host, and host–host contributions. Radial distribution functions and three-dimensional density distributions provide insight into the changes in guest orientation and interactions with the host framework as a function of guest composition. Both energetic and structural analyses provide complementary information to previous experimental studies of the system. The experimentally observed isotropic orientation of CH 4 molecules in both small and large cages is confirmed and the description of the anisotropic orientation of CO 2 molecules in the large cage is confirmed and further enhanced. In mixed hydrates, the presence of CH 4 alters the orientation of CO 2 , an indication that the interactions between guests, either direct (guest–guest) or mediated through interactions with the host (host–guest), are an important phenomenon in these systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Free and internal energies for the adsorption of short alkanes into the zeolite SSZ-13 from ab initio molecular dynamics simulations
We useab initiomolecular dynamics simulations to calculate the temperature dependent free energy and internal energy of adsorption of short alkanes into the zeolite SSZ-13.
Chemistry↗
Lithiation of Sulfur-Graphene Compounds Using Reactive Force-Field Molecular Dynamics Simulations
We performed molecular dynamics simulations of lithium-sulfur-graphene compounds using reactive force fields, providing a time scale to observe atomistic features relevant to the microscopic behavior of the of the bulk of sulfur-based cathodes to be used beyond our present Li-ion batteries. The samples we used were set to realistic geometries through sophisticated protocols to simulate ultrafast reactions that occur within the picosecond range, thus allowing us to get some insights into the characteristics of the bulk material in working cathodes of Li–S batteries, which are mixed with carbon to increase the poor electronic conductivity of S. We report chemical speciation and geometrical data at atomistic levels. We observed that slowly lithiated cathodes were more stable and with higher density than those that were suddenly fully-lithiated. We did not observe molecular Li 2 S formation; however, we observed an amorphous solid arrangement with the same stoichiometry of Li and S, with S–Li–S angles of ~111° and smaller ones due to the interaction between polysulfides that did not reacted totally. In addition, graphene keeps its planar shape; however, S8 changes its shape from rings to chains. Lithiated structures are more stable with lower energies, and more close-packed structures than structures with Li already inserted.
25 ENERGY STORAGE↗
Docking dynamics simulation for AAP
Docking dynamics simulation for Apollo Applications Program
Ravera, R. J.↗
Data Systems Dynamic Simulator
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.
Rouff, Christopher↗
Investigating the Effect of Water on the Mechanical Properties of Cellulose from Multiscale Molecular Dynamics Simulations
Classical molecular dynamics (MD) simulations provide insight into the structure and physicochemical properties of materials with atomic resolution. However, the length and time scales accessible to atomistic MD are orders of magnitude smaller than many relevant processes such as the response of a bulk material to experimentally accessible strain rates, which presents challenges when comparing models to experimental measurements. Bottom-up coarse-graining provides a means for systematically mapping atomistic information to lower resolution models to increase the length and time scales achievable by simulation. Cellulose is an abundant carbohydrate biopolymer with applications to many fields of research, such as materials science and renewable energy, due to its desirable mechanical properties and viability for conversion into biofuel. The effect of moisture content on the Young's modulus of cellulose is of special interest due to its native environment often being in the hydrated secondary plant cell wall and the grinding energy requirements for biomass feedstock preprocessing. The current work investigates the effects of water solvent on the Young's modulus of cellulose calculated from coarse-grained MD mechanical stress simulations. The coarse-grained model was parametrized from atomistic MD calculations of cellulose-cellulose potentials of mean force using umbrella sampling techniques under vacuum and solvated conditions. The Young's moduli of the coarse-grained cellulose assemblies parametrized from cellulose in vacuum or solvated in water were computed via mechanical stress simulations to highlight the importance of capturing solvent interactions for modeling the mechanical behavior of cellulose.
BASIC BIOLOGICAL SCIENCES,RADIATION PROTECTION AND↗
Equation of state for He bubbles in W and model of He bubble growth and bursting near W{100} surfaces derived from molecular dynamics simulations
Abstract Molecular dynamics (MD) simulations are performed to derive an equation of state (EOS) for helium (He) bubbles in tungsten (W) and to study the growth of He bubbles under a W(100) surface until they burst. We study the growth as a function of the initial nucleation depth of the bubbles. During growth, successive loop-punching events are observed, accompanied by shifts in the depth of the bubble towards the surface. Subsequently, the MD data are used to derive models that describe the conditions that cause the loop punching and bursting events. Simulations have been performed at 500, 933, 1500, 2000, and 2500 K to fit the parameters in the models. To compute the pressure in the bubble at the loop punching and bursting events from the models, we derive an EOS for He bubbles in tungsten with an accompanying volume model to compute the bubble volume for a given number of vacancies ( $$N_\text {V}$$ N V ), He atoms ( $$N_\text {He}$$ N He ), and temperature ( T ). To derive the bubble EOS, we firstly derive the EOS for a free He gas. The derived free-gas EOS can accurately predict all MD data included in the analysis (which span up to 54 GPa at 2500 K). Subsequently, the bubble EOS is derived based on the free-gas EOS by correcting the gas density to account for the interaction between He and W atoms. The EOS for the bubbles is fitted to data from MD simulations of He bubbles in bulk W that span a wide range of gas density and sizes up to about 3 nm in diameter. The pressure of subsurface bubbles at the loop punching events as calculated using the bubble-EOS and the volume model agrees well with the pressure obtained directly from the MD simulations. In the loop punching model, for bubbles consisting of $$N_\text {V}$$ N V vacancies and $$N_\text {He}$$ N He helium atoms, the $$N_\text {He}/N_\text {V}$$ N He / N V ratio that causes the event, the resulting increase in $$N_\text {V}$$ N V , and the associated shift of the bubble depth are formulated as a function of $$N_\text {V}$$ N V and T . In the bursting model, a bubble must simultaneously reach a certain depth and $$N_\text {He}/N_\text {V}$$ N He / N V ratio in order to burst. The burst depth and $$N_\text {He}/N_\text {V}$$ N He / N V are also modeled as a function of $$N_\text {V}$$ N V and T . The majority of the loop punching events occur at bubble pressures between 20 and 60 GPa, depending on the bubble size and temperature. The larger the bubble and the higher the temperature, the lower the bubble pressure. Furthermore, our results indicate that at a higher temperature, a bubble can burst from a deeper region.
36 MATERIALS SCIENCE↗
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations
Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
59 BASIC BIOLOGICAL SCIENCES↗
Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations
We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Aspherical particle models for molecular dynamics simulation
In traditional molecular dynamics (MD) simulations, atoms and coarse-grained particles are modeled as point masses interacting via isotropic potentials. For studies where particle shape plays a vital role, more complex models are required. Here, we describe a spectrum of approaches for modeling aspherical particles, all of which are now available (some recently) as options within the LAMMPS MD package. Broadly these include two classes of models. In the first, individual particles are aspherical, either via a pairwise anisotropic potential which implicitly assigns a simple geometric shape to each particle, or in a more general way where particles store internal state which can explicitly define a complex geometric shape. In the second class of models, individual particles are simple points or spheres, but rigid body constraints are used to create composite aspherical particles in a variety of complex shapes. This work discusses parallel algorithms and associated data structures for both kinds of models, which enable dynamics simulations of aspherical particle systems across a wide range of length and time scales. We also highlight parallel performance and scalability and give a few illustrative examples of aspherical models in different contexts.
74 ATOMIC AND MOLECULAR PHYSICS↗
Parareal in Time for Dynamic Simulations of Power Systems
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.
Gurrala, Gurunath↗